Changes between Initial Version and Version 1 of Ticket #15919


Ignore:
Timestamp:
Sep 10, 2024, 11:03:58 AM (14 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #15919

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

  • Ticket #15919 – Description

    initial v1  
    6161  "threads" : 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    236     "name" : "libopenblas64_.0.dylib"
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    254     "name" : "libopenblas.0.dylib"
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    272     "name" : "libCoreVMClient.dylib"
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    280     "path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Libraries\/libCVMSPluginSupport.dylib",
    281     "name" : "libCVMSPluginSupport.dylib"
    282   }
     63[deleted to fit within ticket limits]
    28364],
    28465  "sharedCache" : {
    … …  
    14341215 
    14351216
    1436 > hide #7 models
    1437 
    1438 > show #7 models
    1439 
    1440 > hide #7 models
    1441 
    1442 > show #7 models
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    1444 > hide #7 models
    1445 
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    1447 
    1448 > hide #17 models
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    1455 
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    1461 
    1462 > show #17 models
    1463 
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    1471 
    1472 > hide #17 models
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    1479 
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    1483 
    1484 > hide #17 models
    1485 
    1486 > show #17 models
    1487 
    1488 > hide #17 models
    1489 
    1490 > show #17 models
    1491 
    1492 > hide #17 models
    1493 
    1494 > show #1 models
    1495 
    1496 > show #3 models
    1497 
    1498 > show #5 models
    1499 
    1500 > show #9 models
    1501 
    1502 > show #11 models
    1503 
    1504 > show #13 models
    1505 
    1506 > show #15 models
    1507 
    1508 > color #1&core indian red
    1509 
    1510 > color #1&dimer pink
    1511 
    1512 > color #3,5&core orange
    1513 
    1514 > color #3,5&dimer khaki
    1515 
    1516 > hide #15 models
    1517 
    1518 > hide #13 models
    1519 
    1520 > hide #11 models
    1521 
    1522 > hide #9 models
    1523 
    1524 > hide #7 models
    1525 
    1526 > hide #1 models
    1527 
    1528 > hide #3 models
    1529 
    1530 > show #3 models
    1531 
    1532 > hide #3 models
    1533 
    1534 > show #3 models
    1535 
    1536 > hide #5 models
    1537 
    1538 > show #5 models
    1539 
    1540 > color #7,9&core medium sea green
    1541 
    1542 > color #7,9&dimer pale green
    1543 
    1544 > hide #3 models
    1545 
    1546 > hide #5 models
    1547 
    1548 > show #7 models
    1549 
    1550 > show #9 models
    1551 
    1552 > hide #9 models
    1553 
    1554 > lighting soft
    1555 
    1556 > graphics silhouettes true
    1557 
    1558 > hide #7 models
    1559 
    1560 > show #7 models
    1561 
    1562 > show #!4 models
    1563 
    1564 > hide #!4 models
    1565 
    1566 > show #5 models
    1567 
    1568 > hide #7 models
    1569 
    1570 > show #7 models
    1571 
    1572 > hide #5 models
    1573 
    1574 > color #7,9&core sea green
    1575 
    1576 > color #7,9&dimer pale green
    1577 
    1578 > show #5 models
    1579 
    1580 > hide #7 models
    1581 
    1582 > show #7 models
    1583 
    1584 > hide #7 models
    1585 
    1586 > hide #5 models
    1587 
    1588 > show #7 models
    1589 
    1590 > show #9 models
    1591 
    1592 > hide #9 models
    1593 
    1594 > show #9 models
    1595 
    1596 > hide #9 models
    1597 
    1598 > show #11 models
    1599 
    1600 > color #11,13,15&core dodger blue
    1601 
    1602 > color #11,13,15&dimer light sky blue
    1603 
    1604 > hide #11 models
    1605 
    1606 > show #11 models
    1607 
    1608 > hide #11 models
    1609 
    1610 > show #11 models
    1611 
    1612 > hide #11 models
    1613 
    1614 > show #11 models
    1615 
    1616 > hide #11 models
    1617 
    1618 > color /B,C gray
    1619 
    1620 > color /B,C light gray
    1621 
    1622 > color /B,C silver
    1623 
    1624 > hide /B,C
    1625 
    1626 > hide /B,C target c
    1627 
    1628 > hide #7 models
    1629 
    1630 > show #5 models
    1631 
    1632 > hide #5 models
    1633 
    1634 > show #5 models
    1635 
    1636 > hide #5 models
    1637 
    1638 > show #!8 models
    1639 
    1640 > hide #!8 models
    1641 
    1642 > show #7 models
    1643 
    1644 > hide #7 models
    1645 
    1646 > show #9 models
    1647 
    1648 > setattr #9/A:145-147 res is_helix 0
    1649 
    1650 Assigning is_helix attribute to 3 items 
    1651 
    1652 > show #9 atoms
    1653 
    1654 > hide #9 cartoons
    1655 
    1656 > color #9 byhetero
    1657 
    1658 > show #9 cartoons
    1659 
    1660 > setattr #9/A:285 res is_helix 1
    1661 
    1662 Assigning is_helix attribute to 1 item 
    1663 
    1664 > setattr #9/A:286 res is_helix 1
    1665 
    1666 Assigning is_helix attribute to 1 item 
    1667 
    1668 > setattr #9/A:286 res is_helix 0
    1669 
    1670 Assigning is_helix attribute to 1 item 
    1671 
    1672 > hide #9 atoms
    1673 
    1674 > show #7 models
    1675 
    1676 > hide #9 models
    1677 
    1678 > show #9 models
    1679 
    1680 > hide #7 models
    1681 
    1682 > show #7 models
    1683 
    1684 > hide #9 models
    1685 
    1686 > cartoon style modeHelix tube radius 1.8 sides 24
    1687 
    1688 > show #9 models
    1689 
    1690 > hide #7 models
    1691 
    1692 > show #7 models
    1693 
    1694 > hide #9 models
    1695 
    1696 > show #9 models
    1697 
    1698 > hide #9 models
    1699 
    1700 > show #9 models
    1701 
    1702 > hide #7 models
    1703 
    1704 > hide #9 models
    1705 
    1706 > show #7 models
    1707 
    1708 > cartoon style modeHelix default width 1.8 thickness 0.3
    1709 
    1710 > setattr #7/A:11 res is_helix 0
    1711 
    1712 Assigning is_helix attribute to 1 item 
    1713 
    1714 > show #9 models
    1715 
    1716 > hide #7 models
    1717 
    1718 > show #7 models
    1719 
    1720 > hide #9 models
    1721 
    1722 > show #9 models
    1723 
    1724 > hide #7 models
    1725 
    1726 > show #7 models
    1727 
    1728 > hide #7 models
    1729 
    1730 > show #7 models
    1731 
    1732 > setattr #7/A:145-147 res is_helix 0
    1733 
    1734 Assigning is_helix attribute to 3 items 
    1735 
    1736 > hide #7 models
    1737 
    1738 > show #7 models
    1739 
    1740 > hide #9 models
    1741 
    1742 > show #9 models
    1743 
    1744 > hide #9 models
    1745 
    1746 > show #9 models
    1747 
    1748 > hide #9 models
    1749 
    1750 > show #9 models
    1751 
    1752 > hide #9 models
    1753 
    1754 > show #9 models
    1755 
    1756 > hide #9 models
    1757 
    1758 > show #9 models
    1759 
    1760 > hide #7 models
    1761 
    1762 > show #7 models
    1763 
    1764 > hide #7 models
    1765 
    1766 > show #7 models
    1767 
    1768 > hide #7 models
    1769 
    1770 > show #7 models
    1771 
    1772 > hide #9 models
    1773 
    1774 > show #9 models
    1775 
    1776 > hide #9 models
    1777 
    1778 > show #9 models
    1779 
    1780 > hide #7 models
    1781 
    1782 > show #7 models
    1783 
    1784 > hide #9 models
    1785 
    1786 > show #9 models
    1787 
    1788 > hide #7 models
    1789 
    1790 > hide #9 models
    1791 
    1792 > show #7 models
    1793 
    1794 > show #5 models
    1795 
    1796 > hide #5 models
    1797 
    1798 > show #3 models
    1799 
    1800 > mcopy #7/A toAtoms #3/A settings h
    1801 
    1802 > hide #3 models
    1803 
    1804 > show #13 models
    1805 
    1806 > setattr #7/A:58,45 res is_strand 0
    1807 
    1808 Assigning is_strand attribute to 2 items 
    1809 
    1810 > hide #13 models
    1811 
    1812 > setattr #7/A:45 res is_strand 1
    1813 
    1814 Assigning is_strand attribute to 1 item 
    1815 
    1816 > setattr #7/A:58 res is_strand 1
    1817 
    1818 Assigning is_strand attribute to 1 item 
    1819 
    1820 > show #13 models
    1821 
    1822 > hide #13 models
    1823 
    1824 > mcopy #7/A toAtoms #1,3/A settings h
    1825 
    1826 > show #5 models
    1827 
    1828 > hide #5 models
    1829 
    1830 > hide #7 models
    1831 
    1832 > show #5 models
    1833 
    1834 > show #11 models
    1835 
    1836 > mcopy #9/A toAtoms #5,11,13,15/A settings h
    1837 
    1838 > show #13 models
    1839 
    1840 > hide #13 models
    1841 
    1842 > hide #11 models
    1843 
    1844 > show #11 models
    1845 
    1846 > hide #5 models
    1847 
    1848 > show #11 atoms
    1849 
    1850 > color #11 byhetero
    1851 
    1852 > hide #11 cartoons
    1853 
    1854 > show #13 models
    1855 
    1856 > hide #13 models
    1857 
    1858 > show #9 models
    1859 
    1860 > show #9,11 atoms
    1861 
    1862 > hide #9,11 cartoons
    1863 
    1864 > show #9,11 cartoons
    1865 
    1866 > hide #9,11 atoms
    1867 
    1868 > show #9,11 atoms
    1869 
    1870 > hide #9 models
    1871 
    1872 > show #9 models
    1873 
    1874 > hide #9,11 atoms
    1875 
    1876 > hide #9 models
    1877 
    1878 > show #13 models
    1879 
    1880 > hide #11 models
    1881 
    1882 > show #11 models
    1883 
    1884 > hide #11 models
    1885 
    1886 > show #11 models
    1887 
    1888 > hide #11 models
    1889 
    1890 > show #11 models
    1891 
    1892 > hide #11 models
    1893 
    1894 > show #11 models
    1895 
    1896 > hide #11 models
    1897 
    1898 > show #11 models
    1899 
    1900 > hide #11 models
    1901 
    1902 > show #11 models
    1903 
    1904 > hide #11 models
    1905 
    1906 > show #11 models
    1907 
    1908 > hide #11 models
    1909 
    1910 > show #13 atoms
    1911 
    1912 > hide #13 cartoons
    1913 
    1914 > color #13 byhetero
    1915 
    1916 > show #13 cartoons
    1917 
    1918 > setattr #13/A:223-226 res is_helix 0
    1919 
    1920 Assigning is_helix attribute to 4 items 
    1921 
    1922 > hide #13 cartoons
    1923 
    1924 [Repeated 1 time(s)]
    1925 
    1926 > show #13 cartoons
    1927 
    1928 > setattr #13/A:223-226 res is_helix 1
    1929 
    1930 Assigning is_helix attribute to 4 items 
    1931 
    1932 > setattr #13/A:223-225 res is_helix 1
    1933 
    1934 Assigning is_helix attribute to 3 items 
    1935 
    1936 > setattr #13/A:223-225 res is_helix 0
    1937 
    1938 Assigning is_helix attribute to 3 items 
    1939 
    1940 > show #13 atoms
    1941 
    1942 > hide #13 cartoons
    1943 
    1944 > show #13 cartoons
    1945 
    1946 > hide #13 cartoons
    1947 
    1948 > setattr #13/A:223-226 res is_helix 0
    1949 
    1950 Assigning is_helix attribute to 4 items 
    1951 
    1952 > show #13 cartoons
    1953 
    1954 > setattr #15/A:223-226 res is_helix 0
    1955 
    1956 Assigning is_helix attribute to 4 items 
    1957 
    1958 > show #15 models
    1959 
    1960 > hide #13 models
    1961 
    1962 > close #17
    1963 
    1964 > show #!16 models
    1965 
    1966 > hide #!16 models
    1967 
    1968 > show #!16 models
    1969 
    1970 > hide #!16 models
    1971 
    1972 > show #13 models
    1973 
    1974 > show #11 models
    1975 
    1976 > show #9 models
    1977 
    1978 > show #7 models
    1979 
    1980 > show #5 models
    1981 
    1982 > show #3 models
    1983 
    1984 > show #1 models
    1985 
    1986 > hide /B,C target ac
    1987 
    1988 > hide atoms
    1989 
    1990 > save
    1991 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    1992 
    1993 ——— End of log from Fri Aug 16 14:59:40 2024 ———
    1994 
    1995 opened ChimeraX session 
    1996 
    1997 > color #7,9&core forest green
    1998 
    1999 > color #7,9&dimer pale green
    2000 
    2001 > color #11,13&core light sea green
    2002 
    2003 > color #11,13&dimer cyan
    2004 
    2005 > hide #1 models
    2006 
    2007 > hide #3 models
    2008 
    2009 > hide #7 models
    2010 
    2011 > hide #5 models
    2012 
    2013 > hide #11 models
    2014 
    2015 > hide #13 models
    2016 
    2017 > hide #15 models
    2018 
    2019 > show #11 models
    2020 
    2021 > hide #9 models
    2022 
    2023 > hide #11 models
    2024 
    2025 > show #13 models
    2026 
    2027 > show #15 models
    2028 
    2029 > hide #13 models
    2030 
    2031 > show #11 models
    2032 
    2033 > hide #11 models
    2034 
    2035 > show #11 models
    2036 
    2037 > hide #11 models
    2038 
    2039 > show #11 models
    2040 
    2041 > hide #11 models
    2042 
    2043 > show #11 models
    2044 
    2045 > hide #11 models
    2046 
    2047 > show #11 models
    2048 
    2049 > hide #11 models
    2050 
    2051 > show #11 models
    2052 
    2053 > hide #15 models
    2054 
    2055 > show #9 models
    2056 
    2057 > hide #9 models
    2058 
    2059 > show #9 models
    2060 
    2061 > hide #9 models
    2062 
    2063 > show #7 models
    2064 
    2065 > hide #7 models
    2066 
    2067 > show #7 models
    2068 
    2069 > hide #7 models
    2070 
    2071 > color /A:1-10 orchid
    2072 
    2073 > cartoon style modeHelix default width 1.8 thickness 0.3
    2074 
    2075 > hide #11 models
    2076 
    2077 > show #1 models
    2078 
    2079 > show #3 models
    2080 
    2081 > show #5 models
    2082 
    2083 > show #7 models
    2084 
    2085 > show #9 models
    2086 
    2087 > show #11 models
    2088 
    2089 > show #13 models
    2090 
    2091 > show #15 models
    2092 
    2093 > save
    2094 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    2095 
    2096 > hide #15 models
    2097 
    2098 > hide #13 models
    2099 
    2100 > hide #11 models
    2101 
    2102 > show #11 models
    2103 
    2104 > hide #11 models
    2105 
    2106 > show #13 models
    2107 
    2108 > hide #13 models
    2109 
    2110 > hide #9 models
    2111 
    2112 > show #9 models
    2113 
    2114 > hide #9 models
    2115 
    2116 > show #9 models
    2117 
    2118 > hide #9 models
    2119 
    2120 > show #9 models
    2121 
    2122 > show #13 models
    2123 
    2124 > hide #13 models
    2125 
    2126 > hide #9 models
    2127 
    2128 > show #9 models
    2129 
    2130 > show #11 models
    2131 
    2132 > hide #11 models
    2133 
    2134 > show #11 models
    2135 
    2136 > hide #11 models
    2137 
    2138 > show :CDL,PTY target a
    2139 
    2140 > show #11 models
    2141 
    2142 > show #13 models
    2143 
    2144 > show #15 models
    2145 
    2146 > hide #1 models
    2147 
    2148 > hide #3 models
    2149 
    2150 > hide #5 models
    2151 
    2152 > hide #7 models
    2153 
    2154 > hide #9 models
    2155 
    2156 > hide #15 models
    2157 
    2158 > show #15 models
    2159 
    2160 > hide #15 models
    2161 
    2162 > hide #13 models
    2163 
    2164 > show #!12 models
    2165 
    2166 > hide #!12 models
    2167 
    2168 > show #!12 models
    2169 
    2170 > color #12 #ffb2b258 models
    2171 
    2172 > color #12 #ffb2b26b models
    2173 
    2174 > ui tool show "Side View"
    2175 
    2176 > show #9 models
    2177 
    2178 > hide #9 models
    2179 
    2180 > show #9 models
    2181 
    2182 > hide #!12 models
    2183 
    2184 > select #11/A:401@C78
    2185 
    2186 1 atom, 1 residue, 1 model selected 
    2187 
    2188 > select add #11/A:401@C79
    2189 
    2190 2 atoms, 1 residue, 1 model selected 
    2191 
    2192 > select add #11/A:401@C80
    2193 
    2194 3 atoms, 1 residue, 1 model selected 
    2195 
    2196 > select add #11/A:401@C81
    2197 
    2198 4 atoms, 1 residue, 1 model selected 
    2199 
    2200 > select add #11/A:401@C82
    2201 
    2202 5 atoms, 1 residue, 1 model selected 
    2203 
    2204 > select add #11/A:401@C83
    2205 
    2206 6 atoms, 1 residue, 1 model selected 
    2207 
    2208 > select add #11/A:401@C84
    2209 
    2210 7 atoms, 1 residue, 1 model selected 
    2211 
    2212 > select add #11/A:401@C85
    2213 
    2214 8 atoms, 1 residue, 1 model selected 
    2215 
    2216 > select add #11/A:401@C86
    2217 
    2218 9 atoms, 1 residue, 1 model selected 
    2219 
    2220 > select add #11/A:401@C87
    2221 
    2222 10 atoms, 1 residue, 1 model selected 
    2223 
    2224 > delete sel
    2225 
    2226 > select #11/A:401@C67
    2227 
    2228 1 atom, 1 residue, 1 model selected 
    2229 
    2230 > select add #11/A:401@C66
    2231 
    2232 2 atoms, 1 residue, 1 model selected 
    2233 
    2234 > select add #11/A:401@C65
    2235 
    2236 3 atoms, 1 residue, 1 model selected 
    2237 
    2238 > select add #11/A:401@C64
    2239 
    2240 4 atoms, 1 residue, 1 model selected 
    2241 
    2242 > select add #11/A:401@C63
    2243 
    2244 5 atoms, 1 residue, 1 model selected 
    2245 
    2246 > select add #11/A:401@C62
    2247 
    2248 6 atoms, 1 residue, 1 model selected 
    2249 
    2250 > select add #11/A:401@C60
    2251 
    2252 7 atoms, 1 residue, 1 model selected 
    2253 
    2254 > select add #11/A:401@C59
    2255 
    2256 8 atoms, 1 residue, 1 model selected 
    2257 
    2258 > select add #11/A:401@C58
    2259 
    2260 9 atoms, 1 residue, 1 model selected 
    2261 
    2262 > delete sel
    2263 
    2264 > select #11/A:401@C61
    2265 
    2266 1 atom, 1 residue, 1 model selected 
    2267 
    2268 > delete sel
    2269 
    2270 > show #!12 models
    2271 
    2272 > hide #!12 models
    2273 
    2274 > select #11/A:401@C43
    2275 
    2276 1 atom, 1 residue, 1 model selected 
    2277 
    2278 > select add #11/A:401@C44
    2279 
    2280 2 atoms, 1 residue, 1 model selected 
    2281 
    2282 > select add #11/A:401@C45
    2283 
    2284 3 atoms, 1 residue, 1 model selected 
    2285 
    2286 > select add #11/A:401@C46
    2287 
    2288 4 atoms, 1 residue, 1 model selected 
    2289 
    2290 > select add #11/A:401@C47
    2291 
    2292 5 atoms, 1 residue, 1 model selected 
    2293 
    2294 > delete sel
    2295 
    2296 > show #!12 models
    2297 
    2298 > hide #!12 models
    2299 
    2300 > select #11/A:401@C19
    2301 
    2302 1 atom, 1 residue, 1 model selected 
    2303 
    2304 > select add #11/A:401@C20
    2305 
    2306 2 atoms, 1 residue, 1 model selected 
    2307 
    2308 > select add #11/A:401@C21
    2309 
    2310 3 atoms, 1 residue, 1 model selected 
    2311 
    2312 > select add #11/A:401@C22
    2313 
    2314 4 atoms, 1 residue, 1 model selected 
    2315 
    2316 > select add #11/A:401@C23
    2317 
    2318 5 atoms, 1 residue, 1 model selected 
    2319 
    2320 > select add #11/A:401@C24
    2321 
    2322 6 atoms, 1 residue, 1 model selected 
    2323 
    2324 > select add #11/A:401@C25
    2325 
    2326 7 atoms, 1 residue, 1 model selected 
    2327 
    2328 > select add #11/A:401@C26
    2329 
    2330 8 atoms, 1 residue, 1 model selected 
    2331 
    2332 > select add #11/A:401@C27
    2333 
    2334 9 atoms, 1 residue, 1 model selected 
    2335 
    2336 > delete sel
    2337 
    2338 > show #!12 models
    2339 
    2340 > hide #!12 models
    2341 
    2342 > select #11/A:402@C17
    2343 
    2344 1 atom, 1 residue, 1 model selected 
    2345 
    2346 > select add #11/A:402@C18
    2347 
    2348 2 atoms, 1 residue, 1 model selected 
    2349 
    2350 > select add #11/A:402@C19
    2351 
    2352 3 atoms, 1 residue, 1 model selected 
    2353 
    2354 > select add #11/A:402@C20
    2355 
    2356 4 atoms, 1 residue, 1 model selected 
    2357 
    2358 > select add #11/A:402@C21
    2359 
    2360 5 atoms, 1 residue, 1 model selected 
    2361 
    2362 > select add #11/A:402@C22
    2363 
    2364 6 atoms, 1 residue, 1 model selected 
    2365 
    2366 > select add #11/A:402@C23
    2367 
    2368 7 atoms, 1 residue, 1 model selected 
    2369 
    2370 > select add #11/A:402@C24
    2371 
    2372 8 atoms, 1 residue, 1 model selected 
    2373 
    2374 > select add #11/A:402@C25
    2375 
    2376 9 atoms, 1 residue, 1 model selected 
    2377 
    2378 > select add #11/A:402@C26
    2379 
    2380 10 atoms, 1 residue, 1 model selected 
    2381 
    2382 > select add #11/A:402@C27
    2383 
    2384 11 atoms, 1 residue, 1 model selected 
    2385 
    2386 > select add #11/A:402@C28
    2387 
    2388 12 atoms, 1 residue, 1 model selected 
    2389 
    2390 > select add #11/A:402@C29
    2391 
    2392 13 atoms, 1 residue, 1 model selected 
    2393 
    2394 > show #!12 models
    2395 
    2396 > hide #!12 models
    2397 
    2398 > delete sel
    2399 
    2400 > show #!12 models
    2401 
    2402 > hide #!12 models
    2403 
    2404 > select #11/A:402@C44
    2405 
    2406 1 atom, 1 residue, 1 model selected 
    2407 
    2408 > select add #11/A:402@C43
    2409 
    2410 2 atoms, 1 residue, 1 model selected 
    2411 
    2412 > select add #11/A:402@C42
    2413 
    2414 3 atoms, 1 residue, 1 model selected 
    2415 
    2416 > select add #11/A:402@C41
    2417 
    2418 4 atoms, 1 residue, 1 model selected 
    2419 
    2420 > select add #11/A:402@C40
    2421 
    2422 5 atoms, 1 residue, 1 model selected 
    2423 
    2424 > delete sel
    2425 
    2426 > show #!12 models
    2427 
    2428 > hide #!12 models
    2429 
    2430 > select #11/A:402@C39
    2431 
    2432 1 atom, 1 residue, 1 model selected 
    2433 
    2434 > select add #11/A:402@C38
    2435 
    2436 2 atoms, 1 residue, 1 model selected 
    2437 
    2438 > show #!12 models
    2439 
    2440 > delete sel
    2441 
    2442 > hide #!12 models
    2443 
    2444 > hide #11 models
    2445 
    2446 > show #11 models
    2447 
    2448 > hide #11 models
    2449 
    2450 > show #13 models
    2451 
    2452 > show #!14 models
    2453 
    2454 > color #14 #b2ffb250 models
    2455 
    2456 > color #14 #b2ffb263 models
    2457 
    2458 > volume #14 level 0.0155
    2459 
    2460 > hide #!14 models
    2461 
    2462 > select #13/A:401@C80
    2463 
    2464 1 atom, 1 residue, 1 model selected 
    2465 
    2466 > select add #13/A:401@C81
    2467 
    2468 2 atoms, 1 residue, 1 model selected 
    2469 
    2470 > select add #13/A:401@C82
    2471 
    2472 3 atoms, 1 residue, 1 model selected 
    2473 
    2474 > select add #13/A:401@C83
    2475 
    2476 4 atoms, 1 residue, 1 model selected 
    2477 
    2478 > select add #13/A:401@C84
    2479 
    2480 5 atoms, 1 residue, 1 model selected 
    2481 
    2482 > select add #13/A:401@C85
    2483 
    2484 6 atoms, 1 residue, 1 model selected 
    2485 
    2486 > select add #13/A:401@C86
    2487 
    2488 7 atoms, 1 residue, 1 model selected 
    2489 
    2490 > select add #13/A:401@C87
    2491 
    2492 8 atoms, 1 residue, 1 model selected 
    2493 
    2494 > delete sel
    2495 
    2496 > show #!14 models
    2497 
    2498 > hide #!14 models
    2499 
    2500 > select #13/A:401@C55
    2501 
    2502 1 atom, 1 residue, 1 model selected 
    2503 
    2504 > select add #13/A:401@C56
    2505 
    2506 2 atoms, 1 residue, 1 model selected 
    2507 
    2508 > select add #13/A:401@C57
    2509 
    2510 3 atoms, 1 residue, 1 model selected 
    2511 
    2512 > select add #13/A:401@C58
    2513 
    2514 4 atoms, 1 residue, 1 model selected 
    2515 
    2516 > select add #13/A:401@C59
    2517 
    2518 5 atoms, 1 residue, 1 model selected 
    2519 
    2520 > select add #13/A:401@C60
    2521 
    2522 6 atoms, 1 residue, 1 model selected 
    2523 
    2524 > select add #13/A:401@C61
    2525 
    2526 7 atoms, 1 residue, 1 model selected 
    2527 
    2528 > select add #13/A:401@C62
    2529 
    2530 8 atoms, 1 residue, 1 model selected 
    2531 
    2532 > select add #13/A:401@C63
    2533 
    2534 9 atoms, 1 residue, 1 model selected 
    2535 
    2536 > select add #13/A:401@C64
    2537 
    2538 10 atoms, 1 residue, 1 model selected 
    2539 
    2540 > select add #13/A:401@C65
    2541 
    2542 11 atoms, 1 residue, 1 model selected 
    2543 
    2544 > select add #13/A:401@C66
    2545 
    2546 12 atoms, 1 residue, 1 model selected 
    2547 
    2548 > select add #13/A:401@C67
    2549 
    2550 13 atoms, 1 residue, 1 model selected 
    2551 
    2552 > delete sel
    2553 
    2554 > show #!14 models
    2555 
    2556 > hide #!14 models
    2557 
    2558 > show #!14 models
    2559 
    2560 > hide #!14 models
    2561 
    2562 > show #!14 models
    2563 
    2564 > volume #14 level 0.01343
    2565 
    2566 > hide #!14 models
    2567 
    2568 > select #13/A:401@C41
    2569 
    2570 1 atom, 1 residue, 1 model selected 
    2571 
    2572 > select add #13/A:401@C42
    2573 
    2574 2 atoms, 1 residue, 1 model selected 
    2575 
    2576 > select add #13/A:401@C43
    2577 
    2578 3 atoms, 1 residue, 1 model selected 
    2579 
    2580 > select add #13/A:401@C44
    2581 
    2582 4 atoms, 1 residue, 1 model selected 
    2583 
    2584 > select add #13/A:401@C45
    2585 
    2586 5 atoms, 1 residue, 1 model selected 
    2587 
    2588 > select add #13/A:401@C46
    2589 
    2590 6 atoms, 1 residue, 1 model selected 
    2591 
    2592 > select add #13/A:401@C47
    2593 
    2594 7 atoms, 1 residue, 1 model selected 
    2595 
    2596 > delete sel
    2597 
    2598 > show #!14 models
    2599 
    2600 > hide #!14 models
    2601 
    2602 > select #13/A:401@C17
    2603 
    2604 1 atom, 1 residue, 1 model selected 
    2605 
    2606 > select add #13/A:401@C18
    2607 
    2608 2 atoms, 1 residue, 1 model selected 
    2609 
    2610 > select add #13/A:401@C19
    2611 
    2612 3 atoms, 1 residue, 1 model selected 
    2613 
    2614 > select add #13/A:401@C20
    2615 
    2616 4 atoms, 1 residue, 1 model selected 
    2617 
    2618 > select add #13/A:401@C21
    2619 
    2620 5 atoms, 1 residue, 1 model selected 
    2621 
    2622 > select add #13/A:401@C22
    2623 
    2624 6 atoms, 1 residue, 1 model selected 
    2625 
    2626 > select add #13/A:401@C23
    2627 
    2628 7 atoms, 1 residue, 1 model selected 
    2629 
    2630 > select add #13/A:401@C24
    2631 
    2632 8 atoms, 1 residue, 1 model selected 
    2633 
    2634 > select add #13/A:401@C25
    2635 
    2636 9 atoms, 1 residue, 1 model selected 
    2637 
    2638 > select add #13/A:401@C26
    2639 
    2640 10 atoms, 1 residue, 1 model selected 
    2641 
    2642 > select add #13/A:401@C27
    2643 
    2644 11 atoms, 1 residue, 1 model selected 
    2645 
    2646 > delete sel
    2647 
    2648 > show #!14 models
    2649 
    2650 > select #13/A:402@C15
    2651 
    2652 1 atom, 1 residue, 1 model selected 
    2653 
    2654 > hide #!14 models
    2655 
    2656 > select add #13/A:402@C16
    2657 
    2658 2 atoms, 1 residue, 1 model selected 
    2659 
    2660 > select add #13/A:402@C17
    2661 
    2662 3 atoms, 1 residue, 1 model selected 
    2663 
    2664 > select add #13/A:402@C18
    2665 
    2666 4 atoms, 1 residue, 1 model selected 
    2667 
    2668 > select add #13/A:402@C19
    2669 
    2670 5 atoms, 1 residue, 1 model selected 
    2671 
    2672 > select add #13/A:402@C20
    2673 
    2674 6 atoms, 1 bond, 1 residue, 1 model selected 
    2675 
    2676 > select add #13/A:402@C21
    2677 
    2678 7 atoms, 1 residue, 1 model selected 
    2679 
    2680 > select add #13/A:402@C22
    2681 
    2682 8 atoms, 1 residue, 1 model selected 
    2683 
    2684 > select add #13/A:402@C23
    2685 
    2686 9 atoms, 1 residue, 1 model selected 
    2687 
    2688 > select add #13/A:402@C25
    2689 
    2690 10 atoms, 1 residue, 1 model selected 
    2691 
    2692 > select add #13/A:402@C26
    2693 
    2694 11 atoms, 1 residue, 1 model selected 
    2695 
    2696 > select add #13/A:402@C27
    2697 
    2698 12 atoms, 1 residue, 1 model selected 
    2699 
    2700 > select add #13/A:402@C28
    2701 
    2702 13 atoms, 1 residue, 1 model selected 
    2703 
    2704 > select add #13/A:402@C29
    2705 
    2706 14 atoms, 1 residue, 1 model selected 
    2707 
    2708 > delete sel
    2709 
    2710 > select #13/A:402@C24
    2711 
    2712 1 atom, 1 residue, 1 model selected 
    2713 
    2714 > delete sel
    2715 
    2716 > show #!14 models
    2717 
    2718 > select #13/A:402@C41
    2719 
    2720 1 atom, 1 residue, 1 model selected 
    2721 
    2722 > select add #13/A:402@C42
    2723 
    2724 2 atoms, 1 residue, 1 model selected 
    2725 
    2726 > hide #!14 models
    2727 
    2728 > select add #13/A:402@C43
    2729 
    2730 3 atoms, 1 residue, 1 model selected 
    2731 
    2732 > select add #13/A:402@C44
    2733 
    2734 4 atoms, 1 residue, 1 model selected 
    2735 
    2736 > show #!14 models
    2737 
    2738 > select add #13/A:402@C40
    2739 
    2740 5 atoms, 1 residue, 1 model selected 
    2741 
    2742 > delete sel
    2743 
    2744 > hide #!14 models
    2745 
    2746 > hide #13 models
    2747 
    2748 > show #13 models
    2749 
    2750 > hide #13 models
    2751 
    2752 > size stickRadius 0.3
    2753 
    2754 Changed 38701 bond radii 
    2755 
    2756 > style #9 ball
    2757 
    2758 Changed 4737 atom styles 
    2759 
    2760 > style #9 stick
    2761 
    2762 Changed 4737 atom styles 
    2763 
    2764 > style #9 ball
    2765 
    2766 Changed 4737 atom styles 
    2767 
    2768 > style #9 ball
    2769 
    2770 Changed 4737 atom styles 
    2771 
    2772 > style #9 stick
    2773 
    2774 Changed 4737 atom styles 
    2775 
    2776 > style #9 ball
    2777 
    2778 Changed 4737 atom styles 
    2779 
    2780 > style #9 stick
    2781 
    2782 Changed 4737 atom styles 
    2783 
    2784 > hide #9 models
    2785 
    2786 > show #9 models
    2787 
    2788 > show #!10 models
    2789 
    2790 > volume #10 level 0.01355
    2791 
    2792 > hide #!10 models
    2793 
    2794 > camera ortho
    2795 
    2796 > save
    2797 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    2798 
    2799 ——— End of log from Fri Aug 16 16:43:58 2024 ———
    2800 
    2801 opened ChimeraX session 
    2802 
    2803 > close #13#14
    2804 
    2805 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    2806 > nd-6F9-K_BTPpH85_state2.pdb
    2807 
    2808 Chain information for NhaA-nd-6F9-K_BTPpH85_state2.pdb #13 
    2809 --- 
    2810 Chain | Description 
    2811 A | No description available 
    2812 B | No description available 
    2813 C | No description available 
    2814  
    2815 
    2816 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    2817 > nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc
    2818 
    2819 Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #14, grid size
    2820 248,248,248, pixel 0.837, shown at level 0.00735, step 1, values float32 
    2821 
    2822 > mmaker #13&dimer_TM to #9/A bring #14
    2823 
    2824 Parameters 
    2825 --- 
    2826 Chain pairing | bb 
    2827 Alignment algorithm | Needleman-Wunsch 
    2828 Similarity matrix | BLOSUM-62 
    2829 SS fraction | 0.3 
    2830 Gap open (HH/SS/other) | 18/18/6 
    2831 Gap extend | 1 
    2832 SS matrix |  |  | H | S | O 
    2833 ---|---|---|--- 
    2834 H | 6 | -9 | -6 
    2835 S |  | 6 | -6 
    2836 O |  |  | 4 
    2837 Iteration cutoff | 2 
    2838  
    2839 Matchmaker NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#9) with NhaA-
    2840 nd-6F9-K_BTPpH85_state2.pdb, chain A (#13), sequence alignment score = 603.7 
    2841 RMSD between 114 pruned atom pairs is 0.605 angstroms; (across all 119 pairs:
    2842 1.054) 
    2843  
    2844 
    2845 > hide #!14 models
    2846 
    2847 > color #11,13&core light sea green
    2848 
    2849 > color #11,13&dimer cyan
    2850 
    2851 > hide #9 models
    2852 
    2853 > show #9 models
    2854 
    2855 > hide #9 models
    2856 
    2857 > color /A:1-10 orchid
    2858 
    2859 > color /B,C silver
    2860 
    2861 > hide #13 atoms
    2862 
    2863 > mcopy #15 toAtoms #13 settings h
    2864 
    2865 > show #15 models
    2866 
    2867 > hide #13,15 atoms
    2868 
    2869 > hide /B,C
    2870 
    2871 > hide /B,C target ac
    2872 
    2873 > show :132,133,163,164,300 target a
    2874 
    2875 > color #13,15 byhetero
    2876 
    2877 > size stickRadius 0.3
    2878 
    2879 Changed 38760 bond radii 
    2880 
    2881 > show #!14 models
    2882 
    2883 > transparency #14,16 40 target s
    2884 
    2885 > volume #14 level 0.01445
    2886 
    2887 > ui tool show "Side View"
    2888 
    2889 > show :H2O target a
    2890 
    2891 > show :O target a
    2892 
    2893 > show :NA target a
    2894 
    2895 > show #13,15 atoms
    2896 
    2897 > lighting simple
    2898 
    2899 > select #15/A:505@NA
    2900 
    2901 1 atom, 1 residue, 1 model selected 
    2902 
    2903 > style sel stick
    2904 
    2905 Changed 1 atom style 
    2906 
    2907 > select clear
    2908 
    2909 > volume #14 level 0.01372
    2910 
    2911 > show #!16 models
    2912 
    2913 > volume #16 level 0.01314
    2914 
    2915 > volume #16 level 0.01212
    2916 
    2917 > volume #16 level 0.01172
    2918 
    2919 > hide #13,15 cartoons
    2920 
    2921 > show #13,15 cartoons
    2922 
    2923 > hide #13,15 atoms
    2924 
    2925 > show :132,133,163,164,300,HOH,NA target a
    2926 
    2927 > hide /B,C target ac
    2928 
    2929 > view name binding_site
    2930 
    2931 > hide #!14 models
    2932 
    2933 > hide #!16 models
    2934 
    2935 > hide #13 models
    2936 
    2937 > show #13 models
    2938 
    2939 > hide #15 models
    2940 
    2941 > show #15 models
    2942 
    2943 > view list
    2944 
    2945 Named views: binding_site 
    2946 
    2947 > view binding_site
    2948 
    2949 > hide #15 models
    2950 
    2951 > show #15 models
    2952 
    2953 > hide #15 models
    2954 
    2955 > show #15 models
    2956 
    2957 > hide #15 models
    2958 
    2959 > show #15 models
    2960 
    2961 > hide #15 models
    2962 
    2963 > show #15 models
    2964 
    2965 > hide #13 models
    2966 
    2967 > show #!16 models
    2968 
    2969 > volume #16 level 0.0105
    2970 
    2971 > show #15 atoms
    2972 
    2973 > show #13 models
    2974 
    2975 > show #!14 models
    2976 
    2977 > hide #15 models
    2978 
    2979 > hide #!16 models
    2980 
    2981 > hide #13 models
    2982 
    2983 > hide #!14 models
    2984 
    2985 > show #15 models
    2986 
    2987 > show #!16 models
    2988 
    2989 > hide #!16 models
    2990 
    2991 > show #!16 models
    2992 
    2993 > hide #!16 models
    2994 
    2995 > ui mousemode right distance
    2996 
    2997 > distance #15/A:300@NZ #15/A:163@OD2
    2998 
    2999 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #15/A LYS 300 NZ and ASP 163 OD2:
    3000 3.986Å 
    3001 
    3002 > hide #!17 models
    3003 
    3004 > hide #17.1 models
    3005 
    3006 > show #!17 models
    3007 
    3008 > hide #15 models
    3009 
    3010 > show #13 models
    3011 
    3012 > show #!14 models
    3013 
    3014 > hide #!14 models
    3015 
    3016 > distance #13/A:300@NZ #13/A:163@OD2
    3017 
    3018 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #13/A LYS 300 NZ and ASP 163
    3019 OD2: 3.294Å 
    3020 
    3021 > show #17.1 models
    3022 
    3023 > show #!14 models
    3024 
    3025 > show #15 models
    3026 
    3027 > volume #14 level 0.01151
    3028 
    3029 > hide #13,15 cartoons
    3030 
    3031 > hide #!17 models
    3032 
    3033 > show #!17 models
    3034 
    3035 > hide #13 models
    3036 
    3037 > hide #!14 models
    3038 
    3039 > distance #15/A:132@O #15/A:164@OD1
    3040 
    3041 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #15/A THR 132 O and ASP 164 OD1:
    3042 4.183Å 
    3043 
    3044 > distance #15/A:132@O #15/A:164@OD2
    3045 
    3046 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #15/A THR 132 O and ASP 164 OD2:
    3047 4.787Å 
    3048 
    3049 > hide #15 models
    3050 
    3051 > show #13 models
    3052 
    3053 > distance #13/A:132@O #13/A:164@OD1
    3054 
    3055 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #13/A THR 132 O and ASP 164
    3056 OD1: 5.033Å 
    3057 
    3058 > distance #13/A:132@O #13/A:164@OD2
    3059 
    3060 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #13/A THR 132 O and ASP 164
    3061 OD2: 6.181Å 
    3062 
    3063 > show #15 models
    3064 
    3065 > hide #13 models
    3066 
    3067 > show #!16 models
    3068 
    3069 > hide #!16 models
    3070 
    3071 > hide #!17 models
    3072 
    3073 > hide #15 models
    3074 
    3075 > show #!14 models
    3076 
    3077 > show #13 models
    3078 
    3079 > show #15 models
    3080 
    3081 > show #!16 models
    3082 
    3083 > hide #!14 models
    3084 
    3085 > show #!14 models
    3086 
    3087 > hide #15 models
    3088 
    3089 > hide #!16 models
    3090 
    3091 > hide #!14 models
    3092 
    3093 > show #15 models
    3094 
    3095 > hide #13 models
    3096 
    3097 > show #15 cartoons
    3098 
    3099 > hide /B,C target ac
    3100 
    3101 > save
    3102 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    3103 
    3104 ——— End of log from Tue Aug 20 16:41:19 2024 ———
    3105 
    3106 opened ChimeraX session 
    3107 
    3108 > lighting soft
    3109 
    3110 > lighting simple
    3111 
    3112 > lighting soft
    3113 
    3114 > hide #15 atoms
    3115 
    3116 > close #17
    3117 
    3118 > rename #15 id 17
    3119 
    3120 > rename #16 id #18
    3121 
    3122 > rename #14 id #16
    3123 
    3124 > rename #13 id #15
    3125 
    3126 > close #11#12
    3127 
    3128 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    3129 > nd-6F9-K_BTPpH85_state1-plugged.pdb
    3130 
    3131 Chain information for NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb #11 
    3132 --- 
    3133 Chain | Description 
    3134 A | No description available 
    3135 B | No description available 
    3136 C | No description available 
    3137  
    3138 
    3139 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    3140 > nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc
    3141 
    3142 Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #12, grid
    3143 size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32 
    3144 
    3145 > close #12
    3146 
    3147 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    3148 > nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc
    3149 
    3150 Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
    3151 size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32 
    3152 
    3153 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    3154 > nd-6F9-K_BTPpH85_state1-unplugged.pdb
    3155 
    3156 Chain information for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13 
    3157 --- 
    3158 Chain | Description 
    3159 A | No description available 
    3160 B | No description available 
    3161 C | No description available 
    3162  
    3163 
    3164 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    3165 > nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc
    3166 
    3167 Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
    3168 size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32 
    3169 
    3170 > hide #!12 models
    3171 
    3172 > hide #!14 models
    3173 
    3174 > mmaker #11 to #7 bring 12
    3175 
    3176 > matchmaker #11 to #7 bring 12
    3177 
    3178 Invalid "bring" argument: invalid models specifier 
    3179 
    3180 > mmaker #11&dimer_TM to #7 bring #12
    3181 
    3182 Parameters 
    3183 --- 
    3184 Chain pairing | bb 
    3185 Alignment algorithm | Needleman-Wunsch 
    3186 Similarity matrix | BLOSUM-62 
    3187 SS fraction | 0.3 
    3188 Gap open (HH/SS/other) | 18/18/6 
    3189 Gap extend | 1 
    3190 SS matrix |  |  | H | S | O 
    3191 ---|---|---|--- 
    3192 H | 6 | -9 | -6 
    3193 S |  | 6 | -6 
    3194 O |  |  | 4 
    3195 Iteration cutoff | 2 
    3196  
    3197 Matchmaker NhaA-nd-6F9-K_BTPpH75_plugged.pdb, chain A (#7) with NhaA-
    3198 nd-6F9-K_BTPpH85_state1-plugged.pdb, chain A (#11), sequence alignment score =
    3199 621.1 
    3200 RMSD between 119 pruned atom pairs is 0.160 angstroms; (across all 119 pairs:
    3201 0.160) 
    3202  
    3203 
    3204 > mmaker #13&dimer_TM to #7 bring #14
    3205 
    3206 Parameters 
    3207 --- 
    3208 Chain pairing | bb 
    3209 Alignment algorithm | Needleman-Wunsch 
    3210 Similarity matrix | BLOSUM-62 
    3211 SS fraction | 0.3 
    3212 Gap open (HH/SS/other) | 18/18/6 
    3213 Gap extend | 1 
    3214 SS matrix |  |  | H | S | O 
    3215 ---|---|---|--- 
    3216 H | 6 | -9 | -6 
    3217 S |  | 6 | -6 
    3218 O |  |  | 4 
    3219 Iteration cutoff | 2 
    3220  
    3221 Matchmaker NhaA-nd-6F9-K_BTPpH75_plugged.pdb, chain A (#7) with NhaA-
    3222 nd-6F9-K_BTPpH85_state1-unplugged.pdb, chain A (#13), sequence alignment score
    3223 = 621.1 
    3224 RMSD between 119 pruned atom pairs is 0.167 angstroms; (across all 119 pairs:
    3225 0.167) 
    3226  
    3227 
    3228 > hide #17 models
    3229 
    3230 > show #15 models
    3231 
    3232 > hide #15 models
    3233 
    3234 > hide #13 models
    3235 
    3236 > hide #11 models
    3237 
    3238 > show #11 models
    3239 
    3240 > show #13 models
    3241 
    3242 > color #11,13,15&core light sea green
    3243 
    3244 > color #11,13,15&dimer cyan
    3245 
    3246 > hide #13 models
    3247 
    3248 > hide #11 models
    3249 
    3250 > show #9 models
    3251 
    3252 > color #7,9&core forest green
    3253 
    3254 > color #7,9&dimer pale green
    3255 
    3256 > color #7,9&core medium sea green
    3257 
    3258 > color #7,9&dimer pale green
    3259 
    3260 > show #11 models
    3261 
    3262 > hide #11 models
    3263 
    3264 > show #11 models
    3265 
    3266 > color #7,9&core forest green
    3267 
    3268 > color #7,9&dimer pale green
    3269 
    3270 > hide #11 models
    3271 
    3272 > color #7,9&core lime green
    3273 
    3274 > color #7,9&dimer pale green
    3275 
    3276 > cartoon style modeHelix default width 1.4 thickness 0.3
    3277 
    3278 > cartoon style modeHelix default width 1.5 thickness 0.3
    3279 
    3280 > cartoon style modeHelix default width 1.6 thickness 0.3
    3281 
    3282 > cartoon style modeHelix default width 1.8 thickness 0.3
    3283 
    3284 > show #11 models
    3285 
    3286 > hide #11 models
    3287 
    3288 > show #11 models
    3289 
    3290 > hide #11 models
    3291 
    3292 > show #11 models
    3293 
    3294 > hide #11 models
    3295 
    3296 > hide /B,C target ac
    3297 
    3298 > color #7,9&core yellow green
    3299 
    3300 > color #7,9&dimer pale green
    3301 
    3302 > color #7,9&core olive drab
    3303 
    3304 > color #7,9&dimer pale green
    3305 
    3306 > show #11 models
    3307 
    3308 > color #7,9&core forest green
    3309 
    3310 > color #7,9&dimer pale green
    3311 
    3312 > color #7,9&core olive drab
    3313 
    3314 > color #7,9&dimer pale green
    3315 
    3316 > color #7,9&core forest green
    3317 
    3318 > color #7,9&dimer pale green
    3319 
    3320 > color #7,9&core olive drab
    3321 
    3322 > color #7,9&dimer pale green
    3323 
    3324 > color #7,9&core lime green
    3325 
    3326 > color #7,9&dimer pale green
    3327 
    3328 > color #11,13,15&core light sea green
    3329 
    3330 > color #11,13,15&dimer cyan
    3331 
    3332 > color #11,13,15&core dark cyan
    3333 
    3334 > color #11,13,15&dimer cyan
    3335 
    3336 > hide #11 models
    3337 
    3338 > show #11 models
    3339 
    3340 > hide #9 models
    3341 
    3342 > show #9 models
    3343 
    3344 > hide #11 models
    3345 
    3346 > color #11,13,15&core light sea green
    3347 
    3348 > color #11,13,15&dimer cyan
    3349 
    3350 > show #11 models
    3351 
    3352 > hide #9 models
    3353 
    3354 > show #9 models
    3355 
    3356 > color #7,9&core forest green
    3357 
    3358 > color #7,9&dimer pale green
    3359 
    3360 > hide #11 models
    3361 
    3362 > show #11 models
    3363 
    3364 > hide #9 models
    3365 
    3366 > hide target a
    3367 
    3368 > color #11,13,15&core dark cyan
    3369 
    3370 > color #11,13,15&dimer cyan
    3371 
    3372 > show #9 models
    3373 
    3374 > hide #9 models
    3375 
    3376 > show #9 models
    3377 
    3378 > hide #9 models
    3379 
    3380 > show #9 models
    3381 
    3382 > hide #9 models
    3383 
    3384 > show #9 models
    3385 
    3386 > hide #9 models
    3387 
    3388 > show #9 models
    3389 
    3390 > hide #9 models
    3391 
    3392 > show #9 models
    3393 
    3394 > hide #9 models
    3395 
    3396 > show #9 models
    3397 
    3398 > hide #9 models
    3399 
    3400 > show #9 models
    3401 
    3402 > hide #9 models
    3403 
    3404 > show #9 models
    3405 
    3406 > hide #9 models
    3407 
    3408 > show #9 models
    3409 
    3410 > hide #9 models
    3411 
    3412 > show #9 models
    3413 
    3414 > hide #9 models
    3415 
    3416 > show #9 models
    3417 
    3418 > hide #9 models
    3419 
    3420 > show #9 models
    3421 
    3422 > hide #9 models
    3423 
    3424 > show #9 models
    3425 
    3426 > hide #9 models
    3427 
    3428 > color #7,9&core forest green
    3429 
    3430 > color #7,9&dimer pale green
    3431 
    3432 > color #11,13,15&core light sea green
    3433 
    3434 > color #11,13,15&dimer cyan
    3435 
    3436 > show #9 models
    3437 
    3438 > hide #9 models
    3439 
    3440 > show #9 models
    3441 
    3442 > hide #9 models
    3443 
    3444 > show #9 models
    3445 
    3446 > hide #9 models
    3447 
    3448 > show #9 models
    3449 
    3450 > hide #9 models
    3451 
    3452 > show #9 models
    3453 
    3454 > hide #9 models
    3455 
    3456 > show #9 models
    3457 
    3458 > hide #9 models
    3459 
    3460 > show #9 models
    3461 
    3462 > hide #9 models
    3463 
    3464 > show #9 models
    3465 
    3466 > hide #9 models
    3467 
    3468 > show #9 models
    3469 
    3470 > hide #9 models
    3471 
    3472 > show #9 models
    3473 
    3474 > hide #9 models
    3475 
    3476 > show #9 models
    3477 
    3478 > hide #11 models
    3479 
    3480 > show #13 models
    3481 
    3482 > hide #13 models
    3483 
    3484 > show #15 models
    3485 
    3486 > hide #9 models
    3487 
    3488 > hide #15 models
    3489 
    3490 > show #15 models
    3491 
    3492 > show #9 models
    3493 
    3494 > show #9,15 cartoons
    3495 
    3496 > hide /B,C target ac
    3497 
    3498 > show #17 models
    3499 
    3500 > hide #9 models
    3501 
    3502 > hide #17 models
    3503 
    3504 > show #13 models
    3505 
    3506 > hide #13 models
    3507 
    3508 > show #9 models
    3509 
    3510 > hide #9 models
    3511 
    3512 > show #13 models
    3513 
    3514 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    3515 > nd-6F9-K_BTPpH75_consensus.pdb
    3516 
    3517 Chain information for NhaA-nd-6F9-K_BTPpH75_consensus.pdb #19 
    3518 --- 
    3519 Chain | Description 
    3520 A D | No description available 
    3521 B E | No description available 
    3522 C F | No description available 
    3523  
    3524 
    3525 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    3526 > nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc
    3527 
    3528 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
    3529 248,248,248, pixel 0.837, shown at level 0.00609, step 1, values float32 
    3530 
    3531 > hide #13,15,19 atoms
    3532 
    3533 > show #13,15,19 cartoons
    3534 
    3535 > hide /B,C target ac
    3536 
    3537 > hide #!20 models
    3538 
    3539 > mmaker #19&dimer_TM to #9 bring #20
    3540 
    3541 Parameters 
    3542 --- 
    3543 Chain pairing | bb 
    3544 Alignment algorithm | Needleman-Wunsch 
    3545 Similarity matrix | BLOSUM-62 
    3546 SS fraction | 0.3 
    3547 Gap open (HH/SS/other) | 18/18/6 
    3548 Gap extend | 1 
    3549 SS matrix |  |  | H | S | O 
    3550 ---|---|---|--- 
    3551 H | 6 | -9 | -6 
    3552 S |  | 6 | -6 
    3553 O |  |  | 4 
    3554 Iteration cutoff | 2 
    3555  
    3556 Matchmaker NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#9) with NhaA-
    3557 nd-6F9-K_BTPpH75_consensus.pdb, chain A (#19), sequence alignment score =
    3558 620.5 
    3559 RMSD between 119 pruned atom pairs is 0.103 angstroms; (across all 119 pairs:
    3560 0.103) 
    3561  
    3562 
    3563 > color #19/A,D:86-180,275-388 forest green
    3564 
    3565 > color #19/A,D:11-85,181-274 pale green
    3566 
    3567 > hide #19 models
    3568 
    3569 > hide #15 models
    3570 
    3571 > color #11,13,15&core light sea green
    3572 
    3573 > color #11,13,15&dimer pale turquoise
    3574 
    3575 > color #11,13,15&core light sea green
    3576 
    3577 > color #11,13,15&dimer cyan
    3578 
    3579 > color #11,13,15&core light sea green
    3580 
    3581 > color #11,13,15&dimer pale turquoise
    3582 
    3583 > show #15 models
    3584 
    3585 > hide #15 models
    3586 
    3587 > show #11 models
    3588 
    3589 > hide #11 models
    3590 
    3591 > show #9 models
    3592 
    3593 > hide #9 models
    3594 
    3595 > show #9 models
    3596 
    3597 > hide #9 models
    3598 
    3599 > show #9 models
    3600 
    3601 > hide #9 models
    3602 
    3603 > color #11,13,15&core light sea green
    3604 
    3605 > color #11,13,15&dimer cyan
    3606 
    3607 > color #11,13,15&core light sea green
    3608 
    3609 > color #11,13,15&dimer pale turquoise
    3610 
    3611 > color /A:1-10 orchid
    3612 
    3613 > color /A,D:1-10 orchid
    3614 
    3615 > show #11 models
    3616 
    3617 > show #15 models
    3618 
    3619 > hide #15 models
    3620 
    3621 > hide #13 models
    3622 
    3623 > show #13 models
    3624 
    3625 > hide #13 models
    3626 
    3627 > show #!10 models
    3628 
    3629 > hide #!10 models
    3630 
    3631 > show #9 models
    3632 
    3633 > hide #9 models
    3634 
    3635 > show #7 models
    3636 
    3637 > mcopy #7 toAtoms #11 settings h
    3638 
    3639 > hide #7 models
    3640 
    3641 > show #9 models
    3642 
    3643 > hide #9 models
    3644 
    3645 > hide #11 models
    3646 
    3647 > show #13 models
    3648 
    3649 > mcopy #9 toAtoms #11,19 settings h
    3650 
    3651 > mcopy #9 toAtoms #13,19 settings h
    3652 
    3653 > show #11 models
    3654 
    3655 > hide #13 models
    3656 
    3657 > mcopy #7 toAtoms #11 settings h
    3658 
    3659 > show #13 models
    3660 
    3661 > hide #13 models
    3662 
    3663 > hide #11 models
    3664 
    3665 > show #7 models
    3666 
    3667 > hide #7 models
    3668 
    3669 > show #!8 models
    3670 
    3671 > hide #!8 models
    3672 
    3673 > show #17 models
    3674 
    3675 > hide #17 models
    3676 
    3677 > show #!16 models
    3678 
    3679 > hide #!16 models
    3680 
    3681 > show #15 models
    3682 
    3683 > hide #15 models
    3684 
    3685 > show #19 models
    3686 
    3687 > mcopy #19/A-C toAtoms #19/D-F settings h
    3688 
    3689 > mcopy #19/A toAtoms #19/D settings h
    3690 
    3691 > mcopy #9 toAtoms #19/A settings h
    3692 
    3693 > mcopy #9/A toAtoms #19/A settings h
    3694 
    3695 > mcopy #9/A toAtoms #19/D settings h
    3696 
    3697 > mcopy #9/A toAtoms #19/D settings h matchResidues false
    3698 
    3699 > mcopy #9/B toAtoms #19/E settings h matchResidues false
    3700 
    3701 > mcopy #9/C toAtoms #19/F settings h matchResidues false
    3702 
    3703 > hide /B,C,E,F target ac
    3704 
    3705 > save
    3706 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    3707 
    3708 > cartoon style modeHelix default width 1.8 thickness 0.3
    3709 
    3710 > size stickRadius 0.3
    3711 
    3712 Changed 53299 bond radii 
    3713 
    3714 > save
    3715 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    3716 
    3717 ——— End of log from Thu Aug 22 17:18:58 2024 ———
    3718 
    3719 opened ChimeraX session 
    3720 
    3721 > lighting soft multiShadow 1024
    3722 
    3723 > show /B,C,E,F target c
    3724 
    3725 > color /B,C,E,F silver
    3726 
    3727 > view
    3728 
    3729 > ui tool show "Side View"
    3730 
    3731 > hide #19/A,D:1-10 target c
    3732 
    3733 > show #19:CDL,PTY target a
    3734 
    3735 > style #19:CDL,PTY ball
    3736 
    3737 Changed 150 atom styles 
    3738 
    3739 > view name dimer_view-all_front
    3740 
    3741 > show #!20 models
    3742 
    3743 > surface dust #20 size 1
    3744 
    3745 > volume #20 level 0.006821
    3746 
    3747 > view
    3748 
    3749 > volume #20 level 0.007734
    3750 
    3751 > volume #20 level 0.0081
    3752 
    3753 > volume #20 level 0.008465
    3754 
    3755 > view
    3756 
    3757 > volume #20 level 0.008648
    3758 
    3759 > view
    3760 
    3761 [Repeated 1 time(s)]
    3762 
    3763 > view name dimer_view-all_front
    3764 
    3765 > transparency #20 60
    3766 
    3767 > lighting simple
    3768 
    3769 > select #19/A:401@C58
    3770 
    3771 1 atom, 1 residue, 1 model selected 
    3772 
    3773 > hide #!20 models
    3774 
    3775 > select add #19/A:401@C59
    3776 
    3777 2 atoms, 1 residue, 1 model selected 
    3778 
    3779 > select add #19/A:401@C60
    3780 
    3781 3 atoms, 1 residue, 1 model selected 
    3782 
    3783 > select add #19/A:401@C61
    3784 
    3785 4 atoms, 1 residue, 1 model selected 
    3786 
    3787 > select add #19/A:401@C62
    3788 
    3789 5 atoms, 1 residue, 1 model selected 
    3790 
    3791 > select add #19/A:401@C63
    3792 
    3793 6 atoms, 1 residue, 1 model selected 
    3794 
    3795 > select add #19/A:401@C64
    3796 
    3797 7 atoms, 1 residue, 1 model selected 
    3798 
    3799 > select add #19/A:401@C65
    3800 
    3801 8 atoms, 1 residue, 1 model selected 
    3802 
    3803 > select add #19/A:401@C66
    3804 
    3805 9 atoms, 1 residue, 1 model selected 
    3806 
    3807 > select add #19/A:401@C67
    3808 
    3809 10 atoms, 1 residue, 1 model selected 
    3810 
    3811 > show #!20 models
    3812 
    3813 > select #19/A:401@C77
    3814 
    3815 1 atom, 1 residue, 1 model selected 
    3816 
    3817 > select add #19/A:401@C58
    3818 
    3819 2 atoms, 1 residue, 1 model selected 
    3820 
    3821 > volume #20 level 0.009561
    3822 
    3823 > select add #19/A:401@C24
    3824 
    3825 3 atoms, 1 residue, 1 model selected 
    3826 
    3827 > select add #19/A:402@C16
    3828 
    3829 4 atoms, 2 residues, 1 model selected 
    3830 
    3831 > select add #19/A:402@C37
    3832 
    3833 5 atoms, 2 residues, 1 model selected 
    3834 
    3835 > hide #!20 models
    3836 
    3837 > select add #19/A:401@C59
    3838 
    3839 6 atoms, 2 residues, 1 model selected 
    3840 
    3841 > select add #19/A:401@C60
    3842 
    3843 7 atoms, 2 residues, 1 model selected 
    3844 
    3845 > select add #19/A:401@C61
    3846 
    3847 8 atoms, 2 residues, 1 model selected 
    3848 
    3849 > select add #19/A:401@C62
    3850 
    3851 9 atoms, 2 residues, 1 model selected 
    3852 
    3853 > select add #19/A:401@C63
    3854 
    3855 10 atoms, 2 residues, 1 model selected 
    3856 
    3857 > select add #19/A:401@C64
    3858 
    3859 11 atoms, 2 residues, 1 model selected 
    3860 
    3861 > select add #19/A:401@C65
    3862 
    3863 12 atoms, 2 residues, 1 model selected 
    3864 
    3865 > select add #19/A:401@C66
    3866 
    3867 13 atoms, 2 residues, 1 model selected 
    3868 
    3869 > select add #19/A:401@C67
    3870 
    3871 14 atoms, 2 residues, 1 model selected 
    3872 
    3873 > select add #19/A:401@C78
    3874 
    3875 15 atoms, 2 residues, 1 model selected 
    3876 
    3877 > select add #19/A:401@C79
    3878 
    3879 16 atoms, 2 residues, 1 model selected 
    3880 
    3881 > select add #19/A:401@C80
    3882 
    3883 17 atoms, 2 residues, 1 model selected 
    3884 
    3885 > select add #19/A:401@C81
    3886 
    3887 18 atoms, 2 residues, 1 model selected 
    3888 
    3889 > select add #19/A:401@C82
    3890 
    3891 19 atoms, 2 residues, 1 model selected 
    3892 
    3893 > select add #19/A:401@C83
    3894 
    3895 20 atoms, 2 residues, 1 model selected 
    3896 
    3897 > select add #19/A:401@C84
    3898 
    3899 21 atoms, 2 residues, 1 model selected 
    3900 
    3901 > select add #19/A:401@C85
    3902 
    3903 22 atoms, 2 residues, 1 model selected 
    3904 
    3905 > select add #19/A:401@C86
    3906 
    3907 23 atoms, 2 residues, 1 model selected 
    3908 
    3909 > select add #19/A:401@C87
    3910 
    3911 24 atoms, 2 residues, 1 model selected 
    3912 
    3913 > select add #19/A:401@C25
    3914 
    3915 25 atoms, 2 residues, 1 model selected 
    3916 
    3917 > select add #19/A:401@C26
    3918 
    3919 26 atoms, 2 residues, 1 model selected 
    3920 
    3921 > select add #19/A:401@C27
    3922 
    3923 27 atoms, 2 residues, 1 model selected 
    3924 
    3925 > select add #19/A:402@C17
    3926 
    3927 28 atoms, 2 residues, 1 model selected 
    3928 
    3929 > select add #19/A:402@C18
    3930 
    3931 29 atoms, 2 residues, 1 model selected 
    3932 
    3933 > select add #19/A:402@C19
    3934 
    3935 30 atoms, 2 residues, 1 model selected 
    3936 
    3937 > select add #19/A:402@C20
    3938 
    3939 31 atoms, 2 residues, 1 model selected 
    3940 
    3941 > select add #19/A:402@C21
    3942 
    3943 32 atoms, 2 residues, 1 model selected 
    3944 
    3945 > select add #19/A:402@C22
    3946 
    3947 33 atoms, 2 residues, 1 model selected 
    3948 
    3949 > select add #19/A:402@C23
    3950 
    3951 34 atoms, 2 residues, 1 model selected 
    3952 
    3953 > select add #19/A:402@C24
    3954 
    3955 35 atoms, 2 residues, 1 model selected 
    3956 
    3957 > select add #19/A:402@C25
    3958 
    3959 36 atoms, 2 residues, 1 model selected 
    3960 
    3961 > select add #19/A:402@C26
    3962 
    3963 37 atoms, 2 residues, 1 model selected 
    3964 
    3965 > select add #19/A:402@C27
    3966 
    3967 38 atoms, 2 residues, 1 model selected 
    3968 
    3969 > select add #19/A:402@C28
    3970 
    3971 39 atoms, 2 residues, 1 model selected 
    3972 
    3973 > select add #19/A:402@C29
    3974 
    3975 40 atoms, 2 residues, 1 model selected 
    3976 
    3977 > select add #19/A:402@C38
    3978 
    3979 41 atoms, 2 residues, 1 model selected 
    3980 
    3981 > select add #19/A:402@C39
    3982 
    3983 42 atoms, 2 residues, 1 model selected 
    3984 
    3985 > select add #19/A:402@C40
    3986 
    3987 43 atoms, 2 residues, 1 model selected 
    3988 
    3989 > select add #19/A:402@C41
    3990 
    3991 44 atoms, 2 residues, 1 model selected 
    3992 
    3993 > select add #19/A:402@C42
    3994 
    3995 45 atoms, 2 residues, 1 model selected 
    3996 
    3997 > select add #19/A:402@C43
    3998 
    3999 46 atoms, 2 residues, 1 model selected 
    4000 
    4001 > select add #19/A:402@C44
    4002 
    4003 47 atoms, 2 residues, 1 model selected 
    4004 
    4005 > delete sel
    4006 
    4007 > show #!20 models
    4008 
    4009 > hide #!20 models
    4010 
    4011 > view list
    4012 
    4013 Named views: binding_site, dimer_view-all_front 
    4014 
    4015 > view dimer_view-all_front
    4016 
    4017 > lighting soft
    4018 
    4019 > view name dimer_view-all_front
    4020 
    4021 > lighting soft multiShadow 1024
    4022 
    4023 > lighting gentle multiShadow 1024
    4024 
    4025 > lighting soft multiShadow 1024
    4026 
    4027 > show #!20 models
    4028 
    4029 > transparency #20 0
    4030 
    4031 > lighting soft
    4032 
    4033 > lighting soft multiShadow 1024
    4034 
    4035 > hide #!20 models
    4036 
    4037 > view dimer_view-all_front
    4038 
    4039 [Repeated 1 time(s)]
    4040 
    4041 > save NhaA-K-pH75-consensus_model_front_no-Nterm.png supersample 3
    4042 > transparentBackground true
    4043 
    4044 > hide #19 models
    4045 
    4046 > show #1 models
    4047 
    4048 > view dimer_view-all_front
    4049 
    4050 > turn y 180
    4051 
    4052 > turn y 10
    4053 
    4054 > turn y -20
    4055 
    4056 > turn y 10
    4057 
    4058 > hide #1 models
    4059 
    4060 > show #!8 models
    4061 
    4062 > hide #!8 models
    4063 
    4064 > show #7 models
    4065 
    4066 > hide #7 models
    4067 
    4068 > show #7 models
    4069 
    4070 > show #9 models
    4071 
    4072 > show #19 models
    4073 
    4074 > view list
    4075 
    4076 Named views: binding_site, dimer_view-all_front 
    4077 
    4078 > view dimer_view-all_front
    4079 
    4080 > turn y 180
    4081 
    4082 [Repeated 13 time(s)]
    4083 
    4084 > view dimer_view-all_front
    4085 
    4086 > hide #9 models
    4087 
    4088 > hide #7 models
    4089 
    4090 > turn y 180
    4091 
    4092 [Repeated 1 time(s)]
    4093 
    4094 > show #7 models
    4095 
    4096 > hide #7 models
    4097 
    4098 > turn y 180
    4099 
    4100 [Repeated 1 time(s)]
    4101 
    4102 > turn z 1
    4103 
    4104 > turn z -1
    4105 
    4106 > turn z 0.05
    4107 
    4108 > turn y 180
    4109 
    4110 [Repeated 2 time(s)]
    4111 
    4112 > view dimer_view-all_front
    4113 
    4114 > turn z 0.1
    4115 
    4116 > turn y 180
    4117 
    4118 [Repeated 3 time(s)]
    4119 
    4120 > view dimer_view-all_front
    4121 
    4122 > turn z 0.04
    4123 
    4124 > turn y 180
    4125 
    4126 [Repeated 1 time(s)]
    4127 
    4128 > view dimer_view-all_front
    4129 
    4130 > turn z 0.06
    4131 
    4132 > turn y 180
    4133 
    4134 [Repeated 7 time(s)]
    4135 
    4136 > view dimer_view-all_front
    4137 
    4138 > turn z 0.08
    4139 
    4140 > turn y 180
    4141 
    4142 [Repeated 1 time(s)]
    4143 
    4144 > view dimer_view-all_front
    4145 
    4146 > turn x 0.08
    4147 
    4148 > view dimer_view-all_front
    4149 
    4150 > turn x -0.08
    4151 
    4152 > turn y 180
    4153 
    4154 [Repeated 1 time(s)]
    4155 
    4156 > view dimer_view-all_front
    4157 
    4158 > turn x -0.1
    4159 
    4160 > turn y 180
    4161 
    4162 [Repeated 7 time(s)]
    4163 
    4164 > view dimer_view-all_front
    4165 
    4166 > turn y 180
    4167 
    4168 > save NhaA-K-pH75-consensus_model_back_no-Nterm.png supersample 3
    4169 > transparentBackground true
    4170 
    4171 > view dimer_view-all_front
    4172 
    4173 > show #1 models
    4174 
    4175 > hide #19 models
    4176 
    4177 > show #19 models
    4178 
    4179 > hide #19 models
    4180 
    4181 > show #19 models
    4182 
    4183 > hide #19 models
    4184 
    4185 > view
    4186 
    4187 > show #1/A:5-8 target a
    4188 
    4189 > hide #1 atoms
    4190 
    4191 > show #1/A:7-9 target a
    4192 
    4193 > hide #1 atoms
    4194 
    4195 > view list
    4196 
    4197 Named views: binding_site, dimer_view-all_front 
    4198 
    4199 > view dimer_view-all_front
    4200 
    4201 > view
    4202 
    4203 > show #5 models
    4204 
    4205 > hide #5 models
    4206 
    4207 > show #5 models
    4208 
    4209 > hide #1 models
    4210 
    4211 > show #1 models
    4212 
    4213 > hide #5 models
    4214 
    4215 > show #!4 models
    4216 
    4217 > hide #!4 models
    4218 
    4219 > show #5 models
    4220 
    4221 > hide #1 models
    4222 
    4223 > show #1 models
    4224 
    4225 > hide #5 models
    4226 
    4227 > view list
    4228 
    4229 Named views: binding_site, dimer_view-all_front 
    4230 
    4231 > view dimer_view-all_front
    4232 
    4233 > view
    4234 
    4235 > turn y 10
    4236 
    4237 > turn y -10
    4238 
    4239 > view name mono_front
    4240 
    4241 > turn y 10
    4242 
    4243 > view name mono_front
    4244 
    4245 > turn y -10
    4246 
    4247 > view name mono_front
    4248 
    4249 > turn y 5
    4250 
    4251 > turn y -5
    4252 
    4253 [Repeated 2 time(s)]
    4254 
    4255 > view list
    4256 
    4257 Named views: binding_site, dimer_view-all_front, mono_front 
    4258 
    4259 > view mono_front
    4260 
    4261 [Repeated 1 time(s)]
    4262 
    4263 > turn y 180
    4264 
    4265 > turn y 5
    4266 
    4267 > show #9 models
    4268 
    4269 > hide #9 models
    4270 
    4271 > show #9 models
    4272 
    4273 > hide #9 models
    4274 
    4275 > show #9 models
    4276 
    4277 > hide #9 models
    4278 
    4279 > show #!10 models
    4280 
    4281 > hide #!10 models
    4282 
    4283 > show #9 models
    4284 
    4285 > hide #9 models
    4286 
    4287 > show #9 models
    4288 
    4289 > hide #9 models
    4290 
    4291 > view name mono_back
    4292 
    4293 > view list
    4294 
    4295 Named views: binding_site, dimer_view-all_front, mono_back, mono_front 
    4296 
    4297 > view mono_back
    4298 
    4299 [Repeated 1 time(s)]
    4300 
    4301 > view name mono_back
    4302 
    4303 > save NhaA-K-pH55-plugged_model_back.png supersample 3 transparentBackground
    4304 > true
    4305 
    4306 > graphics silhouettes width 2
    4307 
    4308 > graphics silhouettes width 3
    4309 
    4310 > graphics silhouettes width 2
    4311 
    4312 > graphics silhouettes width 3
    4313 
    4314 > graphics silhouettes width 2
    4315 
    4316 > show #3 models
    4317 
    4318 > hide #1 models
    4319 
    4320 > save NhaA-K-pH63-plugged_model_back.png supersample 3 transparentBackground
    4321 > true
    4322 
    4323 > show #!4 models
    4324 
    4325 > hide #!4 models
    4326 
    4327 > show #5 models
    4328 
    4329 > hide #3 models
    4330 
    4331 > lighting gentle multiShadow 1024
    4332 
    4333 > lighting soft multiShadow 1024
    4334 
    4335 > save NhaA-K-pH63-unplugged_model_back.png supersample 3
    4336 > transparentBackground true
    4337 
    4338 > hide #5 models
    4339 
    4340 > show #7 models
    4341 
    4342 > save NhaA-K-pH75-plugged_model_back_6F9.png supersample 3
    4343 > transparentBackground true
    4344 
    4345 > show #9 models
    4346 
    4347 > hide #7 models
    4348 
    4349 > save NhaA-K-pH75-unplugged_model_back_6F9.png supersample 3
    4350 > transparentBackground true
    4351 
    4352 > hide #9 models
    4353 
    4354 > show #11 models
    4355 
    4356 > hide #11 models
    4357 
    4358 > show #1 models
    4359 
    4360 > hide /B,C target a
    4361 
    4362 > hide /B,C target c
    4363 
    4364 > view
    4365 
    4366 > show #!4 models
    4367 
    4368 > hide #!4 models
    4369 
    4370 > show #3 models
    4371 
    4372 > hide #3 models
    4373 
    4374 > view
    4375 
    4376 > view name mono_back_
    4377 
    4378 > graphics silhouettes width 3
    4379 
    4380 > graphics silhouettes width 2
    4381 
    4382 > save NhaA-K-pH55-plugged_model_back.png supersample 3 transparentBackground
    4383 > true
    4384 
    4385 > show #3 models
    4386 
    4387 > hide #1 models
    4388 
    4389 > save NhaA-K-pH63-plugged_model_back.png supersample 3 transparentBackground
    4390 > true
    4391 
    4392 > view list
    4393 
    4394 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    4395 mono_front 
    4396 
    4397 > view mono_back_
    4398 
    4399 > view name mono_back_
    4400 
    4401 > save NhaA-K-pH63-plugged_model_back.png supersample 3 transparentBackground
    4402 > true
    4403 
    4404 > show #1 models
    4405 
    4406 > hide #3 models
    4407 
    4408 > save NhaA-K-pH55-plugged_model_back.png supersample 3 transparentBackground
    4409 > true
    4410 
    4411 > hide #1 models
    4412 
    4413 > show #5 models
    4414 
    4415 > save NhaA-K-pH63-unplugged_model_back.png supersample 3
    4416 > transparentBackground true
    4417 
    4418 > show #7 models
    4419 
    4420 > hide #5 models
    4421 
    4422 > save NhaA-K-pH75-plugged_model_back.png supersample 3 transparentBackground
    4423 > true
    4424 
    4425 > show #!8 models
    4426 
    4427 > hide #!8 models
    4428 
    4429 > hide #7 models
    4430 
    4431 > show #9 models
    4432 
    4433 > save NhaA-K-pH75-unplugged_model_back.png supersample 3
    4434 > transparentBackground true
    4435 
    4436 > show #11 models
    4437 
    4438 > hide #9 models
    4439 
    4440 > save NhaA-K-pH85-plugged_model_back.png supersample 3 transparentBackground
    4441 > true
    4442 
    4443 > show #13 models
    4444 
    4445 > hide #11 models
    4446 
    4447 > save NhaA-K-pH85-unplugged_model_back.png supersample 3
    4448 > transparentBackground true
    4449 
    4450 > show #15 models
    4451 
    4452 > hide #13 models
    4453 
    4454 > save NhaA-K-pH85-state2-unplugged_model_back.png supersample 3
    4455 > transparentBackground true
    4456 
    4457 > hide #15 models
    4458 
    4459 > show #17 models
    4460 
    4461 > save NhaA-Na-pH85-unplugged_model_back.png supersample 3
    4462 > transparentBackground true
    4463 
    4464 > show #15 models
    4465 
    4466 > hide #15 models
    4467 
    4468 > show #15 models
    4469 
    4470 > hide #15 models
    4471 
    4472 > show #15 models
    4473 
    4474 > hide #15 models
    4475 
    4476 > show #15 models
    4477 
    4478 > hide #15 models
    4479 
    4480 > show #15 models
    4481 
    4482 > hide #15 models
    4483 
    4484 > view name mono_back_
    4485 
    4486 > turn x 90
    4487 
    4488 > turn x -90
    4489 
    4490 > turn x -95
    4491 
    4492 > turn x 95
    4493 
    4494 [Repeated 1 time(s)]
    4495 
    4496 > hide #17 models
    4497 
    4498 > show #13 models
    4499 
    4500 > hide #13 models
    4501 
    4502 > show #7 models
    4503 
    4504 > view list
    4505 
    4506 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    4507 mono_front 
    4508 
    4509 > view mono_back_
    4510 
    4511 > turn x 90
    4512 
    4513 > show #7/A:7-9 target a
    4514 
    4515 > hide #7 atoms
    4516 
    4517 > hide #7 models
    4518 
    4519 > show #1 models
    4520 
    4521 > save NhaA-K-pH55-plugged_model_top.png supersample 3 transparentBackground
    4522 > true
    4523 
    4524 > show #3 models
    4525 
    4526 > hide #1 models
    4527 
    4528 > save NhaA-K-pH63-plugged_model_top.png supersample 3 transparentBackground
    4529 > true
    4530 
    4531 > show #5 models
    4532 
    4533 > hide #3 models
    4534 
    4535 > save NhaA-K-pH63-unplugged_model_top.png supersample 3 transparentBackground
    4536 > true
    4537 
    4538 > show #7 models
    4539 
    4540 > hide #5 models
    4541 
    4542 > save NhaA-K-pH75-plugged_model_top.png supersample 3 transparentBackground
    4543 > true
    4544 
    4545 > show #9 models
    4546 
    4547 > hide #7 models
    4548 
    4549 > save NhaA-K-pH75-unplugged_model_top.png supersample 3 transparentBackground
    4550 > true
    4551 
    4552 > show #11 models
    4553 
    4554 > hide #9 models
    4555 
    4556 > save NhaA-K-pH85-state1-plugged_model_top.png supersample 3
    4557 > transparentBackground true
    4558 
    4559 > show #13 models
    4560 
    4561 > hide #11 models
    4562 
    4563 > save NhaA-K-pH85-state1-unplugged_model_top.png supersample 3
    4564 > transparentBackground true
    4565 
    4566 > show #15 models
    4567 
    4568 > hide #13 models
    4569 
    4570 > save NhaA-K-pH85-state2-unplugged_model_top.png supersample 3
    4571 > transparentBackground true
    4572 
    4573 > show #17 models
    4574 
    4575 > hide #15 models
    4576 
    4577 > save NhaA-Na-pH85-unplugged_model_top.png supersample 3
    4578 > transparentBackground true
    4579 
    4580 > save
    4581 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    4582 
    4583 > view list
    4584 
    4585 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    4586 mono_front 
    4587 
    4588 > view dimer_view-all_front
    4589 
    4590 > hide #17 models
    4591 
    4592 > show #19 models
    4593 
    4594 > show #!20 models
    4595 
    4596 > volume #20 level 0.01212
    4597 
    4598 > volume #20 level 0.01376
    4599 
    4600 > hide #!20 models
    4601 
    4602 > color #19/A,D:86-180,275-388 forest green
    4603 
    4604 > color #19/A,D:11-85,181-274 pale green
    4605 
    4606 > color /B,C,E,F gray
    4607 
    4608 > color /B,C,E,F silver
    4609 
    4610 > color #20:CDL,PTY gray
    4611 
    4612 > color #20:CDL,PTY gray target a
    4613 
    4614 > color #19:CDL,PTY gray
    4615 
    4616 > show #!20 models
    4617 
    4618 > color zone #20 near #19
    4619 
    4620 > color zone #20 near #19 distance 3
    4621 
    4622 > color zone #20 near #19 distance 3.5
    4623 
    4624 > volume #20 level 0.01358
    4625 
    4626 > color #19/A,D:86-180,275-388 forest green
    4627 
    4628 > color #19/A,D:1-85,181-274 pale green
    4629 
    4630 > color zone #20 near #19 distance 3.5
    4631 
    4632 > color zone #20 near #19
    4633 
    4634 > volume #20 level 0.01504
    4635 
    4636 > surface dust #20 size 5
    4637 
    4638 > surface dust #20 size 4
    4639 
    4640 > surface dust #20 size 3
    4641 
    4642 > surface dust #20 size 4
    4643 
    4644 > surface dust #20 size 10
    4645 
    4646 > surface dust #20 size 1
    4647 
    4648 > surface dust #20 size 4
    4649 
    4650 > surface dust #20 size 3
    4651 
    4652 > surface dust #20 size 4
    4653 
    4654 > volume splitbyzone #20
    4655 
    4656 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #21.1, grid
    4657 size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32 
    4658 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #21.2, grid
    4659 size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32 
    4660 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #21.3, grid
    4661 size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32 
    4662 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #21.4, grid
    4663 size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32 
    4664 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #21.5, grid
    4665 size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32 
    4666 
    4667 > hide #!21.1 models
    4668 
    4669 > show #!21.1 models
    4670 
    4671 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    4672 > nd-6F9-K_BTPpH75_consensus_lp6.mrc
    4673 
    4674 Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
    4675 pixel 0.837, shown at level 0.00427, step 1, values float32 
    4676 
    4677 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    4678 > nd-6F9-K_BTPpH75_consensus.pdb
    4679 
    4680 Chain information for NhaA-nd-6F9-K_BTPpH75_consensus.pdb #23 
    4681 --- 
    4682 Chain | Description 
    4683 A D | No description available 
    4684 B E | No description available 
    4685 C F | No description available 
    4686  
    4687 
    4688 > mmaker #23 to #19 bring #22
    4689 
    4690 Parameters 
    4691 --- 
    4692 Chain pairing | bb 
    4693 Alignment algorithm | Needleman-Wunsch 
    4694 Similarity matrix | BLOSUM-62 
    4695 SS fraction | 0.3 
    4696 Gap open (HH/SS/other) | 18/18/6 
    4697 Gap extend | 1 
    4698 SS matrix |  |  | H | S | O 
    4699 ---|---|---|--- 
    4700 H | 6 | -9 | -6 
    4701 S |  | 6 | -6 
    4702 O |  |  | 4 
    4703 Iteration cutoff | 2 
    4704  
    4705 Matchmaker NhaA-nd-6F9-K_BTPpH75_consensus.pdb, chain A (#19) with NhaA-
    4706 nd-6F9-K_BTPpH75_consensus.pdb, chain A (#23), sequence alignment score =
    4707 1997.6 
    4708 RMSD between 388 pruned atom pairs is 0.000 angstroms; (across all 388 pairs:
    4709 0.000) 
    4710  
    4711 
    4712 > hide #23 models
    4713 
    4714 > volume #22 level 0.002198
    4715 
    4716 > volume #22 level 0.002307
    4717 
    4718 > transparency #22 1
    4719 
    4720 > transparency #22 95
    4721 
    4722 > color #22 snow
    4723 
    4724 > transparency #22 99
    4725 
    4726 > transparency #22 98
    4727 
    4728 > transparency #22 95
    4729 
    4730 > hide #19 models
    4731 
    4732 > surface dust #21,22 size 4
    4733 
    4734 > surface dust #21,22 size 3
    4735 
    4736 > surface dust #21,22 size 4
    4737 
    4738 > color #21.1 gray
    4739 
    4740 > color #21.5 gainsboro
    4741 
    4742 > color #21.1 dark gray
    4743 
    4744 > color #21.1 gray
    4745 
    4746 > color #21.1 dark gray
    4747 
    4748 > graphics silhouettes false
    4749 
    4750 > graphics silhouettes true
    4751 
    4752 > transparency #22 100
    4753 
    4754 > lighting soft multiShadow 1024
    4755 
    4756 > lighting flat
    4757 
    4758 > lighting soft
    4759 
    4760 > lighting soft multiShadow 1024
    4761 
    4762 > save NhaA-K-pH75-consensus_map_front.png supersample 3 transparentBackground
    4763 > true
    4764 
    4765 > hide #!21 models
    4766 
    4767 > close #23
    4768 
    4769 > hide #!22 models
    4770 
    4771 > show #19 models
    4772 
    4773 > color #19 byhetero
    4774 
    4775 > show #19 cartoons
    4776 
    4777 > hide #19/A,D:1-10
    4778 
    4779 > hide #19/A,D:1-10 target c
    4780 
    4781 > color /B,C,E,F gainsboro
    4782 
    4783 > view list
    4784 
    4785 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    4786 mono_front 
    4787 
    4788 > view dimer_view-all_front
    4789 
    4790 > hide #19 models
    4791 
    4792 > show #19 models
    4793 
    4794 > save
    4795 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    4796 
    4797 ——— End of log from Fri Aug 23 11:48:49 2024 ———
    4798 
    4799 opened ChimeraX session 
    4800 
    4801 > hide #19 models
    4802 
    4803 > show #17 models
    4804 
    4805 > view list
    4806 
    4807 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    4808 mono_front 
    4809 
    4810 > view mono_back_
    4811 
    4812 > show :NA target a
    4813 
    4814 > style :NA ball
    4815 
    4816 Changed 1 atom style 
    4817 
    4818 > style :NA stick
    4819 
    4820 Changed 1 atom style 
    4821 
    4822 > style :NA sphere
    4823 
    4824 Changed 1 atom style 
    4825 
    4826 > color :NA byhetero target a
    4827 
    4828 > ui tool show "Side View"
    4829 
    4830 > select ~sel & ##selected
    4831 
    4832 Nothing selected 
    4833 
    4834 > lighting #17:NA shadows 0
    4835 
    4836 Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
    4837 keyword 
    4838 
    4839 > lighting model #17:NA shadows false
    4840 
    4841 > lighting model #17:NA shadows true
    4842 
    4843 > lighting model #17:NA multishadows 0
    4844 
    4845 Expected a keyword 
    4846 
    4847 > lighting model #17:NA multiShadow false
    4848 
    4849 > lighting model #17:NA multiShadow true
    4850 
    4851 > lighting model #17:NA shadows true
    4852 
    4853 > lighting model #17:NA shadows false
    4854 
    4855 > color :NA orange red target a
    4856 
    4857 > hide #17/A target c
    4858 
    4859 > show #17/A target c
    4860 
    4861 > view list
    4862 
    4863 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    4864 mono_front 
    4865 
    4866 > view binding_site
    4867 
    4868 > name /A:132,133,163,164,300,NA,HOH binding_site_res
    4869 
    4870 "binding_site_res": invalid atom specifier 
    4871 
    4872 > name binding_site_res /A:132,133,163,164,300,NA,HOH
    4873 
    4874 "/A:132,133,163,164,300,NA,HOH ": contains extra trailing text 
    4875 
    4876 > name binding_site_res /A:132,133,163,164,300,NA,HOH
    4877 
    4878 > show #17&binding_site_res target a
    4879 
    4880 > lighting simple
    4881 
    4882 > lighting gentle multiShadow 1024
    4883 
    4884 > lighting soft multiShadow 1024
    4885 
    4886 > lighting soft
    4887 
    4888 > lighting simple
    4889 
    4890 > lighting soft multiShadow 1024
    4891 
    4892 > color :NA orange target a
    4893 
    4894 > color :NA gode tar a
    4895 
    4896 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    4897 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    4898 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    4899 
    4900 > color :NA gold target a
    4901 
    4902 > color :NA goldenrod target a
    4903 
    4904 > color :NA tomato target a
    4905 
    4906 > color :NA gold target a
    4907 
    4908 > show #15 models
    4909 
    4910 > show #17,15&binding_site_res target a
    4911 
    4912 > color #15,17 byhetero
    4913 
    4914 > show #13 models
    4915 
    4916 > hide #13 models
    4917 
    4918 > show #13 models
    4919 
    4920 > hide #13 models
    4921 
    4922 > show #13 models
    4923 
    4924 > hide #13 models
    4925 
    4926 > show #13 models
    4927 
    4928 > show #17,15,13&binding_site_res target a
    4929 
    4930 > hide #13 models
    4931 
    4932 > hide #15 models
    4933 
    4934 > hbonds #17 reveal true
    4935 
    4936 6877 hydrogen bonds found 
    4937 
    4938 > close #23
    4939 
    4940 > hide #17 atoms
    4941 
    4942 > show #17,15&binding_site_res target a
    4943 
    4944 [Repeated 1 time(s)]
    4945 
    4946 > cartoon #15,17/A:132 suppressBackboneDisplay false
    4947 
    4948 > show #17,15&binding_site_res target a
    4949 
    4950 > cartoon #15,17/A:132,133 suppressBackboneDisplay false
    4951 
    4952 > cartoon #15,17/A:133 suppressBackboneDisplay true
    4953 
    4954 > view name binding_site
    4955 
    4956 > view list
    4957 
    4958 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    4959 mono_front 
    4960 
    4961 > lighting simple
    4962 
    4963 > select #17/A:161
    4964 
    4965 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4966 
    4967 > show sel target a
    4968 
    4969 > cartoon sel suppressBackboneDisplay false
    4970 
    4971 > hide sel target a
    4972 
    4973 > cartoon sel suppressBackboneDisplay true
    4974 
    4975 > select #17/A:160
    4976 
    4977 5 atoms, 4 bonds, 1 residue, 1 model selected 
    4978 
    4979 > show sel target a
    4980 
    4981 > cartoon sel suppressBackboneDisplay false
    4982 
    4983 > view list
    4984 
    4985 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    4986 mono_front 
    4987 
    4988 > view binding_site
    4989 
    4990 [Repeated 1 time(s)]
    4991 
    4992 > select #17/A:505@NA
    4993 
    4994 1 atom, 1 residue, 1 model selected 
    4995 
    4996 > select clear
    4997 
    4998 > style :NA stick
    4999 
    5000 Changed 1 atom style 
    5001 
    5002 > style :NA ball
    5003 
    5004 Changed 1 atom style 
    5005 
    5006 > style :NA stick
    5007 
    5008 Changed 1 atom style 
    5009 
    5010 > ui mousemode right distance
    5011 
    5012 > distance #17/A:164@OD1 #17/A:505@NA
    5013 
    5014 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 164 OD1 and NA 505 NA:
    5015 2.181Å 
    5016 
    5017 > distance #17/A:163@OD1 #17/A:505@NA
    5018 
    5019 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 163 OD1 and NA 505 NA:
    5020 3.219Å 
    5021 
    5022 > close #23
    5023 
    5024 > distance #17/A:505@NA #17/A:164@OD1
    5025 
    5026 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A NA 505 NA and ASP 164 OD1:
    5027 2.181Å 
    5028 
    5029 > distance #17/A:505@NA #17/A:163@OD1
    5030 
    5031 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A NA 505 NA and ASP 163 OD1:
    5032 3.219Å 
    5033 
    5034 > distance #17/A:505@NA #17/A:132@O
    5035 
    5036 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A NA 505 NA and THR 132 O:
    5037 2.185Å 
    5038 
    5039 > distance #17/A:505@NA #17/A:504@O
    5040 
    5041 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A NA 505 NA and HOH 504 O:
    5042 2.987Å 
    5043 
    5044 > distance #17/A:505@NA #17/A:160@O
    5045 
    5046 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A NA 505 NA and ALA 160 O:
    5047 3.209Å 
    5048 
    5049 > hide #23.1 models
    5050 
    5051 > delete sel
    5052 
    5053 > ui tool show Distances
    5054 
    5055 > ~distance #17/A:505@NA #17/A:160@O
    5056 
    5057 > view list
    5058 
    5059 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    5060 mono_front 
    5061 
    5062 > view binding_site
    5063 
    5064 > select #17/A:160
    5065 
    5066 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5067 
    5068 > hide sel target a
    5069 
    5070 > cartoon sel suppressBackboneDisplay true
    5071 
    5072 > select clear
    5073 
    5074 > view binding_site
    5075 
    5076 > cartoon style modeHelix default width 1.0 thickness 0.3
    5077 
    5078 > color #23 silver target p
    5079 
    5080 > style :HOH ball
    5081 
    5082 Changed 4 atom styles 
    5083 
    5084 > style :HOH,NA ball
    5085 
    5086 Changed 5 atom styles 
    5087 
    5088 > style :NA sphere
    5089 
    5090 Changed 1 atom style 
    5091 
    5092 > show #!18 models
    5093 
    5094 > color #18 snow
    5095 
    5096 > transparency #18 70
    5097 
    5098 > style :HOH,NA ball
    5099 
    5100 Changed 5 atom styles 
    5101 
    5102 > hide #!18 models
    5103 
    5104 > hide #17 models
    5105 
    5106 > show #!16 models
    5107 
    5108 > show #!15 models
    5109 
    5110 > hide #!15 models
    5111 
    5112 > show #!18 models
    5113 
    5114 > transparency #18 0
    5115 
    5116 > color #18 bluw
    5117 
    5118 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    5119 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    5120 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    5121 
    5122 > color #18 blue
    5123 
    5124 > volume #16 level 0.01372
    5125 
    5126 > volume #16 level 0.012
    5127 
    5128 > volume #16 level 0.01225
    5129 
    5130 > view list
    5131 
    5132 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    5133 mono_front 
    5134 
    5135 > view binding_site
    5136 
    5137 > hide #!16 models
    5138 
    5139 > show #!16 models
    5140 
    5141 > hide #!18 models
    5142 
    5143 > show #!18 models
    5144 
    5145 > hide #!16 models
    5146 
    5147 > color #18 snow
    5148 
    5149 > transparency #18 70
    5150 
    5151 > show #17 models
    5152 
    5153 > lighting soft multiShadow 1024
    5154 
    5155 > save
    5156 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    5157 
    5158 ——— End of log from Fri Aug 23 12:47:33 2024 ———
    5159 
    5160 opened ChimeraX session 
    5161 
    5162 > surface zone #18 nearAtoms #17&binding_site_res
    5163 
    5164 > color #18 gainsboro
    5165 
    5166 > color #18 whitesmoke
    5167 
    5168 > color #18 snow
    5169 
    5170 > color #18 whitesmoke
    5171 
    5172 > color #18 gainsboro
    5173 
    5174 > color #18 whitesmoke
    5175 
    5176 > transparency #18 70
    5177 
    5178 > transparency #18 60
    5179 
    5180 > transparency #18 70
    5181 
    5182 > transparency #17/A 80 target c
    5183 
    5184 > hide #!23 models
    5185 
    5186 > show #!23 models
    5187 
    5188 > hide #!23 models
    5189 
    5190 > transparency #17 100 target a
    5191 
    5192 > save NhaA-Na-pH85_binding-site_tra.png supersample 3 transparentBackground
    5193 > true
    5194 
    5195 > save NhaA-Na-pH85_binding-site_map_tra.png supersample 3
    5196 > transparentBackground true
    5197 
    5198 > hide #!18 models
    5199 
    5200 > show #!18 models
    5201 
    5202 > hide #!18 models
    5203 
    5204 > cartoon tether #17 opacity 0
    5205 
    5206 > cartoon tether #17/A:132 opacity 0
    5207 
    5208 > cartoon tether #17/A:132 scale 0
    5209 
    5210 > save NhaA-Na-pH85_binding-site_tra.png supersample 3 transparentBackground
    5211 > true
    5212 
    5213 > hide #17/A target ac
    5214 
    5215 > show #17&(binding_site_res&sidechain|:132,NA,HOH) target a
    5216 
    5217 > transparency #17/A 100 target a
    5218 
    5219 > transparency #23 100 target p
    5220 
    5221 > show #!23 models
    5222 
    5223 > hide sel
    5224 
    5225 > graphics silhouettes width 6
    5226 
    5227 > save NhaA-Na-pH85_binding-site_sil.png supersample 3 transparentBackground
    5228 > true
    5229 
    5230 > hide #17/A target ac
    5231 
    5232 > show #17&(binding_site_res&sidechain|:132,NA,HOH) target a
    5233 
    5234 > transparency #17/A 0 target a
    5235 
    5236 > transparency #23 100 target p
    5237 
    5238 > save NhaA-Na-pH85_binding-site_sil.png supersample 3 transparentBackground
    5239 > true
    5240 
    5241 > show #17/A target c
    5242 
    5243 > show #17&binding_site_res target a
    5244 
    5245 > cartoon #17/A:132 suppressBackboneDisplay false
    5246 
    5247 > cartoon tether #17/A:132 scale 0
    5248 
    5249 > show #17/A target c
    5250 
    5251 > show #17&binding_site_res target a
    5252 
    5253 > cartoon #17/A:132 suppressBackboneDisplay false
    5254 
    5255 > cartoon tether #17/A:132 scale 0
    5256 
    5257 > graphics silhouettes width 2
    5258 
    5259 > hide #!23 models
    5260 
    5261 > show #!18 models
    5262 
    5263 > show #17/A target c
    5264 
    5265 > show #17&binding_site_res target a
    5266 
    5267 > transparency #17 100 target a
    5268 
    5269 > cartoon #17/A:132 suppressBackboneDisplay false
    5270 
    5271 > cartoon tether #17/A:132 scale 0
    5272 
    5273 > graphics silhouettes width 2
    5274 
    5275 > hide #!18 models
    5276 
    5277 > show #17/A target c
    5278 
    5279 > transparency #17/A 70 target c
    5280 
    5281 > show #17&binding_site_res target a
    5282 
    5283 > transparency #17 100 target a
    5284 
    5285 > cartoon #17/A:132 suppressBackboneDisplay false
    5286 
    5287 > cartoon tether #17/A:132 scale 0
    5288 
    5289 > graphics silhouettes width 2
    5290 
    5291 > save NhaA-Na-pH85_binding-site_tra.png supersample 3 transparentBackground
    5292 > true
    5293 
    5294 > show #!18 models
    5295 
    5296 > color #18 gainsboro
    5297 
    5298 > color #18 black
    5299 
    5300 > color #18 gainsboro
    5301 
    5302 > transparency #18 70
    5303 
    5304 > transparency #18 50
    5305 
    5306 > transparency #18 10
    5307 
    5308 > transparency #18 0
    5309 
    5310 > transparency #18 1
    5311 
    5312 > transparency #17 0
    5313 
    5314 > transparency #17 0 target ac
    5315 
    5316 > transparency #18 60
    5317 
    5318 > transparency #18 70
    5319 
    5320 > transparency #18 80
    5321 
    5322 > save NhaA-Na-pH85_binding-site_no-tra.png supersample 3
    5323 > transparentBackground true
    5324 
    5325 > transparency #18 70
    5326 
    5327 > save NhaA-Na-pH85_binding-site_no-tra.png supersample 3
    5328 > transparentBackground true
    5329 
    5330 > hide #!18 models
    5331 
    5332 > hide #17/A target ac
    5333 
    5334 > show #17&(binding_site_res&sidechain|:132,NA,HOH) target a
    5335 
    5336 > transparency #17/A 100 target a
    5337 
    5338 > transparency #23 0 target p
    5339 
    5340 > graphics silhouettes width 6
    5341 
    5342 > hide sel
    5343 
    5344 > select clear
    5345 
    5346 > show #!23 models
    5347 
    5348 > transparency #23 1
    5349 
    5350 > transparency #23 1 target p
    5351 
    5352 > transparency #18 0 target a
    5353 
    5354 > transparency #17 0 target a
    5355 
    5356 > save NhaA-Na-pH85_binding-site_sil.png supersample 3 transparentBackground
    5357 > true
    5358 
    5359 > style :NA sphere
    5360 
    5361 Changed 1 atom style 
    5362 
    5363 > show #!18 models
    5364 
    5365 > show #17/A target c
    5366 
    5367 > show #17&binding_site_res target a
    5368 
    5369 > cartoon #17/A:132 suppressBackboneDisplay false
    5370 
    5371 > cartoon tether #17/A:132 scale 0
    5372 
    5373 > graphics silhouettes width 2
    5374 
    5375 > volume #18 level 0.009684
    5376 
    5377 > volume #18 level 0.009887
    5378 
    5379 > volume #18 level 0.0098
    5380 
    5381 > volume #18 level 0.01
    5382 
    5383 > view list
    5384 
    5385 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    5386 mono_front 
    5387 
    5388 > view binding_site
    5389 
    5390 > style :NA ball
    5391 
    5392 Changed 1 atom style 
    5393 
    5394 > style :NA stick
    5395 
    5396 Changed 1 atom style 
    5397 
    5398 > color :NA gold
    5399 
    5400 > hide #!23 models
    5401 
    5402 > select ~sel & ##selected
    5403 
    5404 Nothing selected 
    5405 
    5406 > color :NA byhetero
    5407 
    5408 > surface style #18 mesh
    5409 
    5410 > surface style #18 mesh squaremesh false
    5411 
    5412 Expected fewer arguments 
    5413 
    5414 > surface style #18 solid
    5415 
    5416 > volume #18 style mesh squareMesh false
    5417 
    5418 > volume #18 style solid
    5419 
    5420 > surface style #18 solid
    5421 
    5422 > volume #18 style mesh squareMesh true
    5423 
    5424 > surface style #18 solid
    5425 
    5426 > color zone #18 near :NA distance 1
    5427 
    5428 > color zone #18 near :NA distance 1.5
    5429 
    5430 > transparency #18 60
    5431 
    5432 > volume #18 style solid
    5433 
    5434 > volume #18 style surface
    5435 
    5436 > color :NA gold target a
    5437 
    5438 > color zone #18 near :NA distance 1.5
    5439 
    5440 > transparency #18 60
    5441 
    5442 > color :NA byhetero target a
    5443 
    5444 > color zone #18 near :NA distance 1.5
    5445 
    5446 > transparency #18 60
    5447 
    5448 > transparency #18 70
    5449 
    5450 > color :NA byhetero transparency 80 target a
    5451 
    5452 > color zone #18 near :NA distance 1.5
    5453 
    5454 > color :NA byhetero target a
    5455 
    5456 > color :NA byhetero transparency 0 target a
    5457 
    5458 > lighting simple
    5459 
    5460 > lighting soft
    5461 
    5462 > lighting simple
    5463 
    5464 > graphics silhouettes false
    5465 
    5466 > graphics silhouettes true
    5467 
    5468 > graphics silhouettes false
    5469 
    5470 > graphics silhouettes true
    5471 
    5472 > graphics silhouettes false
    5473 
    5474 > graphics silhouettes true
    5475 
    5476 > graphics silhouettes false
    5477 
    5478 > graphics silhouettes true
    5479 
    5480 > lighting soft
    5481 
    5482 > lighting soft multiShadow 1024
    5483 
    5484 > color :NA byelement target a
    5485 
    5486 > save NhaA-Na-pH85_binding-site_tra.png supersample 3 transparentBackground
    5487 > true
    5488 
    5489 > color zone #18 near :NA distance 1.5
    5490 
    5491 > transparency #18 60
    5492 
    5493 > save NhaA-Na-pH85_binding-site_tra.png supersample 3 transparentBackground
    5494 > true
    5495 
    5496 > hide #17/A target ac
    5497 
    5498 > show #17&(binding_site_res&sidechain|:132,NA,HOH) target a
    5499 
    5500 > transparency #17/A 100 target a
    5501 
    5502 > transparency #23 1 target p
    5503 
    5504 > graphics silhouettes width 6
    5505 
    5506 > hide #!18 models
    5507 
    5508 > hide sel
    5509 
    5510 > hide #17/A target ac
    5511 
    5512 > show #17&(binding_site_res&sidechain|:132,NA,HOH) target a
    5513 
    5514 > transparency #17/A 0 target a
    5515 
    5516 > transparency #23 1 target p
    5517 
    5518 > graphics silhouettes width 6
    5519 
    5520 > show #!22 models
    5521 
    5522 > hide #!22 models
    5523 
    5524 > show #!23 models
    5525 
    5526 > select clear
    5527 
    5528 > save NhaA-Na-pH85_binding-site_sil.png supersample 3 transparentBackground
    5529 > true
    5530 
    5531 > show #17/A target c
    5532 
    5533 > show #17&binding_site_res target a
    5534 
    5535 > cartoon #17/A:132 suppressBackboneDisplay false
    5536 
    5537 > cartoon tether #17/A:132 scale 0
    5538 
    5539 > graphics silhouettes width 2
    5540 
    5541 > hide #!23 models
    5542 
    5543 > view list
    5544 
    5545 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    5546 mono_front 
    5547 
    5548 > view mono_back
    5549 
    5550 > view mono_back_
    5551 
    5552 > hide #17 atoms
    5553 
    5554 > show :NA target a
    5555 
    5556 > style :NA sphere
    5557 
    5558 Changed 1 atom style 
    5559 
    5560 > cartoon style modeHelix default width 1.8 thickness 0.3
    5561 
    5562 > combine #17
    5563 
    5564 > hide #24 target c
    5565 
    5566 > lighting model #24 multiShadow false
    5567 
    5568 > hide #17:NA
    5569 
    5570 > hide #17:NA target a
    5571 
    5572 > lighting model #24 multiShadow true
    5573 
    5574 > lighting model #24 shadows false
    5575 
    5576 > lighting model #24 multiShadow false
    5577 
    5578 > lighting model #24 shadows true
    5579 
    5580 > ui tool show "Side View"
    5581 
    5582 > lighting simple
    5583 
    5584 > lighting full
    5585 
    5586 > lighting soft
    5587 
    5588 > lighting simple
    5589 
    5590 > lighting soft multiShadow 1024
    5591 
    5592 > lighting soft
    5593 
    5594 > lighting simple
    5595 
    5596 > hide #24 models
    5597 
    5598 > show :NA target a
    5599 
    5600 > transparency #17 100 target c
    5601 
    5602 > transparency :NA 1 target a
    5603 
    5604 > lighting full
    5605 
    5606 [Repeated 1 time(s)]
    5607 
    5608 > lighting soft
    5609 
    5610 > lighting simple
    5611 
    5612 > save NhaA-Na-pH85_model_back_simple.png supersample 3 transparentBackground
    5613 > true
    5614 
    5615 > lighting soft multiShadow 1024
    5616 
    5617 > transparency #17 0 target c
    5618 
    5619 > view list
    5620 
    5621 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    5622 mono_front 
    5623 
    5624 > view mono_back_
    5625 
    5626 > show #24 models
    5627 
    5628 > hide #24 models
    5629 
    5630 > show #24 models
    5631 
    5632 > select #17/A:505@NA
    5633 
    5634 1 atom, 1 residue, 1 model selected 
    5635 
    5636 > hide #17 models
    5637 
    5638 > select clear
    5639 
    5640 > select #24/A:505@NA
    5641 
    5642 1 atom, 1 residue, 1 model selected 
    5643 
    5644 > show sel surfaces
    5645 
    5646 > hide #24 target a
    5647 
    5648 > hide #!24 models
    5649 
    5650 > close #24.1
    5651 
    5652 > select clear
    5653 
    5654 > show #24 models
    5655 
    5656 > hide #24 models
    5657 
    5658 > show #!18 models
    5659 
    5660 > show #17 models
    5661 
    5662 > hide #!18 models
    5663 
    5664 > lighting simple
    5665 
    5666 > lighting full
    5667 
    5668 > lighting simple
    5669 
    5670 > lighting full
    5671 
    5672 > lighting simple
    5673 
    5674 > lighting full
    5675 
    5676 > view list
    5677 
    5678 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    5679 mono_front 
    5680 
    5681 > view binding_site
    5682 
    5683 > style :NA stick
    5684 
    5685 Changed 2 atom styles 
    5686 
    5687 > show #17/A target c
    5688 
    5689 > show #17&binding_site_res target a
    5690 
    5691 > cartoon #17/A:132 suppressBackboneDisplay false
    5692 
    5693 > cartoon tether #17/A:132 scale 0
    5694 
    5695 > graphics silhouettes width 2
    5696 
    5697 > style :NA sphere
    5698 
    5699 Changed 2 atom styles 
    5700 
    5701 > style :NA stick
    5702 
    5703 Changed 2 atom styles 
    5704 
    5705 > style :NA ball
    5706 
    5707 Changed 2 atom styles 
    5708 
    5709 > style :NA stick
    5710 
    5711 Changed 2 atom styles 
    5712 
    5713 > cartoon style modeHelix default width 1.0 thickness 0.3
    5714 
    5715 > lighting full
    5716 
    5717 > lighting simple
    5718 
    5719 > lighting full
    5720 
    5721 > show #!18 models
    5722 
    5723 > lighting simple
    5724 
    5725 > lighting full
    5726 
    5727 > lighting shadows false
    5728 
    5729 > lighting full
    5730 
    5731 > lighting shadows false
    5732 
    5733 > lighting simple
    5734 
    5735 > lighting shadows true
    5736 
    5737 > lighting shadows false
    5738 
    5739 > lighting full
    5740 
    5741 > lighting shadows false
    5742 
    5743 > lighting soft
    5744 
    5745 > lighting shadows true intensity 0.5
    5746 
    5747 > lighting simple
    5748 
    5749 > lighting soft
    5750 
    5751 > lighting shadows true intensity 0.5
    5752 
    5753 > lighting full
    5754 
    5755 > lighting simple
    5756 
    5757 > lighting soft
    5758 
    5759 > lighting shadows true intensity 0.5
    5760 
    5761 > lighting shadows false
    5762 
    5763 > lighting soft
    5764 
    5765 > lighting soft multiShadow 1024
    5766 
    5767 > lighting shadows true intensity 0.5
    5768 
    5769 > save NhaA-Na-pH85_binding-site_simple_tra.png supersample 3
    5770 > transparentBackground true
    5771 
    5772 > hide #17/A target ac
    5773 
    5774 > show #17&(binding_site_res&sidechain|:132,NA,HOH) target a
    5775 
    5776 > transparency #17/A 100 target a
    5777 
    5778 > transparency #23 1 target p
    5779 
    5780 > graphics silhouettes width 6
    5781 
    5782 > hide #!18 models
    5783 
    5784 > hide sel
    5785 
    5786 > select clear
    5787 
    5788 > show #!23 models
    5789 
    5790 > save NhaA-Na-pH85_binding-site_simple_sil.png supersample 3
    5791 > transparentBackground true
    5792 
    5793 > style :NA stick
    5794 
    5795 Changed 2 atom styles 
    5796 
    5797 > show #17/A target c
    5798 
    5799 > show #17&binding_site_res target a
    5800 
    5801 > cartoon #17/A:132 suppressBackboneDisplay false
    5802 
    5803 > cartoon tether #17/A:132 scale 0
    5804 
    5805 > graphics silhouettes width 2
    5806 
    5807 > transparency #17 0 target a
    5808 
    5809 > save
    5810 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    5811 
    5812 > view list
    5813 
    5814 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    5815 mono_front 
    5816 
    5817 > view mono_back_
    5818 
    5819 > hide #!23 models
    5820 
    5821 > view binding_site
    5822 
    5823 > hide #17 models
    5824 
    5825 > show #!15 models
    5826 
    5827 > hide #!15 atoms
    5828 
    5829 > style :NA stick
    5830 
    5831 Changed 2 atom styles 
    5832 
    5833 > show #15/A target c
    5834 
    5835 > show #15&binding_site_res target a
    5836 
    5837 > cartoon #15/A:132 suppressBackboneDisplay false
    5838 
    5839 > cartoon tether #15/A:132 scale 0
    5840 
    5841 > graphics silhouettes width 2
    5842 
    5843 > lighting soft
    5844 
    5845 > lighting soft multiShadow 1024
    5846 
    5847 > lighting shadows true intensity 0.5
    5848 
    5849 > show #!16 models
    5850 
    5851 > lighting shadows false
    5852 
    5853 > lighting soft
    5854 
    5855 > lighting shadows true intensity 0.5
    5856 
    5857 > lighting shadows false
    5858 
    5859 > lighting simple
    5860 
    5861 > lighting full
    5862 
    5863 > lighting soft
    5864 
    5865 > lighting shadows true intensity 0.5
    5866 
    5867 > lighting shadows false
    5868 
    5869 > lighting soft multiShadow 1024
    5870 
    5871 > lighting shadows true intensity 0.5
    5872 
    5873 > lighting shadows false
    5874 
    5875 > lighting shadows true
    5876 
    5877 > lighting shadows false
    5878 
    5879 > lighting shadows true
    5880 
    5881 > lighting shadows false
    5882 
    5883 > volume #18 change image level -0.001229,0 level 0.005411,0.8 level 0.07594,1
    5884 
    5885 > volume #16 level 0.01176
    5886 
    5887 > volume #16 level 0.01225
    5888 
    5889 > ui mousemode right "mark center"
    5890 
    5891 Enclosed volume for marked surface: 0.452 
    5892 
    5893 > marker #25 position 117.7,81.62,99.72 color yellow radius 1
    5894 
    5895 Enclosed volume for marked surface: 0.218 
    5896 
    5897 > marker #25 position 116.7,82.14,101.9 color yellow radius 1
    5898 
    5899 Enclosed volume for marked surface: 0.383 
    5900 
    5901 > marker #25 position 115.9,80.84,101.2 color yellow radius 1
    5902 
    5903 Enclosed volume for marked surface: 0.0893 
    5904 
    5905 > marker #25 position 115.1,81.5,103.3 color yellow radius 1
    5906 
    5907 Enclosed volume for marked surface: 0.103 
    5908 
    5909 > marker #25 position 114.3,82.15,103.4 color yellow radius 1
    5910 
    5911 > hide #25 models
    5912 
    5913 > select clear
    5914 
    5915 > show #25 models
    5916 
    5917 > hide #25 models
    5918 
    5919 > surface zone #16 nearAtoms #25|(#15&binding_site_res)
    5920 
    5921 > color #16 gainsboro
    5922 
    5923 > transparency #16 60
    5924 
    5925 > surface unzone #16
    5926 
    5927 Enclosed volume for marked surface: 2.23 
    5928 
    5929 > marker #25 position 113.2,82.87,100.8 color yellow radius 1
    5930 
    5931 > show #25 models
    5932 
    5933 > hide #25 models
    5934 
    5935 > select clear
    5936 
    5937 > surface zone #16 nearAtoms #25|(#15&binding_site_res)
    5938 
    5939 > color #16 gainsboro
    5940 
    5941 > transparency #16 60
    5942 
    5943 > view binding_site
    5944 
    5945 > surface zone #16 nearAtoms #25|(#15&binding_site_res) distance 2
    5946 
    5947 > color #16 gainsboro
    5948 
    5949 > transparency #16 60
    5950 
    5951 > surface zone #16 nearAtoms #25|(#15&binding_site_res) distance 1.8
    5952 
    5953 > color #16 gainsboro
    5954 
    5955 > transparency #16 60
    5956 
    5957 > surface zone #16 nearAtoms #25|(#15&binding_site_res) distance 1.9
    5958 
    5959 > color #16 gainsboro
    5960 
    5961 > transparency #16 60
    5962 
    5963 > surface zone #16 nearAtoms #25|(#15&binding_site_res)
    5964 
    5965 > color #16 gainsboro
    5966 
    5967 > transparency #16 60
    5968 
    5969 > save NhaA-K-pH85-state2_binding-site_tra.png supersample 3
    5970 > transparentBackground true
    5971 
    5972 > hide #15/A target ac
    5973 
    5974 > show #15&(binding_site_res&sidechain|:132,NA,HOH) target a
    5975 
    5976 > transparency #15/A 100 target a
    5977 
    5978 > transparency #23 1 target p
    5979 
    5980 > graphics silhouettes width 6
    5981 
    5982 > hide #!16 models
    5983 
    5984 > hide sel
    5985 
    5986 > save NhaA-K-pH85-state2_binding-site_sil.png supersample 3
    5987 > transparentBackground true
    5988 
    5989 > hide #15/A target ac
    5990 
    5991 > show #15&(binding_site_res&sidechain|:132,NA,HOH) target a
    5992 
    5993 > transparency #15/A 0 target a
    5994 
    5995 > transparency #23 1 target p
    5996 
    5997 > graphics silhouettes width 6
    5998 
    5999 > save NhaA-K-pH85-state2_binding-site_sil.png supersample 3
    6000 > transparentBackground true
    6001 
    6002 > hide #!15 models
    6003 
    6004 > select clear
    6005 
    6006 > show #17 models
    6007 
    6008 > hide #17/A target ac
    6009 
    6010 > show #17&(binding_site_res&sidechain|:132,NA,HOH) target a
    6011 
    6012 > transparency #17/A 0 target a
    6013 
    6014 > transparency #23 1 target p
    6015 
    6016 > graphics silhouettes width 6
    6017 
    6018 > hide sel
    6019 
    6020 > show #!23 models
    6021 
    6022 > transparency #23 0 target p
    6023 
    6024 > color #23 gray target p
    6025 
    6026 > color #23 dark gray target p
    6027 
    6028 > save NhaA-Na-pH85_binding-site_simple_sil.png supersample 3
    6029 > transparentBackground true
    6030 
    6031 > hide #!23 models
    6032 
    6033 > ui mousemode right distance
    6034 
    6035 > distance #17/A:164@OD1 #17/A:132@O
    6036 
    6037 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 164 OD1 and THR 132 O:
    6038 4.183Å 
    6039 
    6040 > show #!23 models
    6041 
    6042 > show #23.1 models
    6043 
    6044 > hide #23.1 models
    6045 
    6046 > show #23.1 models
    6047 
    6048 > hide #!23 models
    6049 
    6050 > show #!23 models
    6051 
    6052 > hide #!17 models
    6053 
    6054 > show #!15 models
    6055 
    6056 > distance #15/A:164@OD1 #15/A:132@O
    6057 
    6058 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A ASP 164 OD1 and THR
    6059 132 O: 5.033Å 
    6060 
    6061 > show #!16 models
    6062 
    6063 > lighting simple
    6064 
    6065 > view list
    6066 
    6067 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    6068 mono_front 
    6069 
    6070 > view binding_site
    6071 
    6072 > hide #!16 models
    6073 
    6074 > hide #23.1 models
    6075 
    6076 > style :NA stick
    6077 
    6078 Changed 2 atom styles 
    6079 
    6080 > show #17/A target c
    6081 
    6082 > show #17&binding_site_res target a
    6083 
    6084 > cartoon #17/A:132 suppressBackboneDisplay false
    6085 
    6086 > cartoon tether #17/A:132 scale 0
    6087 
    6088 > graphics silhouettes width 2
    6089 
    6090 > style :NA stick
    6091 
    6092 Changed 2 atom styles 
    6093 
    6094 > show #15/A target c
    6095 
    6096 > show #15&binding_site_res target a
    6097 
    6098 > cartoon #15/A:132 suppressBackboneDisplay false
    6099 
    6100 > cartoon tether #15/A:132 scale 0
    6101 
    6102 > graphics silhouettes width 2
    6103 
    6104 > view list
    6105 
    6106 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    6107 mono_front 
    6108 
    6109 > view mono_back_
    6110 
    6111 > hide #!23 models
    6112 
    6113 > hide #15 models
    6114 
    6115 > show #!7 models
    6116 
    6117 > show #!8 models
    6118 
    6119 > hide #!8 models
    6120 
    6121 > hide #!7 atoms
    6122 
    6123 > show #!9 models
    6124 
    6125 > hide #7#!9 atoms
    6126 
    6127 > select clear
    6128 
    6129 > ui mousemode right translate
    6130 
    6131 > ui mousemode right zoom
    6132 
    6133 > view list
    6134 
    6135 Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
    6136 mono_front 
    6137 
    6138 > view mono_back
    6139 
    6140 > view mono_back_
    6141 
    6142 [Repeated 1 time(s)]
    6143 
    6144 > turn x 90
    6145 
    6146 > hide #9 models
    6147 
    6148 > show #!8 models
    6149 
    6150 > volume #8 level 0.01256
    6151 
    6152 > surface dust #8 size 3
    6153 
    6154 > surface dust #8 size 5
    6155 
    6156 > surface dust #8 size 4
    6157 
    6158 > surface dust #8 size 5
    6159 
    6160 > surface dust #8 size 6
    6161 
    6162 > surface dust #8 size 5
    6163 
    6164 > surface dust #8 size 6
    6165 
    6166 > show #9 models
    6167 
    6168 > hide #!8 models
    6169 
    6170 > show #!10 models
    6171 
    6172 > show #!8 models
    6173 
    6174 > volume #10 level 0.01179
    6175 
    6176 > surface dust #8,10 size 6
    6177 
    6178 > surface dust #8,10 size 7
    6179 
    6180 > hide #!8 models
    6181 
    6182 > show #!8 models
    6183 
    6184 > hide #!8 models
    6185 
    6186 > hide #7 models
    6187 
    6188 > surface dust #8,10 size 0
    6189 
    6190 > surface dust #8,10 size 1
    6191 
    6192 > surface dust #8,10 size 0
    6193 
    6194 > ui mousemode right translate
    6195 
    6196 > ui mousemode right zoom
    6197 
    6198 > ui mousemode right translate
    6199 
    6200 > color zone #10 near #8
    6201 
    6202 color zone: No atoms specified. 
    6203 
    6204 > color zone #10 near #9
    6205 
    6206 > hide #!10 models
    6207 
    6208 > hide #9 models
    6209 
    6210 > show #19 models
    6211 
    6212 > color :CDL,PTY gray target a
    6213 
    6214 > hide #19 models
    6215 
    6216 > show #9 models
    6217 
    6218 > show #!10 models
    6219 
    6220 > color zone #10 near #9
    6221 
    6222 > color #10 snow
    6223 
    6224 > color zone #10 near #9
    6225 
    6226 > color #10 gainsboro
    6227 
    6228 > color #10 silver
    6229 
    6230 > color zone #10 near #9
    6231 
    6232 > color zone #10 near #9 distance 3
    6233 
    6234 > color zone #10 near #9 distance 2.5
    6235 
    6236 > transparency #10 50
    6237 
    6238 > transparency #10 60
    6239 
    6240 > lighting soft
    6241 
    6242 > lighting shadows true intensity 0.5
    6243 
    6244 > lighting simple
    6245 
    6246 > lighting full
    6247 
    6248 > lighting soft
    6249 
    6250 > lighting shadows true intensity 0.5
    6251 
    6252 > lighting shadows false
    6253 
    6254 > lighting full
    6255 
    6256 > lighting shadows false
    6257 
    6258 > transparency #10 60
    6259 
    6260 > color zone #10 near #9 distance 2.5
    6261 
    6262 > transparency #10 60
    6263 
    6264 > color zone #10 near #9 distance 2.5
    6265 
    6266 > transparency #10 60
    6267 
    6268 > view name N-term_density_top
    6269 
    6270 > lighting soft
    6271 
    6272 > lighting shadows true intensity 0.5
    6273 
    6274 > lighting shadows false
    6275 
    6276 > lighting full
    6277 
    6278 > lighting shadows false
    6279 
    6280 > lighting simple
    6281 
    6282 > lighting shadows true
    6283 
    6284 > lighting shadows false
    6285 
    6286 > lighting gentle multiShadow 1024
    6287 
    6288 > lighting soft multiShadow 1024
    6289 
    6290 > lighting shadows true intensity 0.5
    6291 
    6292 > lighting shadows false
    6293 
    6294 > color #10 silver
    6295 
    6296 > transparency #10 60
    6297 
    6298 > color #10 dark gray
    6299 
    6300 > color #10 gray
    6301 
    6302 > lighting soft
    6303 
    6304 > color #10 silver
    6305 
    6306 > lighting soft
    6307 
    6308 > lighting simple
    6309 
    6310 > lighting full
    6311 
    6312 > lighting soft multiShadow 1024
    6313 
    6314 > lighting shadows true intensity 0.5
    6315 
    6316 > lighting shadows false
    6317 
    6318 > lighting full
    6319 
    6320 > lighting simple
    6321 
    6322 > lighting full
    6323 
    6324 > lighting shadows false
    6325 
    6326 > lighting soft multiShadow 1024
    6327 
    6328 > lighting shadows true intensity 0.5
    6329 
    6330 > lighting shadows false
    6331 
    6332 > lighting full
    6333 
    6334 [Repeated 1 time(s)]
    6335 
    6336 > lighting shadows false
    6337 
    6338 > hide #9 models
    6339 
    6340 > show #9 models
    6341 
    6342 > hide #!10 models
    6343 
    6344 > hide #9 models
    6345 
    6346 > show #9 models
    6347 
    6348 > hide #9 models
    6349 
    6350 > show #19 models
    6351 
    6352 > hide #19 atoms
    6353 
    6354 > show #!20 models
    6355 
    6356 > color #20 gray
    6357 
    6358 > color #20 silver
    6359 
    6360 > transparency #20 60
    6361 
    6362 > surface dust #20 0
    6363 
    6364 Expected a keyword 
    6365 
    6366 > surface dust #20 size 0
    6367 
    6368 > show #!10 models
    6369 
    6370 > hide #!10 models
    6371 
    6372 > show #!10 models
    6373 
    6374 > transparency #20 0
    6375 
    6376 > volume #20 level 0.008648
    6377 
    6378 > hide #!10 models
    6379 
    6380 > show #!10 models
    6381 
    6382 > hide #!10 models
    6383 
    6384 > show #!10 models
    6385 
    6386 > hide #!10 models
    6387 
    6388 > show #!10 models
    6389 
    6390 > hide #!10 models
    6391 
    6392 > volume #20 level 0.0081
    6393 
    6394 > show #!10 models
    6395 
    6396 > hide #!10 models
    6397 
    6398 > show #!10 models
    6399 
    6400 > hide #!10 models
    6401 
    6402 > transparency #20 60
    6403 
    6404 > color zone #20 near #7,9:1-20
    6405 
    6406 > color zone #20 near #7,9:1-10
    6407 
    6408 > transparency #20 60
    6409 
    6410 > graphics silhouettes false
    6411 
    6412 > graphics silhouettes true
    6413 
    6414 > graphics silhouettes false
    6415 
    6416 > lighting full
    6417 
    6418 > lighting shadows false
    6419 
    6420 > lighting soft
    6421 
    6422 > lighting simple
    6423 
    6424 > lighting shadows true
    6425 
    6426 > lighting shadows false
    6427 
    6428 > lighting full
    6429 
    6430 > lighting shadows false
    6431 
    6432 > save NhaA-K-pH75-consensus-Nterm-density_no-sil.png supersample 3
    6433 > transparentBackground true
    6434 
    6435 > hide #!20 models
    6436 
    6437 > graphics silhouettes true
    6438 
    6439 > graphics silhouettes 3
    6440 
    6441 Expected true or false or a keyword 
    6442 
    6443 > graphics silhouettes width 3
    6444 
    6445 > save NhaA-K-pH75-consensus-Nterm-density_ribbon.png supersample 3
    6446 > transparentBackground true
    6447 
    6448 > hide #19 models
    6449 
    6450 > show #!18 models
    6451 
    6452 > hide #!18 models
    6453 
    6454 > show #9 models
    6455 
    6456 > save NhaA-K-pH75-unplugged-Nterm-density_ribbon.png supersample 3
    6457 > transparentBackground true
    6458 
    6459 > hide #9 models
    6460 
    6461 > show #7 models
    6462 
    6463 > save NhaA-K-pH75-plugged-Nterm-density_ribbon.png supersample 3
    6464 > transparentBackground true
    6465 
    6466 > show #!8 models
    6467 
    6468 > hide #7 models
    6469 
    6470 > hide #!8 models
    6471 
    6472 > show #!10 models
    6473 
    6474 > graphics silhouettes false
    6475 
    6476 > color zone #10 near #9:1-10
    6477 
    6478 > transparency #10 60
    6479 
    6480 > save NhaA-K-pH75-unplugged-Nterm-density_no-sil.png supersample 3
    6481 > transparentBackground true
    6482 
    6483 > hide #!10 models
    6484 
    6485 > show #!8 models
    6486 
    6487 > color #8 silver
    6488 
    6489 > color zone #8 near #7:1-10
    6490 
    6491 > transparency #8 60
    6492 
    6493 > save NhaA-K-pH75-plugged-Nterm-density_no-sil.png supersample 3
    6494 > transparentBackground true
    6495 
    6496 > show #7 models
    6497 
    6498 > transparency #8 60
    6499 
    6500 > save NhaA-K-pH75-plugged-Nterm-density_no-sil.png supersample 3
    6501 > transparentBackground true
    6502 
    6503 > hide #!8 models
    6504 
    6505 > hide #7 models
    6506 
    6507 > show #9 models
    6508 
    6509 > show #!10 models
    6510 
    6511 > save NhaA-K-pH75-unplugged-Nterm-density_no-sil.png supersample 3
    6512 > transparentBackground true
    6513 
    6514 > graphics silhouettes true
    6515 
    6516 > graphics silhouettes false
    6517 
    6518 > transparency #10 40
    6519 
    6520 > save NhaA-K-pH75-unplugged-Nterm-density_no-sil.png supersample 3
    6521 > transparentBackground true
    6522 
    6523 > hide #!10 models
    6524 
    6525 > show #!10 models
    6526 
    6527 > hide #9 models
    6528 
    6529 > show #!21 models
    6530 
    6531 > hide #!21 models
    6532 
    6533 > show #!21 models
    6534 
    6535 > hide #!21 models
    6536 
    6537 > show #!20 models
    6538 
    6539 > hide #!10 models
    6540 
    6541 > show #19 models
    6542 
    6543 > color zone #20 near #7,9:1-10
    6544 
    6545 > ui mousemode right zoom
    6546 
    6547 > ui mousemode right translate
    6548 
    6549 > ui mousemode right zoom
    6550 
    6551 > ui mousemode right translate
    6552 
    6553 > transparency #20 40
    6554 
    6555 > color zone #20 near #7,9:1-10
    6556 
    6557 > transparency #20 40
    6558 
    6559 > color zone #20 near #7,9:1-10
    6560 
    6561 > transparency #20 30
    6562 
    6563 > color zone #20 near #7,9:1-10
    6564 
    6565 > save NhaA-K-pH75-consensus-Nterm-density_no-sil.png supersample 3
    6566 > transparentBackground true
    6567 
    6568 > hide #!20 models
    6569 
    6570 > graphics silhouettes true
    6571 
    6572 > save NhaA-K-pH75-consensus-Nterm-density_ribbon.png supersample 3
    6573 > transparentBackground true
    6574 
    6575 > hide #19 models
    6576 
    6577 > show #19 models
    6578 
    6579 > show #!10 models
    6580 
    6581 > hide #!10 models
    6582 
    6583 > show #!10 models
    6584 
    6585 > show #9 models
    6586 
    6587 > hide #!10 models
    6588 
    6589 > hide #19 models
    6590 
    6591 > show #19 models
    6592 
    6593 > hide #19 models
    6594 
    6595 > hide #7,9:1-10 target c
    6596 
    6597 > save NhaA-K-pH75-unplugged-Nterm-density_ribbon.png supersample 3
    6598 > transparentBackground true
    6599 
    6600 > hide #9 models
    6601 
    6602 > show #7 models
    6603 
    6604 > save NhaA-K-pH75-plugged-Nterm-density_ribbon.png supersample 3
    6605 > transparentBackground true
    6606 
    6607 > show #!8 models
    6608 
    6609 > hide #7 models
    6610 
    6611 > graphics silhouettes false
    6612 
    6613 > transparency #8,10 30
    6614 
    6615 > color zone #8 near #7:1-10
    6616 
    6617 > transparency #8,10 30
    6618 
    6619 > show #7 models
    6620 
    6621 > color zone #8 near #7:1-10
    6622 
    6623 > transparency #8 30
    6624 
    6625 > color zone #8 near #7:1-10
    6626 
    6627 > hide #!8 models
    6628 
    6629 > show #!20 models
    6630 
    6631 > hide #!20 models
    6632 
    6633 > show #!8 models
    6634 
    6635 > color #10 silver
    6636 
    6637 > color #8 silver
    6638 
    6639 > transparency #8 30
    6640 
    6641 > color zone #8 near #7:1-10
    6642 
    6643 > save NhaA-K-pH75-plugged-Nterm-density_no-sil.png supersample 3
    6644 > transparentBackground true
    6645 
    6646 > hide #!8 models
    6647 
    6648 > hide #7 models
    6649 
    6650 > show #9 models
    6651 
    6652 > show #!10 models
    6653 
    6654 > transparency #10 30
    6655 
    6656 > color zone #10 near #9:1-10
    6657 
    6658 > save NhaA-K-pH75-unplugged-Nterm-density_no-sil.png supersample 3
    6659 > transparentBackground true
    6660 
    6661 > hide #!10 models
    6662 
    6663 > hide #9 models
    6664 
    6665 > show #19 models
    6666 
    6667 > show #!20 models
    6668 
    6669 > color #20 gray
    6670 
    6671 > transparency #20 30
    6672 
    6673 > color #20 silver
    6674 
    6675 > transparency #20 30
    6676 
    6677 > color zone #20 near #7,9:1-10
    6678 
    6679 > save NhaA-K-pH75-consensus-Nterm-density_no-sil.png supersample 3
    6680 > transparentBackground true
    6681 
    6682 > hide #!20 models
    6683 
    6684 > graphics silhouettes true
    6685 
    6686 > graphics silhouettes width 4
    6687 
    6688 > graphics silhouettes width 3
    6689 
    6690 > graphics silhouettes width 4
    6691 
    6692 > save NhaA-K-pH75-consensus-Nterm-density_ribbon.png supersample 3
    6693 > transparentBackground true
    6694 
    6695 > hide #19 models
    6696 
    6697 > show #9 models
    6698 
    6699 > save NhaA-K-pH75-unplugged-Nterm-density_ribbon.png supersample 3
    6700 > transparentBackground true
    6701 
    6702 > hide #9 models
    6703 
    6704 > show #7 models
    6705 
    6706 > save NhaA-K-pH75-plugged-Nterm-density_ribbon.png supersample 3
    6707 > transparentBackground true
    6708 
    6709 > view list
    6710 
    6711 Named views: N-term_density_top, binding_site, dimer_view-all_front,
    6712 mono_back, mono_back_, mono_front 
    6713 
    6714 > view name N-term_density_top
    6715 
    6716 > save
    6717 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    6718 
    6719 ——— End of log from Sat Aug 24 11:29:55 2024 ———
    6720 
    6721 opened ChimeraX session 
    6722 
    6723 > graphics silhouettes width 2
    6724 
    6725 > view list
    6726 
    6727 Named views: N-term_density_top, binding_site, dimer_view-all_front,
    6728 mono_back, mono_back_, mono_front 
    6729 
    6730 > view mono_back_
    6731 
    6732 > show /A:1-10 target c
    6733 
    6734 > show #9 models
    6735 
    6736 > hide #7 models
    6737 
    6738 > hide #9 models
    6739 
    6740 > show #!13 models
    6741 
    6742 > hide #!13 atoms
    6743 
    6744 > hide #13 models
    6745 
    6746 > show #15 models
    6747 
    6748 > show #17 models
    6749 
    6750 > hide #15,17&dimer target c
    6751 
    6752 > mmaker #17&dimer_TM to #15/A bring #18
    6753 
    6754 Parameters 
    6755 --- 
    6756 Chain pairing | bb 
    6757 Alignment algorithm | Needleman-Wunsch 
    6758 Similarity matrix | BLOSUM-62 
    6759 SS fraction | 0.3 
    6760 Gap open (HH/SS/other) | 18/18/6 
    6761 Gap extend | 1 
    6762 SS matrix |  |  | H | S | O 
    6763 ---|---|---|--- 
    6764 H | 6 | -9 | -6 
    6765 S |  | 6 | -6 
    6766 O |  |  | 4 
    6767 Iteration cutoff | 2 
    6768  
    6769 Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with NhaA-
    6770 nd-6F9-Na_BTPpH85.pdb, chain A (#17), sequence alignment score = 619.9 
    6771 RMSD between 119 pruned atom pairs is 0.146 angstroms; (across all 119 pairs:
    6772 0.146) 
    6773  
    6774 
    6775 > ui tool show "Side View"
    6776 
    6777 > hide #15,17 atoms
    6778 
    6779 > show #15,17/A:163,132 target a
    6780 
    6781 > hide #15,17 atoms
    6782 
    6783 > show #15,17/A:164,132 target a
    6784 
    6785 > cartoon style modeHelix tube radius 1.8 sides 24
    6786 
    6787 > cartoon style modeHelix default width 1.0 thickness 0.3
    6788 
    6789 > cartoon style modeHelix default width 1.8 thickness 0.3
    6790 
    6791 > cartoon style modeHelix default width 1.4 thickness 0.3
    6792 
    6793 > cartoon style modeHelix default width 1.2 thickness 0.3
    6794 
    6795 > show #15,17/A:164,132,133 target a
    6796 
    6797 > hide #15,17 atoms
    6798 
    6799 > show #15,17/A:164,132 target a
    6800 
    6801 > lighting full
    6802 
    6803 > lighting shadows false
    6804 
    6805 > size stickRadius 0.5
    6806 
    6807 Changed 58102 bond radii 
    6808 
    6809 > size stickRadius 0.4
    6810 
    6811 Changed 58102 bond radii 
    6812 
    6813 > view name core_inner_side
    6814 
    6815 > save NhaA-Na-pH85_vs_K-pH85_inside.png supersample 3 transparentBackground
    6816 > true
    6817 
    6818 > show #15,17/A:150-274,130-144 target c
    6819 
    6820 > hide #15,17&dimer target c
    6821 
    6822 > show #15,17/A:150-174,130-144 target c
    6823 
    6824 > hide #15,17 cartoons
    6825 
    6826 > show #15,17/A:150-174,130-144 target c
    6827 
    6828 > graphics silhouettes width 4
    6829 
    6830 > graphics silhouettes width 6
    6831 
    6832 > graphics silhouettes width 4
    6833 
    6834 > graphics silhouettes width 6
    6835 
    6836 > graphics silhouettes width 5
    6837 
    6838 > save NhaA-Na-pH85_vs_K-pH85_inside_TM4c-5.png supersample 3
    6839 > transparentBackground true
    6840 
    6841 > cartoon style modeHelix default width 1 thickness 0.3
    6842 
    6843 > cartoon style modeHelix default width 1.2 thickness 0.3
    6844 
    6845 > save
    6846 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    6847 
    6848 ——— End of log from Sat Aug 24 21:20:57 2024 ———
    6849 
    6850 opened ChimeraX session 
    6851 
    6852 > cartoon style modeHelix default width 1.0 thickness 0.3
    6853 
    6854 > size stickRadius 0.3
    6855 
    6856 Changed 58102 bond radii 
    6857 
    6858 > graphics silhouettes 2
    6859 
    6860 Expected true or false or a keyword 
    6861 
    6862 > graphics silhouettes width 2
    6863 
    6864 > show /A target c
    6865 
    6866 > view list
    6867 
    6868 Named views: N-term_density_top, binding_site, core_inner_side, dimer_view-
    6869 all_front, mono_back, mono_back_, mono_front 
    6870 
    6871 > view binding_site
    6872 
    6873 > show #15,17&binding_site_res target a
    6874 
    6875 > hide :NA,HOH target a
    6876 
    6877 > transparency #15,17 50 target c
    6878 
    6879 > show #!23 models
    6880 
    6881 > color #23 dark gray target p
    6882 
    6883 > hide #17 models
    6884 
    6885 > distance #15/A:163@OD2 #15/A:300@NZ
    6886 
    6887 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A ASP 163 OD2 and LYS
    6888 300 NZ: 3.294Å 
    6889 
    6890 > show #17 models
    6891 
    6892 > hide #15 models
    6893 
    6894 > distance #17/A:163@OD2 #17/A:300@NZ
    6895 
    6896 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 163 OD2 and LYS 300 NZ:
    6897 3.986Å 
    6898 
    6899 > show #15 models
    6900 
    6901 > color #23 dark gray target p
    6902 
    6903 > hide #!23 models
    6904 
    6905 > transparency 100 target a
    6906 
    6907 > transparency 0 target a
    6908 
    6909 > save NhaA-Na-pH85_vs_K-pH85_binding-site.png supersample 3
    6910 > transparentBackground true
    6911 
    6912 > hide #15,17 cartoons
    6913 
    6914 > show #15,17 cartoons
    6915 
    6916 > hide #15,17/A target ac
    6917 
    6918 > show #15,17&(binding_site_res&sidechain|:132) target a
    6919 
    6920 > transparency #15,17/A 0 target a
    6921 
    6922 > transparency #23 1 target p
    6923 
    6924 > graphics silhouettes width 6
    6925 
    6926 > ui mousemode right translate
    6927 
    6928 > hide sel
    6929 
    6930 > select clear
    6931 
    6932 > show #!16 models
    6933 
    6934 > hide #!16 models
    6935 
    6936 > show #!23 models
    6937 
    6938 > transparency 0 target a
    6939 
    6940 > transparency 100 target a
    6941 
    6942 > transparency 0 target a
    6943 
    6944 > color sel royal blue target p
    6945 
    6946 > color sel blue target p
    6947 
    6948 > color sel royal blue target p
    6949 
    6950 > color sel deep sky blue target p
    6951 
    6952 > color sel dodger blue target p
    6953 
    6954 > color sel light sea green target p
    6955 
    6956 > select clear
    6957 
    6958 > show #23.1 models
    6959 
    6960 > hide #23.1 models
    6961 
    6962 > graphics silhouettes width 8
    6963 
    6964 > hide #!23 models
    6965 
    6966 > show #!23 models
    6967 
    6968 > hide #!15 models
    6969 
    6970 > show #!15 models
    6971 
    6972 > hide #!17 models
    6973 
    6974 > show #!17 models
    6975 
    6976 > graphics silhouettes width 6
    6977 
    6978 > save NhaA-Na-pH85_vs_K-pH85_binding-site_sil.png supersample 3
    6979 > transparentBackground true
    6980 
    6981 > show #23.1 models
    6982 
    6983 > hide #!23 models
    6984 
    6985 > style :NA stick
    6986 
    6987 Changed 2 atom styles 
    6988 
    6989 > show #17/A target c
    6990 
    6991 > show #17&binding_site_res target a
    6992 
    6993 > cartoon #17/A:132 suppressBackboneDisplay false
    6994 
    6995 > cartoon tether #17/A:132 scale 0
    6996 
    6997 > graphics silhouettes width 2
    6998 
    6999 > hide :NA,HOH target a
    7000 
    7001 > style :NA stick
    7002 
    7003 Changed 2 atom styles 
    7004 
    7005 > show #15,17/A target c
    7006 
    7007 > show #15,17&binding_site_res target a
    7008 
    7009 > cartoon #15,17/A:132 suppressBackboneDisplay false
    7010 
    7011 > cartoon tether #15,17/A:132 scale 0
    7012 
    7013 > graphics silhouettes width 2
    7014 
    7015 > hide :NA,HOH target a
    7016 
    7017 > transparency 100 target a
    7018 
    7019 > save NhaA-Na-pH85_vs_K-pH85_binding-site.png supersample 3
    7020 > transparentBackground true
    7021 
    7022 > transparency 0 target a
    7023 
    7024 > hide /B,C,E,F target ac
    7025 
    7026 > transparency 0 target c
    7027 
    7028 > view list
    7029 
    7030 Named views: N-term_density_top, binding_site, core_inner_side, dimer_view-
    7031 all_front, mono_back, mono_back_, mono_front 
    7032 
    7033 > view mono_back_
    7034 
    7035 > hide target a
    7036 
    7037 > hide #17 models
    7038 
    7039 > hide #15 models
    7040 
    7041 > show #7 models
    7042 
    7043 > show #!8 models
    7044 
    7045 > hide #!8 models
    7046 
    7047 > view mono_back_
    7048 
    7049 > show /A:1-10 target a
    7050 
    7051 > color #7 byhetero
    7052 
    7053 > show #!8 models
    7054 
    7055 > color #8 gray
    7056 
    7057 > transparency #8 60
    7058 
    7059 > color #8 silver
    7060 
    7061 > hide #!8 models
    7062 
    7063 > show #!8 models
    7064 
    7065 > show /A:1-10,81,82,78,252,253,256 target a
    7066 
    7067 > hide /A:1-10 target c
    7068 
    7069 > show /A:1-10 target c
    7070 
    7071 > hide /A:1-3 target a
    7072 
    7073 > hide /A:1-4 target a
    7074 
    7075 > hide /A:1-4,10 target a
    7076 
    7077 > hide #!8 models
    7078 
    7079 > ui mousemode right distance
    7080 
    7081 > distance #7/A:82@OE1 #7/A:6@NH1
    7082 
    7083 Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A GLU 82 OE1 and ARG 6
    7084 NH1: 2.988Å 
    7085 
    7086 > show #!23 models
    7087 
    7088 > show #!8 models
    7089 
    7090 > hide #!8 models
    7091 
    7092 > distance #7/A:82@OE1 #7/A:6@NH2
    7093 
    7094 Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A GLU 82 OE1 and ARG 6
    7095 NH2: 3.052Å 
    7096 
    7097 > ui tool show Distances
    7098 
    7099 > ~distance #7/A:82@OE1 #7/A:6@NH2
    7100 
    7101 > distance #7/A:6@NH2 #7/A:78@OE1
    7102 
    7103 Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A ARG 6 NH2 and GLU 78
    7104 OE1: 2.803Å 
    7105 
    7106 > show #!8 models
    7107 
    7108 > hide #!8 models
    7109 
    7110 > distance #7/A:81@NH1 #7/A:252@OE1
    7111 
    7112 Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A ARG 81 NH1 and GLU 252
    7113 OE1: 3.594Å 
    7114 
    7115 > ui tool show Distances
    7116 
    7117 > ~distance #7/A:81@NH1 #7/A:252@OE1
    7118 
    7119 > hide #7 models
    7120 
    7121 > show #9 models
    7122 
    7123 > color #9 byhetero
    7124 
    7125 > distance #9/A:81@NH1 #9/A:82@OE1
    7126 
    7127 Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A ARG 81 NH1 and GLU
    7128 82 OE1: 3.128Å 
    7129 
    7130 > distance #9/A:81@NH2 #9/A:252@OE2
    7131 
    7132 Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A ARG 81 NH2 and GLU
    7133 252 OE2: 2.826Å 
    7134 
    7135 > show #!10 models
    7136 
    7137 > hide #!10 models
    7138 
    7139 > hide #9 models
    7140 
    7141 > show #3 models
    7142 
    7143 > color #3 byhetero
    7144 
    7145 > distance #3/A:6@NH1 #3/A:82@OE2
    7146 
    7147 Distance between NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3/A ARG 6 NH1 and GLU 82
    7148 OE2: 2.952Å 
    7149 
    7150 > distance #3/A:6@NH2 #3/A:78@OE1
    7151 
    7152 Distance between NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3/A ARG 6 NH2 and GLU 78
    7153 OE1: 2.641Å 
    7154 
    7155 > show #7 models
    7156 
    7157 > hide #7 models
    7158 
    7159 > show #7 models
    7160 
    7161 > hide #7 models
    7162 
    7163 > show #7 models
    7164 
    7165 > hide #7 models
    7166 
    7167 > show #7 models
    7168 
    7169 > hide #3 models
    7170 
    7171 > distance #7/A:256@NE2 #7/A:252@OE2
    7172 
    7173 Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A HIS 256 NE2 and GLU
    7174 252 OE2: 3.442Å 
    7175 
    7176 > ui tool show Distances
    7177 
    7178 > ~distance #7/A:256@NE2 #7/A:252@OE2
    7179 
    7180 > show #5 models
    7181 
    7182 > hide #7 models
    7183 
    7184 > show #7 models
    7185 
    7186 > hide #7 models
    7187 
    7188 > color #5 byhetero
    7189 
    7190 > distance #5/A:81@NH1 #5/A:82@OE2
    7191 
    7192 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A ARG 81 NH1 and GLU
    7193 82 OE2: 3.215Å 
    7194 
    7195 > show #9 models
    7196 
    7197 > hide #9 models
    7198 
    7199 > distance #5/A:252@OE2 #5/A:81@NH2
    7200 
    7201 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A GLU 252 OE2 and ARG
    7202 81 NH2: 2.623Å 
    7203 
    7204 > distance #5/A:81@NH2 #5/A:78@OE1
    7205 
    7206 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A ARG 81 NH2 and GLU
    7207 78 OE1: 2.384Å 
    7208 
    7209 > distance #5/A:252@OE1 #5/A:81@NE
    7210 
    7211 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A GLU 252 OE1 and ARG
    7212 81 NE: 2.675Å 
    7213 
    7214 > distance #5/A:252@OE2 #5/A:81@NE
    7215 
    7216 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A GLU 252 OE2 and ARG
    7217 81 NE: 2.946Å 
    7218 
    7219 > ui tool show Distances
    7220 
    7221 > ~distance #5/A:252@OE1 #5/A:81@NE
    7222 
    7223 > ~distance #5/A:252@OE2 #5/A:81@NE
    7224 
    7225 > hide #5 models
    7226 
    7227 > show #1 models
    7228 
    7229 > color #1 byhetero
    7230 
    7231 > show #!2 models
    7232 
    7233 > hide #!2 models
    7234 
    7235 > distance #1/A:81@NH1 #1/A:82@OE1
    7236 
    7237 Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A ARG 81 NH1 and GLU 82 OE1:
    7238 3.309Å 
    7239 
    7240 > distance #1/A:81@NH2 #1/A:78@OE2
    7241 
    7242 Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A ARG 81 NH2 and GLU 78 OE2:
    7243 3.308Å 
    7244 
    7245 > distance #1/A:81@NE #1/A:252@OE1
    7246 
    7247 Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A ARG 81 NE and GLU 252 OE1:
    7248 3.245Å 
    7249 
    7250 > distance #1/A:81@NH2 #1/A:252@OE2
    7251 
    7252 Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A ARG 81 NH2 and GLU 252 OE2:
    7253 3.627Å 
    7254 
    7255 > show #3 models
    7256 
    7257 > hide #3 models
    7258 
    7259 > show #3 models
    7260 
    7261 > hide #1 models
    7262 
    7263 > hide #3 models
    7264 
    7265 > show #1 models
    7266 
    7267 > save
    7268 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    7269 
    7270 ——— End of log from Sun Aug 25 17:46:16 2024 ———
    7271 
    7272 opened ChimeraX session 
    7273 
    7274 > view list
    7275 
    7276 Named views: N-term_density_top, binding_site, core_inner_side, dimer_view-
    7277 all_front, mono_back, mono_back_, mono_front 
    7278 
    7279 > view N-term_density_top
    7280 
    7281 > view mono_back_
    7282 
    7283 > hide #!23 models
    7284 
    7285 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    7286 > nd-6F9-K_BTPpH85_state1-unplugged.pdb
    7287 
    7288 Chain information for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #26 
    7289 --- 
    7290 Chain | Description 
    7291 A | No description available 
    7292 B | No description available 
    7293 C | No description available 
    7294  
    7295 
    7296 > hide #1 models
    7297 
    7298 > show #13 models
    7299 
    7300 > mmaker #26 to #13
    7301 
    7302 Parameters 
    7303 --- 
    7304 Chain pairing | bb 
    7305 Alignment algorithm | Needleman-Wunsch 
    7306 Similarity matrix | BLOSUM-62 
    7307 SS fraction | 0.3 
    7308 Gap open (HH/SS/other) | 18/18/6 
    7309 Gap extend | 1 
    7310 SS matrix |  |  | H | S | O 
    7311 ---|---|---|--- 
    7312 H | 6 | -9 | -6 
    7313 S |  | 6 | -6 
    7314 O |  |  | 4 
    7315 Iteration cutoff | 2 
    7316  
    7317 Matchmaker NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb, chain A (#13) with
    7318 NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb, chain A (#26), sequence alignment
    7319 score = 2000 
    7320 RMSD between 388 pruned atom pairs is 0.003 angstroms; (across all 388 pairs:
    7321 0.003) 
    7322  
    7323 
    7324 > mcopy #13 toAtoms #26 settings hscv
    7325 
    7326 > cartoon style modeHelix default width 1.0 thickness 0.3
    7327 
    7328 > cartoon style modeHelix default width 1.1 thickness 0.2
    7329 
    7330 > cartoon style modeHelix default width 1.0 thickness 0.3
    7331 
    7332 > hide #13 models
    7333 
    7334 > close #13
    7335 
    7336 > rename #26 id #13
    7337 
    7338 > ui tool show "Side View"
    7339 
    7340 > coulombic #13
    7341 
    7342 Using Amber 20 recommended default charges and atom types for standard
    7343 residues 
    7344 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_A SES surface
    7345 #13.1: minimum, -16.52, mean 0.04, maximum 15.63 
    7346 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_B SES surface
    7347 #13.2: minimum, -19.83, mean -1.80, maximum 8.49 
    7348 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_C SES surface
    7349 #13.3: minimum, -13.89, mean -1.84, maximum 10.03 
    7350 To also show corresponding color key, enter the above coulombic command and
    7351 add key true 
    7352 
    7353 > surface cap false
    7354 
    7355 [Repeated 1 time(s)]
    7356 
    7357 > show /A:163,164 target a
    7358 
    7359 > save
    7360 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    7361 
    7362 > show #15 models
    7363 
    7364 > hide #!13 models
    7365 
    7366 > coulombic #15
    7367 
    7368 Using Amber 20 recommended default charges and atom types for standard
    7369 residues 
    7370 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_A SES surface #15.1:
    7371 minimum, -17.07, mean 0.02, maximum 20.09 
    7372 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_B SES surface #15.2:
    7373 minimum, -18.53, mean -1.82, maximum 10.93 
    7374 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_C SES surface #15.3:
    7375 minimum, -14.51, mean -2.14, maximum 12.50 
    7376 To also show corresponding color key, enter the above coulombic command and
    7377 add key true 
    7378 
    7379 > hide #!15 models
    7380 
    7381 > show #!16 models
    7382 
    7383 > hide #!16 models
    7384 
    7385 > show #!15 models
    7386 
    7387 > hide #!15 models
    7388 
    7389 > show #17 models
    7390 
    7391 > coulombic #17
    7392 
    7393 Using Amber 20 recommended default charges and atom types for standard
    7394 residues 
    7395 Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_A SES surface #17.1: minimum,
    7396 -15.88, mean 0.07, maximum 15.24 
    7397 Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_B SES surface #17.2: minimum,
    7398 -20.11, mean -1.82, maximum 11.17 
    7399 Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_C SES surface #17.3: minimum,
    7400 -14.41, mean -2.05, maximum 16.84 
    7401 To also show corresponding color key, enter the above coulombic command and
    7402 add key true 
    7403 
    7404 > hide /B,C target cs
    7405 
    7406 > show :NA target a
    7407 
    7408 > show #!15 models
    7409 
    7410 > hide #!17 models
    7411 
    7412 > show #!17 models
    7413 
    7414 > hide #!17 models
    7415 
    7416 > show #!17 models
    7417 
    7418 > hide #!17 models
    7419 
    7420 > show #!17 models
    7421 
    7422 > hide #!17 models
    7423 
    7424 > show #!17 models
    7425 
    7426 > hide #!17 models
    7427 
    7428 > show #!17 models
    7429 
    7430 > hide #!15 models
    7431 
    7432 > show #!15 models
    7433 
    7434 > hide #!15 models
    7435 
    7436 > show #!15 models
    7437 
    7438 > hide #!15 models
    7439 
    7440 > show #!15 models
    7441 
    7442 > hide #!15 models
    7443 
    7444 > show #!15 models
    7445 
    7446 > hide #!17 models
    7447 
    7448 > show #!13 models
    7449 
    7450 > hide #!15 models
    7451 
    7452 > view name cutaway
    7453 
    7454 > save
    7455 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    7456 
    7457 > show #11 models
    7458 
    7459 > hide #!13 models
    7460 
    7461 > coulombic #11
    7462 
    7463 Using Amber 20 recommended default charges and atom types for standard
    7464 residues 
    7465 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb_A SES surface
    7466 #11.1: minimum, -16.15, mean -0.06, maximum 16.72 
    7467 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb_B SES surface
    7468 #11.2: minimum, -19.94, mean -1.89, maximum 14.08 
    7469 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb_C SES surface
    7470 #11.3: minimum, -13.83, mean -1.90, maximum 13.43 
    7471 To also show corresponding color key, enter the above coulombic command and
    7472 add key true 
    7473 
    7474 > hide #!11 models
    7475 
    7476 > show #9 models
    7477 
    7478 > coulombic #9
    7479 
    7480 Using Amber 20 recommended default charges and atom types for standard
    7481 residues 
    7482 Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_A SES surface #9.1:
    7483 minimum, -15.35, mean 0.08, maximum 15.24 
    7484 Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_B SES surface #9.2:
    7485 minimum, -18.25, mean -1.97, maximum 8.02 
    7486 Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_C SES surface #9.3:
    7487 minimum, -13.57, mean -1.87, maximum 9.81 
    7488 To also show corresponding color key, enter the above coulombic command and
    7489 add key true 
    7490 
    7491 > show #!11 models
    7492 
    7493 > hide #!9 models
    7494 
    7495 > show #!9 models
    7496 
    7497 > hide #!11 models
    7498 
    7499 > show #!13 models
    7500 
    7501 > hide #!9 models
    7502 
    7503 > show #5 models
    7504 
    7505 > hide #!13 models
    7506 
    7507 > coulombic #5
    7508 
    7509 Using Amber 20 recommended default charges and atom types for standard
    7510 residues 
    7511 Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_A SES surface #5.1:
    7512 minimum, -15.26, mean 0.23, maximum 19.25 
    7513 Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_B SES surface #5.2:
    7514 minimum, -17.29, mean -2.01, maximum 8.10 
    7515 Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_C SES surface #5.3:
    7516 minimum, -13.33, mean -1.95, maximum 8.36 
    7517 To also show corresponding color key, enter the above coulombic command and
    7518 add key true 
    7519 
    7520 > hide #!5 models
    7521 
    7522 > show #!5 models
    7523 
    7524 > show #!9 models
    7525 
    7526 > hide #!5 models
    7527 
    7528 > show #!5 models
    7529 
    7530 > view list
    7531 
    7532 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    7533 dimer_view-all_front, mono_back, mono_back_, mono_front 
    7534 
    7535 > view cutaway
    7536 
    7537 > hide #!9 models
    7538 
    7539 > hide #!5 models
    7540 
    7541 > show #!11 models
    7542 
    7543 > show #!13 models
    7544 
    7545 > hide #!11 models
    7546 
    7547 > show #!11 models
    7548 
    7549 > hide #!11 models
    7550 
    7551 > show #!9 models
    7552 
    7553 > hide #!9 models
    7554 
    7555 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    7556 > nd-6F9-K_BTPpH85_state1-unplugged.pdb
    7557 
    7558 Chain information for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #26 
    7559 --- 
    7560 Chain | Description 
    7561 A | No description available 
    7562 B | No description available 
    7563 C | No description available 
    7564  
    7565 
    7566 > mmaker #26 to #13
    7567 
    7568 Parameters 
    7569 --- 
    7570 Chain pairing | bb 
    7571 Alignment algorithm | Needleman-Wunsch 
    7572 Similarity matrix | BLOSUM-62 
    7573 SS fraction | 0.3 
    7574 Gap open (HH/SS/other) | 18/18/6 
    7575 Gap extend | 1 
    7576 SS matrix |  |  | H | S | O 
    7577 ---|---|---|--- 
    7578 H | 6 | -9 | -6 
    7579 S |  | 6 | -6 
    7580 O |  |  | 4 
    7581 Iteration cutoff | 2 
    7582  
    7583 Matchmaker NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb, chain A (#13) with
    7584 NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb, chain A (#26), sequence alignment
    7585 score = 2000 
    7586 RMSD between 388 pruned atom pairs is 0.000 angstroms; (across all 388 pairs:
    7587 0.000) 
    7588  
    7589 
    7590 > mcopy #13 toAtoms #26 settings hscv
    7591 
    7592 > cartoon style modeHelix default width 1.1 thickness 0.2
    7593 
    7594 > cartoon style modeHelix default width 1.0 thickness 0.3
    7595 
    7596 > hide #!13 models
    7597 
    7598 > coulombic #26
    7599 
    7600 Using Amber 20 recommended default charges and atom types for standard
    7601 residues 
    7602 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_A SES surface
    7603 #26.1: minimum, -16.52, mean 0.01, maximum 15.63 
    7604 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_B SES surface
    7605 #26.2: minimum, -19.83, mean -1.80, maximum 8.49 
    7606 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_C SES surface
    7607 #26.3: minimum, -13.89, mean -1.84, maximum 10.03 
    7608 To also show corresponding color key, enter the above coulombic command and
    7609 add key true 
    7610 
    7611 > hide #!26 models
    7612 
    7613 > show #!26 models
    7614 
    7615 > show #!9 models
    7616 
    7617 > hide #!9 models
    7618 
    7619 > show #!9 models
    7620 
    7621 > hide #!26 models
    7622 
    7623 > hide #!9 models
    7624 
    7625 > show #!13 models
    7626 
    7627 > hide #!13 models
    7628 
    7629 > close #13
    7630 
    7631 > show #!26 models
    7632 
    7633 > rename #26 id #13
    7634 
    7635 > save
    7636 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    7637 
    7638 > view list
    7639 
    7640 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    7641 dimer_view-all_front, mono_back, mono_back_, mono_front 
    7642 
    7643 > view cutaway
    7644 
    7645 > show #!15 models
    7646 
    7647 > hide #!13 models
    7648 
    7649 > show #!13 models
    7650 
    7651 > show #!17 models
    7652 
    7653 > hide #!13 models
    7654 
    7655 > hide #!15 models
    7656 
    7657 > show #!13 models
    7658 
    7659 > view cutaway
    7660 
    7661 > hide #!17 models
    7662 
    7663 > show #!15 models
    7664 
    7665 > hide #!13 models
    7666 
    7667 > show #!17 models
    7668 
    7669 > hide #!15 models
    7670 
    7671 > show #!15 models
    7672 
    7673 > hide #!17 models
    7674 
    7675 > show #!13 models
    7676 
    7677 > hide #!15 models
    7678 
    7679 > show #!9 models
    7680 
    7681 > hide #!13 models
    7682 
    7683 > show #!5 models
    7684 
    7685 > hide #!9 models
    7686 
    7687 > show #!9 models
    7688 
    7689 > hide #!5 models
    7690 
    7691 > show #!17 models
    7692 
    7693 > hide #!17 models
    7694 
    7695 > show #!17 models
    7696 
    7697 > hide #!17 models
    7698 
    7699 > show #19 models
    7700 
    7701 > hide #19 models
    7702 
    7703 > show #19 models
    7704 
    7705 > hide #19 models
    7706 
    7707 > show #19 models
    7708 
    7709 > hide #19 models
    7710 
    7711 > show #!17 models
    7712 
    7713 > hide #!9 models
    7714 
    7715 > show #!5 models
    7716 
    7717 > hide #!17 models
    7718 
    7719 > show #!17 models
    7720 
    7721 > show #!9 models
    7722 
    7723 > hide #!5 models
    7724 
    7725 > hide /B,C target acs
    7726 
    7727 > hide #!9 models
    7728 
    7729 > show #!9 models
    7730 
    7731 > view list
    7732 
    7733 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    7734 dimer_view-all_front, mono_back, mono_back_, mono_front 
    7735 
    7736 > view cutaway
    7737 
    7738 > hide #!9 models
    7739 
    7740 > show #!9 models
    7741 
    7742 > hide #!17 models
    7743 
    7744 > view cutaway
    7745 
    7746 > show #!13 models
    7747 
    7748 > hide #!9 models
    7749 
    7750 > show #!17 models
    7751 
    7752 > hide #!17 models
    7753 
    7754 > show #!15 models
    7755 
    7756 > hide #!13 models
    7757 
    7758 > show #!17 models
    7759 
    7760 > hide #!15 models
    7761 
    7762 > show #!15 models
    7763 
    7764 > hide #!17 models
    7765 
    7766 > show #!13 models
    7767 
    7768 > hide #!15 models
    7769 
    7770 > show #!15 models
    7771 
    7772 > hide #!13 models
    7773 
    7774 > show #!17 models
    7775 
    7776 > hide #!15 models
    7777 
    7778 > hide #!17 models
    7779 
    7780 > show #!17 models
    7781 
    7782 > show #!15 models
    7783 
    7784 > hide #!15 models
    7785 
    7786 > show #!13 models
    7787 
    7788 > hide #!17 models
    7789 
    7790 > show #!15 models
    7791 
    7792 > hide #!15 models
    7793 
    7794 > hide #!13 models
    7795 
    7796 > show #!13 models
    7797 
    7798 > show #!9 models
    7799 
    7800 > hide #!13 models
    7801 
    7802 > show #!13 models
    7803 
    7804 > hide #!13 models
    7805 
    7806 > show #!13 models
    7807 
    7808 > hide #!13 models
    7809 
    7810 > show #!13 models
    7811 
    7812 > hide #!9 models
    7813 
    7814 > show #!9 models
    7815 
    7816 > hide #!13 models
    7817 
    7818 > show #!15 models
    7819 
    7820 > view list
    7821 
    7822 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    7823 dimer_view-all_front, mono_back, mono_back_, mono_front 
    7824 
    7825 > view cutaway
    7826 
    7827 > view name cutaway
    7828 
    7829 > hide #!15 models
    7830 
    7831 > clip near -0.8 position #9/A:164
    7832 
    7833 > clip near -0.0 position #9/A:164
    7834 
    7835 > clip near -1.5 position #9/A:164
    7836 
    7837 > clip near -1.6 position #9/A:164
    7838 
    7839 > clip near -2 position #9/A:164
    7840 
    7841 > show #!17 models
    7842 
    7843 > hide #!17 models
    7844 
    7845 > show #!17 models
    7846 
    7847 > hide #!9 models
    7848 
    7849 > show #!9 models
    7850 
    7851 > hide #!9 models
    7852 
    7853 > clip near -2 position #17/A:164
    7854 
    7855 > clip near -2 position #17/A:163
    7856 
    7857 > clip near -3 position #17/A:163
    7858 
    7859 > show #!9 models
    7860 
    7861 > hide #!17 models
    7862 
    7863 > clip near -3 position #9/A:163
    7864 
    7865 > hide #!9 models
    7866 
    7867 > show #!13 models
    7868 
    7869 > clip near -3 position #13/A:163
    7870 
    7871 > clip near -3 position #13/A:164@CG
    7872 
    7873 > clip near 0 position #13/A:164@CG
    7874 
    7875 > clip near -2 position #13/A:164@CG
    7876 
    7877 > clip near -1 position #13/A:164@CG
    7878 
    7879 > hide #!13 models
    7880 
    7881 > show #!15 models
    7882 
    7883 > show #!17 models
    7884 
    7885 > hide #!15 models
    7886 
    7887 > show #!15 models
    7888 
    7889 > hide #!17 models
    7890 
    7891 > show #!9 models
    7892 
    7893 > hide #!15 models
    7894 
    7895 > clip near -1 position #9/A:164@CG
    7896 
    7897 > show #!17 models
    7898 
    7899 > hide #!9 models
    7900 
    7901 > show #!9 models
    7902 
    7903 > hide #!17 models
    7904 
    7905 > view list
    7906 
    7907 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    7908 dimer_view-all_front, mono_back, mono_back_, mono_front 
    7909 
    7910 > view cutaway
    7911 
    7912 > show #!13 models
    7913 
    7914 > hide #!9 models
    7915 
    7916 > show #!9 models
    7917 
    7918 > hide #!13 models
    7919 
    7920 > hide #!9 models
    7921 
    7922 > show #!13 models
    7923 
    7924 > show #!15 models
    7925 
    7926 > hide #!13 models
    7927 
    7928 > show #!17 models
    7929 
    7930 > hide #!15 models
    7931 
    7932 > show #!15 models
    7933 
    7934 > hide #!17 models
    7935 
    7936 > show #!13 models
    7937 
    7938 > hide #!15 models
    7939 
    7940 > show #!15 models
    7941 
    7942 > hide #!13 models
    7943 
    7944 > show #!13 models
    7945 
    7946 > hide #!15 models
    7947 
    7948 > view list
    7949 
    7950 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    7951 dimer_view-all_front, mono_back, mono_back_, mono_front 
    7952 
    7953 > view cutaway
    7954 
    7955 > show #!17 models
    7956 
    7957 > hide #!17 models
    7958 
    7959 > show #!9 models
    7960 
    7961 > hide #!13 models
    7962 
    7963 > show #!13 models
    7964 
    7965 > hide #!13 models
    7966 
    7967 > show #!13 models
    7968 
    7969 > hide #!9 models
    7970 
    7971 > show #!9 models
    7972 
    7973 > hide #!13 models
    7974 
    7975 > show #!13 models
    7976 
    7977 > hide #!9 models
    7978 
    7979 > show #!9 models
    7980 
    7981 > hide #!13 models
    7982 
    7983 > show #!13 models
    7984 
    7985 > hide #!9 models
    7986 
    7987 > show #!15 models
    7988 
    7989 > hide #!13 models
    7990 
    7991 > show #!17 models
    7992 
    7993 > hide #!15 models
    7994 
    7995 > view name cutaway
    7996 
    7997 > save
    7998 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    7999 
    8000 > surface cap true
    8001 
    8002 [Repeated 1 time(s)]
    8003 
    8004 > show #!15 models
    8005 
    8006 > hide #!17 models
    8007 
    8008 > show #!17 models
    8009 
    8010 > hide #!17 models
    8011 
    8012 > hide #!15 models
    8013 
    8014 > show #!13 models
    8015 
    8016 > show #!9 models
    8017 
    8018 > hide #!13 models
    8019 
    8020 > show #!17 models
    8021 
    8022 > hide #!9 models
    8023 
    8024 > hide #!17 atoms
    8025 
    8026 > hide #!17 cartoons
    8027 
    8028 > color /A:NA,163,164 byhetero target a
    8029 
    8030 > color ##name="cap front" black target s
    8031 
    8032 [Repeated 1 time(s)]
    8033 
    8034 > color ##name="cap near" black target s
    8035 
    8036 > lighting soft
    8037 
    8038 > lighting full
    8039 
    8040 > lighting simple
    8041 
    8042 > lighting soft
    8043 
    8044 > lighting soft multiShadow 1024
    8045 
    8046 > save
    8047 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    8048 
    8049 ——— End of log from Mon Aug 26 17:49:42 2024 ———
    8050 
    8051 opened ChimeraX session 
    8052 
    8053 > lighting soft multiShadow 1024
    8054 
    8055 > color ##name="cap near" black target s
    8056 
    8057 > save NhaA-Na-pH85_cutaway.png supersample 3 transparentBackground false
    8058 
    8059 > clip model /A:NA,163,164 false
    8060 
    8061 > show :NA target a
    8062 
    8063 > show /A:163,164&sidechain target a
    8064 
    8065 > color /A:NA,163,164 byhetero target a
    8066 
    8067 > transparency ##name="cap near" 100
    8068 
    8069 > transparency #17 70 target s
    8070 
    8071 > clip model /A:NA,163,164 false
    8072 
    8073 > show :NA target a
    8074 
    8075 > show /A:163,164&sidechain target a
    8076 
    8077 > color /A:NA,163,164 byhetero target a
    8078 
    8079 > color ##name="cap near" white transparency 100 target s
    8080 
    8081 > transparency #17 70 target s
    8082 
    8083 > view
    8084 
    8085 > view list
    8086 
    8087 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    8088 dimer_view-all_front, mono_back, mono_back_, mono_front 
    8089 
    8090 > view cutaway
    8091 
    8092 > ui tool show "Side View"
    8093 
    8094 > clip front -0.8 position #17:NA
    8095 
    8096 > clip front 0 position #17:NA
    8097 
    8098 > clip front 1 position #17:NA
    8099 
    8100 > clip front 0.5 position #17:NA
    8101 
    8102 > clip front 0.4 position #17:NA
    8103 
    8104 > hide #!17 models
    8105 
    8106 > show #!11 models
    8107 
    8108 > hide #!11 models
    8109 
    8110 > show #!9 models
    8111 
    8112 > show #!5 models
    8113 
    8114 > hide #!9 models
    8115 
    8116 > show #!9 models
    8117 
    8118 > hide #!5 models
    8119 
    8120 > hide #!9 models
    8121 
    8122 > show #!17 models
    8123 
    8124 > view name cutaway
    8125 
    8126 > clip model /A:NA,163,164 false
    8127 
    8128 > show :NA target a
    8129 
    8130 > show /A:163,164&sidechain target a
    8131 
    8132 > color /A:NA,163,164 byhetero target a
    8133 
    8134 > transparency ##name="cap near" 100
    8135 
    8136 > transparency #17 70 target s
    8137 
    8138 > clip model /A:NA,163,164 false
    8139 
    8140 > show :NA target a
    8141 
    8142 > show /A:163,164&sidechain target a
    8143 
    8144 > color /A:NA,163,164 byhetero target a
    8145 
    8146 > color ##name="cap near" white transparency 100 target s
    8147 
    8148 > transparency #17 70 target s
    8149 
    8150 > clip model /A:NA,163,164 false
    8151 
    8152 > show :NA target a
    8153 
    8154 > show /A:163,164&sidechain target a
    8155 
    8156 > color /A:NA,163,164 byhetero target a
    8157 
    8158 > color ##name="cap near" white transparency 100 target s
    8159 
    8160 > transparency #17 70 target s
    8161 
    8162 > clip model /A:NA,163,164 false
    8163 
    8164 > show :NA target a
    8165 
    8166 > show /A:163,164&sidechain target a
    8167 
    8168 > color /A:NA,163,164 byhetero target a
    8169 
    8170 > color ##name="cap front" white transparency 100 target s
    8171 
    8172 > transparency #17 70 target s
    8173 
    8174 > hide #!17 atoms
    8175 
    8176 > save NhaA-Na-pH85_cutaway_surf.png supersample 3 transparentBackground false
    8177 
    8178 > color ##name="cap near" black target s
    8179 
    8180 > transparency 0 target s
    8181 
    8182 > color ##name="cap near" black target s
    8183 
    8184 > transparency 0 target s
    8185 
    8186 > color ##name="cap front" black target s
    8187 
    8188 > transparency 0 target s
    8189 
    8190 > save NhaA-Na-pH85_cutaway.png supersample 3 transparentBackground false
    8191 
    8192 > hide #!17 models
    8193 
    8194 > show #!15 models
    8195 
    8196 > hide #!15 cartoons
    8197 
    8198 > hide #!15 atoms
    8199 
    8200 > color ##name="cap front" black target s
    8201 
    8202 > transparency 0 target s
    8203 
    8204 > save NhaA-K-pH85-state2_cutaway.png supersample 3 transparentBackground
    8205 > false
    8206 
    8207 > show #!13 models
    8208 
    8209 > hide #!15 models
    8210 
    8211 > hide #!13 cartoons
    8212 
    8213 > hide #!13 atoms
    8214 
    8215 > color ##name="cap front" black target s
    8216 
    8217 > transparency 0 target s
    8218 
    8219 > save NhaA-K-pH85-state1-unplugged_cutaway.png supersample 3
    8220 > transparentBackground false
    8221 
    8222 > show #!9 models
    8223 
    8224 > hide #!13 models
    8225 
    8226 > hide #!9 cartoons
    8227 
    8228 > hide #!9 atoms
    8229 
    8230 > color ##name="cap front" black target s
    8231 
    8232 > transparency 0 target s
    8233 
    8234 > save NhaA-K-pH75-unplugged_cutaway.png supersample 3 transparentBackground
    8235 > false
    8236 
    8237 > hide #!9 models
    8238 
    8239 > show #!5 models
    8240 
    8241 > hide #!5 cartoons
    8242 
    8243 > hide #!5 atoms
    8244 
    8245 > color ##name="cap front" black target s
    8246 
    8247 > transparency 0 target s
    8248 
    8249 > save NhaA-K-pH63-unplugged_cutaway.png supersample 3 transparentBackground
    8250 > false
    8251 
    8252 > color ##name="cap front" white transparency 100 target s
    8253 
    8254 > transparency #17 70 target s
    8255 
    8256 > color ##name="cap front" white transparency 100 target s
    8257 
    8258 > transparency 70 target s
    8259 
    8260 > save NhaA-K-pH63-unplugged_cutaway_surf.png supersample 3
    8261 > transparentBackground false
    8262 
    8263 > show #!9 models
    8264 
    8265 > hide #!5 models
    8266 
    8267 > color ##name="cap front" white transparency 100 target s
    8268 
    8269 > transparency 70 target s
    8270 
    8271 > save NhaA-K-pH75-unplugged_cutaway_surf.png supersample 3
    8272 > transparentBackground false
    8273 
    8274 > show #!13 models
    8275 
    8276 > hide #!9 models
    8277 
    8278 > color ##name="cap front" white transparency 100 target s
    8279 
    8280 > transparency 70 target s
    8281 
    8282 > save NhaA-K-pH85-state1-unplugged_cutaway_surf.png supersample 3
    8283 > transparentBackground false
    8284 
    8285 > show #!15 models
    8286 
    8287 > hide #!13 models
    8288 
    8289 > color ##name="cap front" white transparency 100 target s
    8290 
    8291 > transparency 70 target s
    8292 
    8293 > save NhaA-K-pH85-state2_cutaway_surf.png supersample 3 transparentBackground
    8294 > false
    8295 
    8296 > show #!17 models
    8297 
    8298 > hide #!15 models
    8299 
    8300 > color ##name="cap front" white transparency 100 target s
    8301 
    8302 > transparency 70 target s
    8303 
    8304 > save NhaA-Na-pH85_cutaway_surf.png supersample 3 transparentBackground false
    8305 
    8306 > hide #!17 models
    8307 
    8308 > show #!17 models
    8309 
    8310 > transparency 0 target s
    8311 
    8312 > hide target s
    8313 
    8314 > clip model /A:NA,163,164 false
    8315 
    8316 > show :NA target a
    8317 
    8318 > show /A:163,164&sidechain target a
    8319 
    8320 > color /A:NA,163,164 byhetero target a
    8321 
    8322 > size stickRadius 0.4
    8323 
    8324 Changed 58102 bond radii 
    8325 
    8326 > graphics silhouettes 6;
    8327 
    8328 Expected true or false or a keyword 
    8329 
    8330 > clip model /A:NA,163,164 false
    8331 
    8332 > show :NA target a
    8333 
    8334 > show /A:163,164&sidechain target a
    8335 
    8336 > color /A:NA,163,164 byhetero target a
    8337 
    8338 > size stickRadius 0.4
    8339 
    8340 Changed 58102 bond radii 
    8341 
    8342 > graphics silhouettes width 6
    8343 
    8344 > ~clip
    8345 
    8346 > clip model /A:NA,163,164 true
    8347 
    8348 > lighting full
    8349 
    8350 > lighting simple
    8351 
    8352 > lighting full
    8353 
    8354 > style :NA sphere
    8355 
    8356 Changed 2 atom styles 
    8357 
    8358 > hide sel
    8359 
    8360 > clip model /A:NA,163,164 false
    8361 
    8362 > show :NA target a
    8363 
    8364 > show /A:163,164&sidechain target a
    8365 
    8366 > color /A:NA,163,164 byhetero target a
    8367 
    8368 > size stickRadius 0.4
    8369 
    8370 Changed 58102 bond radii 
    8371 
    8372 > graphics silhouettes width 4
    8373 
    8374 > clip model /A:NA,163,164 false
    8375 
    8376 > show :NA target a
    8377 
    8378 > show /A:163,164&sidechain target a
    8379 
    8380 > color /A:NA,163,164 byhetero target a
    8381 
    8382 > size stickRadius 0.4
    8383 
    8384 Changed 58102 bond radii 
    8385 
    8386 > graphics silhouettes width 5
    8387 
    8388 > clip model /A:NA,163,164 false
    8389 
    8390 > show :NA target a
    8391 
    8392 > show /A:163,164&sidechain target a
    8393 
    8394 > color /A:NA,163,164 byhetero target a
    8395 
    8396 > size stickRadius 0.4
    8397 
    8398 Changed 58102 bond radii 
    8399 
    8400 > graphics silhouettes width 4
    8401 
    8402 > clip model /A:NA,163,164 false
    8403 
    8404 > show :NA target a
    8405 
    8406 > show /A:163,164&sidechain target a
    8407 
    8408 > color /A:NA,163,164 byhetero target a
    8409 
    8410 > size stickRadius 0.5
    8411 
    8412 Changed 58102 bond radii 
    8413 
    8414 > graphics silhouettes width 4
    8415 
    8416 > clip model /A:NA,163,164 false
    8417 
    8418 > show :NA target a
    8419 
    8420 > show /A:163,164&sidechain target a
    8421 
    8422 > color /A:NA,163,164 byhetero target a
    8423 
    8424 > size stickRadius 0.5
    8425 
    8426 Changed 58102 bond radii 
    8427 
    8428 > graphics silhouettes width 5
    8429 
    8430 > save NhaA-Na-pH85_cutaway_res.png supersample 3 transparentBackground false
    8431 
    8432 > save NhaA-Na-pH85_cutaway_res.png supersample 3 transparentBackground true
    8433 
    8434 > hide #!17 models
    8435 
    8436 > show #!15 models
    8437 
    8438 > hide sel
    8439 
    8440 > save NhaA-K-pH85_cutaway_res.png supersample 3 transparentBackground true
    8441 
    8442 > hide #!15 models
    8443 
    8444 > show #!13 models
    8445 
    8446 > select clear
    8447 
    8448 > hide sel
    8449 
    8450 > save NhaA-K-pH85-state1-unplugged_cutaway_res.png supersample 3
    8451 > transparentBackground true
    8452 
    8453 > hide #!13 models
    8454 
    8455 > show #!15 models
    8456 
    8457 > hide #!15 models
    8458 
    8459 > show #!9 models
    8460 
    8461 > hide sel
    8462 
    8463 > save NhaA-K-pH75-unplugged_cutaway_res.png supersample 3
    8464 > transparentBackground true
    8465 
    8466 > hide #!9 models
    8467 
    8468 > show #!5 models
    8469 
    8470 > hide sel
    8471 
    8472 > save NhaA-K-pH63-unplugged_cutaway_res.png supersample 3
    8473 > transparentBackground true
    8474 
    8475 > hide #!5 models
    8476 
    8477 > show #!5 models
    8478 
    8479 > select clear
    8480 
    8481 > show #!5 atoms
    8482 
    8483 > hide #!5 atoms
    8484 
    8485 > hide /A:NA,163,164 target a
    8486 
    8487 > size stickRadius 0.3
    8488 
    8489 Changed 58102 bond radii 
    8490 
    8491 > graphics silhouettes width 2
    8492 
    8493 > show #!9 models
    8494 
    8495 > show #!13 models
    8496 
    8497 > show #!15 models
    8498 
    8499 > show #!17 models
    8500 
    8501 > show #!5,9,13,15,17 surfaces
    8502 
    8503 > hide #!17 models
    8504 
    8505 > hide #!15 models
    8506 
    8507 > hide #!13 models
    8508 
    8509 > hide #!9 models
    8510 
    8511 > hide #!5 models
    8512 
    8513 > show #!5 models
    8514 
    8515 > lighting soft
    8516 
    8517 > lighting soft multiShadow 1024
    8518 
    8519 > clip front 0.4 position #17:NA
    8520 
    8521 > color ##name="cap front" black target s
    8522 
    8523 > hide /B,C target asc
    8524 
    8525 > save NhaA-K-pH63-unplugged_cutaway.png supersample 3 transparentBackground
    8526 > true
    8527 
    8528 > show #!9 models
    8529 
    8530 > hide #!5 models
    8531 
    8532 > color ##name="cap front" black target s
    8533 
    8534 > save NhaA-K-pH75-unplugged_cutaway.png supersample 3 transparentBackground
    8535 > true
    8536 
    8537 > hide #!9 models
    8538 
    8539 > show #!11 models
    8540 
    8541 > hide #!11 models
    8542 
    8543 > show #!13 models
    8544 
    8545 > color ##name="cap front" black target s
    8546 
    8547 > save NhaA-K-pH85-state1-unplugged_cutaway.png supersample 3
    8548 > transparentBackground true
    8549 
    8550 > hide #!13 models
    8551 
    8552 > show #!15 models
    8553 
    8554 > color ##name="cap front" black target s
    8555 
    8556 > save NhaA-K-pH85-state2_cutaway.png supersample 3 transparentBackground true
    8557 
    8558 > hide #!15 models
    8559 
    8560 > show #!17 models
    8561 
    8562 > color ##name="cap front" black target s
    8563 
    8564 > save NhaA-Na-pH85_cutaway.png supersample 3 transparentBackground true
    8565 
    8566 > color ##name="cap near" white transparency 100 target s
    8567 
    8568 > transparency 70 target s
    8569 
    8570 > color ##name="cap front" white transparency 100 target s
    8571 
    8572 > transparency 70 target s
    8573 
    8574 > save NhaA-Na-pH85_cutaway_surf.png supersample 3 transparentBackground true
    8575 
    8576 > hide #!17 models
    8577 
    8578 > show #!15 models
    8579 
    8580 > color ##name="cap front" white transparency 100 target s
    8581 
    8582 > transparency 70 target s
    8583 
    8584 > save NhaA-K-pH85-state2_cutaway_surf.png supersample 3 transparentBackground
    8585 > true
    8586 
    8587 > hide #!15 models
    8588 
    8589 > show #!13 models
    8590 
    8591 > color ##name="cap front" white transparency 100 target s
    8592 
    8593 > transparency 70 target s
    8594 
    8595 > save NhaA-K-pH85-state1-unplugged_cutaway_surf.png supersample 3
    8596 > transparentBackground true
    8597 
    8598 > hide #!13 models
    8599 
    8600 > show #!9 models
    8601 
    8602 > color ##name="cap front" white transparency 100 target s
    8603 
    8604 > transparency 70 target s
    8605 
    8606 > save NhaA-K-pH75-unplugged_cutaway_surf.png supersample 3
    8607 > transparentBackground true
    8608 
    8609 > hide #!9 models
    8610 
    8611 > show #!5 models
    8612 
    8613 > color ##name="cap front" white transparency 100 target s
    8614 
    8615 > transparency 70 target s
    8616 
    8617 > save NhaA-K-pH63-unplugged_cutaway_surf.png supersample 3
    8618 > transparentBackground true
    8619 
    8620 > transparency 0 target s
    8621 
    8622 > hide #!5 models
    8623 
    8624 > show #!5 models
    8625 
    8626 > ~clip
    8627 
    8628 > hide #5.1 models
    8629 
    8630 > show #5.1 models
    8631 
    8632 > hide target s
    8633 
    8634 > show :NA target a
    8635 
    8636 > show /A:163,164&sidechain target a
    8637 
    8638 > color /A:NA,163,164 byhetero target a
    8639 
    8640 > size stickRadius 0.5
    8641 
    8642 Changed 58102 bond radii 
    8643 
    8644 > graphics silhouettes width 5
    8645 
    8646 > show :NA target a
    8647 
    8648 > show /A:163,164&sidechain target a
    8649 
    8650 > color /A:NA,163,164 byhetero target a
    8651 
    8652 > size stickRadius 0.5
    8653 
    8654 Changed 58102 bond radii 
    8655 
    8656 > graphics silhouettes width 5
    8657 
    8658 > graphics silhouettes color white
    8659 
    8660 > select up
    8661 
    8662 4643 atoms, 1 pseudobond, 612 residues, 5 models selected 
    8663 
    8664 > select down
    8665 
    8666 1 pseudobond, 1 model selected 
    8667 
    8668 > hide sel
    8669 
    8670 > save NhaA-K-pH63-unplugged_cutaway_res_wh-sil.png supersample 3
    8671 > transparentBackground true
    8672 
    8673 > select up
    8674 
    8675 1 pseudobond, 1 model selected 
    8676 
    8677 > select clear
    8678 
    8679 > show :NA target a
    8680 
    8681 > show /A:163,164&sidechain target a
    8682 
    8683 > color /A:NA,163,164 byhetero target a
    8684 
    8685 > size stickRadius 0.5
    8686 
    8687 Changed 58102 bond radii 
    8688 
    8689 > graphics silhouettes width 5
    8690 
    8691 > graphics silhouettes color black
    8692 
    8693 > hide /A:NA,163,164 target a
    8694 
    8695 > size stickRadius 0.3
    8696 
    8697 Changed 58102 bond radii 
    8698 
    8699 > graphics silhouettes width 2
    8700 
    8701 > show :NA target a
    8702 
    8703 > show /A:163,164&sidechain target a
    8704 
    8705 > color /A:NA,163,164 byhetero target a
    8706 
    8707 > size stickRadius 0.5
    8708 
    8709 Changed 58102 bond radii 
    8710 
    8711 > graphics silhouettes width 5
    8712 
    8713 > lighting full
    8714 
    8715 > lighting shadows false
    8716 
    8717 > show :NA target a
    8718 
    8719 > show /A:163,164&sidechain target a
    8720 
    8721 > color /A:NA,163,164 byhetero target a
    8722 
    8723 > size stickRadius 0.6
    8724 
    8725 Changed 58102 bond radii 
    8726 
    8727 > graphics silhouettes width 5
    8728 
    8729 > show :NA target a
    8730 
    8731 > show /A:163,164&sidechain target a
    8732 
    8733 > color /A:NA,163,164 byhetero target a
    8734 
    8735 > size stickRadius 0.6
    8736 
    8737 Changed 58102 bond radii 
    8738 
    8739 > graphics silhouettes width 4
    8740 
    8741 > show :NA target a
    8742 
    8743 > show /A:163,164&sidechain target a
    8744 
    8745 > color /A:NA,163,164 byhetero target a
    8746 
    8747 > size stickRadius 0.8
    8748 
    8749 Changed 58102 bond radii 
    8750 
    8751 > graphics silhouettes width 4
    8752 
    8753 > show :NA target a
    8754 
    8755 > show /A:163,164&sidechain target a
    8756 
    8757 > color /A:NA,163,164 byhetero target a
    8758 
    8759 > size stickRadius 0.7
    8760 
    8761 Changed 58102 bond radii 
    8762 
    8763 > graphics silhouettes width 4
    8764 
    8765 > show :NA target a
    8766 
    8767 > show /A:163,164&sidechain target a
    8768 
    8769 > color /A:NA,163,164 byhetero target a
    8770 
    8771 > size stickRadius 0.7
    8772 
    8773 Changed 58102 bond radii 
    8774 
    8775 > graphics silhouettes width 2
    8776 
    8777 > show :NA target a
    8778 
    8779 > show /A:163,164&sidechain target a
    8780 
    8781 > color /A:NA,163,164 byhetero target a
    8782 
    8783 > size stickRadius 0.7
    8784 
    8785 Changed 58102 bond radii 
    8786 
    8787 > graphics silhouettes width 4
    8788 
    8789 > show :NA target a
    8790 
    8791 > show /A:163,164&sidechain target a
    8792 
    8793 > color /A:NA,163,164 byhetero target a
    8794 
    8795 > size stickRadius 0.7
    8796 
    8797 Changed 58102 bond radii 
    8798 
    8799 > graphics silhouettes width 2
    8800 
    8801 > lighting simple
    8802 
    8803 > lighting full
    8804 
    8805 > lighting simple
    8806 
    8807 > lighting full
    8808 
    8809 > lighting simple
    8810 
    8811 > lighting full
    8812 
    8813 > lighting simple
    8814 
    8815 > lighting full
    8816 
    8817 > lighting simple
    8818 
    8819 > lighting full
    8820 
    8821 > lighting simple
    8822 
    8823 > lighting full
    8824 
    8825 > lighting shadows false
    8826 
    8827 > select clear
    8828 
    8829 > hide sel
    8830 
    8831 > select clear
    8832 
    8833 > save NhaA-K-pH63-unplugged_cutaway_res.png supersample 3
    8834 > transparentBackground true
    8835 
    8836 > hide #!5 models
    8837 
    8838 > show #!17 models
    8839 
    8840 > lighting simple
    8841 
    8842 > lighting full
    8843 
    8844 > lighting simple
    8845 
    8846 > lighting full
    8847 
    8848 > lighting soft
    8849 
    8850 > lighting simple
    8851 
    8852 > lighting full
    8853 
    8854 > hide #!17 models
    8855 
    8856 > show #!5 models
    8857 
    8858 > hide #!5 models
    8859 
    8860 > show #!9 models
    8861 
    8862 > hide sel
    8863 
    8864 > lighting shadows false
    8865 
    8866 > lighting shadows true
    8867 
    8868 > lighting shadows false
    8869 
    8870 > save NhaA-K-pH75-unplugged_cutaway_res.png supersample 3
    8871 > transparentBackground true
    8872 
    8873 > hide #!9 models
    8874 
    8875 > show #!13 models
    8876 
    8877 > select clear
    8878 
    8879 [Repeated 1 time(s)]
    8880 
    8881 > hide sel
    8882 
    8883 > save NhaA-K-pH85-state1-unplugged_cutaway_res.png supersample 3
    8884 > transparentBackground true
    8885 
    8886 > hide #!13 models
    8887 
    8888 > show #!15 models
    8889 
    8890 > hide sel
    8891 
    8892 > save NhaA-K-pH85-state2_cutaway_res.png supersample 3 transparentBackground
    8893 > true
    8894 
    8895 > hide #!15 models
    8896 
    8897 > show #!17 models
    8898 
    8899 > select up
    8900 
    8901 4643 atoms, 1 pseudobond, 612 residues, 5 models selected 
    8902 
    8903 > select up
    8904 
    8905 4749 atoms, 4850 bonds, 1 pseudobond, 617 residues, 5 models selected 
    8906 
    8907 > select down
    8908 
    8909 4643 atoms, 1 pseudobond, 612 residues, 5 models selected 
    8910 
    8911 > select down
    8912 
    8913 1 pseudobond, 1 model selected 
    8914 
    8915 > hide sel
    8916 
    8917 > save NhaA-Na-pH85_cutaway_res.png supersample 3 transparentBackground true
    8918 
    8919 > hide /A:NA,163,164 target a
    8920 
    8921 > size stickRadius 0.3
    8922 
    8923 Changed 58102 bond radii 
    8924 
    8925 > graphics silhouettes width 2
    8926 
    8927 > clip front 0.4 position #17:NA
    8928 
    8929 > transparency 70 target s
    8930 
    8931 > color ##name="cap front" white transparency 100 target s
    8932 
    8933 > show #!15 models
    8934 
    8935 > show #!13 models
    8936 
    8937 > show #!9 models
    8938 
    8939 > show #!5 models
    8940 
    8941 > show #!5,9,13,15,17 surfaces
    8942 
    8943 > hide /B,C target s
    8944 
    8945 > hide #!5 models
    8946 
    8947 > hide #!9 models
    8948 
    8949 > hide #!13 models
    8950 
    8951 > hide #!15 models
    8952 
    8953 > lighting soft
    8954 
    8955 > lighting soft multiShadow 1024
    8956 
    8957 > transparency 70 target s
    8958 
    8959 > color ##name="cap front" white transparency 100 target s
    8960 
    8961 > save NhaA-Na-pH85_cutaway_surf.png supersample 3 transparentBackground true
    8962 
    8963 > hide #!17 models
    8964 
    8965 > show #!15 models
    8966 
    8967 > transparency 70 target s
    8968 
    8969 > color ##name="cap front" white transparency 100 target s
    8970 
    8971 > save NhaA-K-pH85-state2_cutaway_surf.png supersample 3 transparentBackground
    8972 > true
    8973 
    8974 > hide #!15 models
    8975 
    8976 > show #!13 models
    8977 
    8978 > transparency 70 target s
    8979 
    8980 > color ##name="cap front" white transparency 100 target s
    8981 
    8982 > save NhaA-K-pH85-state1-unplugged_cutaway_surf.png supersample 3
    8983 > transparentBackground true
    8984 
    8985 > hide #!13 models
    8986 
    8987 > show #!9 models
    8988 
    8989 > transparency 70 target s
    8990 
    8991 > color ##name="cap front" white transparency 100 target s
    8992 
    8993 > save NhaA-K-pH75-unplugged_cutaway_surf.png supersample 3
    8994 > transparentBackground true
    8995 
    8996 > hide #!9 models
    8997 
    8998 > show #!5 models
    8999 
    9000 > transparency 70 target s
    9001 
    9002 > color ##name="cap front" white transparency 100 target s
    9003 
    9004 > save NhaA-K-pH63-unplugged_cutaway_surf.png supersample 3
    9005 > transparentBackground true
    9006 
    9007 > hide #!5 models
    9008 
    9009 > show #7 models
    9010 
    9011 > hide #7 models
    9012 
    9013 > show #!9 models
    9014 
    9015 > transparency 50 target s
    9016 
    9017 > color ##name="cap front" white transparency 100 target s
    9018 
    9019 > transparency 10 target s
    9020 
    9021 > color ##name="cap front" white transparency 100 target s
    9022 
    9023 > save NhaA-K-pH75-unplugged_cutaway_surf_.png supersample 3
    9024 > transparentBackground true
    9025 
    9026 > transparency 70 target s
    9027 
    9028 > color ##name="cap front" white transparency 100 target s
    9029 
    9030 > transparency 20 target s
    9031 
    9032 > color ##name="cap front" white transparency 100 target s
    9033 
    9034 > transparency 30 target s
    9035 
    9036 > color ##name="cap front" white transparency 100 target s
    9037 
    9038 > save NhaA-K-pH75-unplugged_cutaway_surf_30.png supersample 3
    9039 > transparentBackground true
    9040 
    9041 > hide #!9 models
    9042 
    9043 > show #!15 models
    9044 
    9045 > transparency 30 target s
    9046 
    9047 > color ##name="cap front" white transparency 100 target s
    9048 
    9049 > save NhaA-K-pH85-state2_cutaway_surf_30.png supersample 3
    9050 > transparentBackground true
    9051 
    9052 > hide #!15 models
    9053 
    9054 > show #!17 models
    9055 
    9056 > transparency 30 target s
    9057 
    9058 > color ##name="cap front" white transparency 100 target s
    9059 
    9060 > save NhaA-Na-pH85_cutaway_surf_30.png supersample 3 transparentBackground
    9061 > true
    9062 
    9063 > hide #!17 models
    9064 
    9065 > show #!14 models
    9066 
    9067 > hide #!14 models
    9068 
    9069 > show #!13 models
    9070 
    9071 > transparency 30 target s
    9072 
    9073 > color ##name="cap front" white transparency 100 target s
    9074 
    9075 > save NhaA-K-pH85-state1-unplugged_cutaway_surf_30.png supersample 3
    9076 > transparentBackground true
    9077 
    9078 > hide #!13 models
    9079 
    9080 > show #!5 models
    9081 
    9082 > transparency 30 target s
    9083 
    9084 > color ##name="cap front" white transparency 100 target s
    9085 
    9086 > save NhaA-K-pH63-unplugged_cutaway_surf_30.png supersample 3
    9087 > transparentBackground true
    9088 
    9089 > hide target s
    9090 
    9091 > ~clip
    9092 
    9093 > show :NA target a
    9094 
    9095 > show /A:163,164&sidechain target a
    9096 
    9097 > color /A:NA,163,164 byhetero target a
    9098 
    9099 > size stickRadius 0.5
    9100 
    9101 Changed 58102 bond radii 
    9102 
    9103 > graphics silhouettes width 5
    9104 
    9105 > show :NA target a
    9106 
    9107 > show /A:163,164&sidechain target a
    9108 
    9109 > color /A:NA,163,164 byhetero target a
    9110 
    9111 > size stickRadius 0.5
    9112 
    9113 Changed 58102 bond radii 
    9114 
    9115 > graphics silhouettes width 4
    9116 
    9117 > show :NA target a
    9118 
    9119 > show /A:163,164&sidechain target a
    9120 
    9121 > color /A:NA,163,164 byhetero target a
    9122 
    9123 > size stickRadius 0.5
    9124 
    9125 Changed 58102 bond radii 
    9126 
    9127 > graphics silhouettes width 5
    9128 
    9129 > show :NA target a
    9130 
    9131 > show /A:163,164&sidechain target a
    9132 
    9133 > color /A:NA,163,164 byhetero target a
    9134 
    9135 > size stickRadius 0.5
    9136 
    9137 Changed 58102 bond radii 
    9138 
    9139 > graphics silhouettes width 4
    9140 
    9141 > show :NA target a
    9142 
    9143 > show /A:163,164&sidechain target a
    9144 
    9145 > color /A:NA,163,164 byhetero target a
    9146 
    9147 > size stickRadius 0.5
    9148 
    9149 Changed 58102 bond radii 
    9150 
    9151 > graphics silhouettes width 3
    9152 
    9153 > hide #!5 models
    9154 
    9155 > show #!13 models
    9156 
    9157 > lighting full
    9158 
    9159 > select clear
    9160 
    9161 [Repeated 3 time(s)]
    9162 
    9163 > hide sel
    9164 
    9165 > select clear
    9166 
    9167 > show :NA target a
    9168 
    9169 > show /A:163,164&sidechain target a
    9170 
    9171 > color /A:NA,163,164 byhetero target a
    9172 
    9173 > size stickRadius 0.5
    9174 
    9175 Changed 58102 bond radii 
    9176 
    9177 > graphics silhouettes width 4
    9178 
    9179 > show :NA target a
    9180 
    9181 > show /A:163,164&sidechain target a
    9182 
    9183 > color /A:NA,163,164 byhetero target a
    9184 
    9185 > size stickRadius 0.5
    9186 
    9187 Changed 58102 bond radii 
    9188 
    9189 > graphics silhouettes width 5
    9190 
    9191 > show :NA target a
    9192 
    9193 > show /A:163,164&sidechain target a
    9194 
    9195 > color /A:NA,163,164 byhetero target a
    9196 
    9197 > size stickRadius 0.5
    9198 
    9199 Changed 58102 bond radii 
    9200 
    9201 > graphics silhouettes width 2
    9202 
    9203 > transparency 0 target a
    9204 
    9205 > transparency 1000 target a
    9206 
    9207 > transparency 100 target a
    9208 
    9209 > graphics silhouettes 6
    9210 
    9211 Expected true or false or a keyword 
    9212 
    9213 > graphics silhouettes width 6
    9214 
    9215 > graphics silhouettes width 8
    9216 
    9217 > graphics silhouettes width 6
    9218 
    9219 > graphics silhouettes width 8
    9220 
    9221 > save NhaA-Na-pH85_cutaway_res_sil.png supersample 3 transparentBackground
    9222 > true
    9223 
    9224 > hide #!13 models
    9225 
    9226 > show #!15 models
    9227 
    9228 > select clear
    9229 
    9230 > hide sel
    9231 
    9232 > save NhaA-K-pH85-state2_cutaway_res_sil.png supersample 3
    9233 > transparentBackground true
    9234 
    9235 > graphics silhouettes width 15
    9236 
    9237 > graphics silhouettes width 20
    9238 
    9239 > save NhaA-K-pH85-state2_cutaway_res_sil.png supersample 3
    9240 > transparentBackground true
    9241 
    9242 > select up
    9243 
    9244 1 pseudobond, 1 model selected 
    9245 
    9246 > select clear
    9247 
    9248 > graphics silhouettes width 2
    9249 
    9250 > transparency 0 target a
    9251 
    9252 > lighting shadows false
    9253 
    9254 > show #!13 models
    9255 
    9256 > show #!11 models
    9257 
    9258 > hide #!11 models
    9259 
    9260 > show #!9 models
    9261 
    9262 > show #7 models
    9263 
    9264 > hide #7 models
    9265 
    9266 > show #!5 models
    9267 
    9268 > show /A target c
    9269 
    9270 > hide #!5,9,13,15 atoms
    9271 
    9272 > hide #!15 models
    9273 
    9274 > show #1 models
    9275 
    9276 > hide #1 models
    9277 
    9278 > show #1 models
    9279 
    9280 > hide #1 models
    9281 
    9282 > show #3 models
    9283 
    9284 > hide #3 models
    9285 
    9286 > show #3 models
    9287 
    9288 > hide #3 models
    9289 
    9290 > hide /A:NA,163,164 target a
    9291 
    9292 > size stickRadius 0.3
    9293 
    9294 Changed 58102 bond radii 
    9295 
    9296 > graphics silhouettes width 2
    9297 
    9298 > show #3 models
    9299 
    9300 > hide #3 models
    9301 
    9302 > show #7 models
    9303 
    9304 > hide #7 models
    9305 
    9306 > show #7 models
    9307 
    9308 > hide #7 models
    9309 
    9310 > show #!11 models
    9311 
    9312 > hide #!11 models
    9313 
    9314 > show #7 models
    9315 
    9316 > show #3 models
    9317 
    9318 > show #1 models
    9319 
    9320 > show #!11 models
    9321 
    9322 > hide #1,3,7#!5,9,11,13 atoms
    9323 
    9324 > show /A:144 target a
    9325 
    9326 > ui mousemode right distance
    9327 
    9328 > distance #1/A:144@CA #13/A:144@CA
    9329 
    9330 Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A LEU 144 CA and NhaA-
    9331 nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A LEU 144 CA: 1.067Å 
    9332 
    9333 > show /A:155 target a
    9334 
    9335 > show /A:150 target a
    9336 
    9337 > hide #3 models
    9338 
    9339 > hide #!5 models
    9340 
    9341 > distance #1/A:150@CA #13/A:150@CA
    9342 
    9343 Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A LEU 150 CA and NhaA-
    9344 nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A LEU 150 CA: 0.906Å 
    9345 
    9346 > save
    9347 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    9348 
    9349 > view list
    9350 
    9351 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    9352 dimer_view-all_front, mono_back, mono_back_, mono_front 
    9353 
    9354 > view mono_back_
    9355 
    9356 > combine #1,3,5,7,9,11,13,15 pH-superposition
    9357 
    9358 Expected a keyword 
    9359 
    9360 > combine #1,3,5,7,9,11,13,15 name pH-superposition
    9361 
    9362 Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3 to 'D' 
    9363 Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3 to 'E' 
    9364 Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3 to 'F' 
    9365 Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5 to 'G' 
    9366 Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5 to 'H' 
    9367 Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5 to 'I' 
    9368 Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7 to 'J' 
    9369 Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7 to 'K' 
    9370 Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7 to 'L' 
    9371 Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9 to 'M' 
    9372 Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9 to 'N' 
    9373 Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9 to 'O' 
    9374 Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb #11 to 'P' 
    9375 Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb #11 to 'Q' 
    9376 Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb #11 to 'R' 
    9377 Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13 to
    9378 'S' 
    9379 Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13 to
    9380 'T' 
    9381 Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13 to
    9382 'U' 
    9383 Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH85_state2.pdb #15 to 'V' 
    9384 Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH85_state2.pdb #15 to 'W' 
    9385 Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH85_state2.pdb #15 to 'X' 
    9386 
    9387 > hide #1 models
    9388 
    9389 > hide #7 models
    9390 
    9391 > hide #!9 models
    9392 
    9393 > hide #!11 models
    9394 
    9395 > hide #!13 models
    9396 
    9397 > cartoon style modeHelix default width 1.0 thickness 0.3
    9398 
    9399 > cartoon style modeHelix tube radius 1.8 sides 24
    9400 
    9401 > cartoon style modeHelix default width 1.0 thickness 0.3
    9402 
    9403 > size stickRadius 0.3
    9404 
    9405 Changed 96905 bond radii 
    9406 
    9407 > close #26
    9408 
    9409 > show #1 models
    9410 
    9411 > show #3 models
    9412 
    9413 > show #!5 models
    9414 
    9415 > show #7 models
    9416 
    9417 > show #!9 models
    9418 
    9419 > show #!11 models
    9420 
    9421 > show #!13 models
    9422 
    9423 > show #!15 models
    9424 
    9425 > view list
    9426 
    9427 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    9428 dimer_view-all_front, mono_back, mono_back_, mono_front 
    9429 
    9430 > view mono_back_
    9431 
    9432 > hide #!15 models
    9433 
    9434 > show #!15 models
    9435 
    9436 > hide #!15 models
    9437 
    9438 > show #!15 models
    9439 
    9440 > view mono_back_
    9441 
    9442 > save
    9443 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    9444 
    9445 ——— End of log from Tue Aug 27 10:43:20 2024 ———
    9446 
    9447 opened ChimeraX session 
    9448 
    9449 > hide #1 models
    9450 
    9451 > hide #3 models
    9452 
    9453 > hide #!5 models
    9454 
    9455 > hide #7 models
    9456 
    9457 > hide #!9 models
    9458 
    9459 > hide #!11 models
    9460 
    9461 > hide #!13 models
    9462 
    9463 > hide #!15 models
    9464 
    9465 > show #!17 models
    9466 
    9467 > show #17/A:163,164 target s
    9468 
    9469 > show #17/A:163,164,132,133 target a
    9470 
    9471 > show :NA target a
    9472 
    9473 > show :NA target s
    9474 
    9475 > hide :NA target a
    9476 
    9477 > hide :NA target s
    9478 
    9479 > show #17/A:163,164,132,133 target s
    9480 
    9481 > show :NA target a
    9482 
    9483 > hide :NA target a
    9484 
    9485 > hide #17/A:163,164,132,133 target sa
    9486 
    9487 > hide #!17 atoms
    9488 
    9489 > hide #!17 models
    9490 
    9491 > show #7 models
    9492 
    9493 > show #!9 models
    9494 
    9495 > hide #!9 models
    9496 
    9497 > hide #7 models
    9498 
    9499 > show #!9 models
    9500 
    9501 > hide #!9 models
    9502 
    9503 > show #7 models
    9504 
    9505 > view list
    9506 
    9507 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    9508 dimer_view-all_front, mono_back, mono_back_, mono_front 
    9509 
    9510 > view cutaway
    9511 
    9512 > clip front 0.4 position #17:NA
    9513 
    9514 > color ##name="cap front" black target s
    9515 
    9516 > coulombic #7
    9517 
    9518 Using Amber 20 recommended default charges and atom types for standard
    9519 residues 
    9520 Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged.pdb_A SES surface #7.1:
    9521 minimum, -15.51, mean 0.31, maximum 15.23 
    9522 Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged.pdb_B SES surface #7.2:
    9523 minimum, -18.75, mean -1.94, maximum 19.89 
    9524 Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged.pdb_C SES surface #7.3:
    9525 minimum, -13.67, mean -1.87, maximum 10.42 
    9526 To also show corresponding color key, enter the above coulombic command and
    9527 add key true 
    9528 
    9529 > hide #7/B,C target s
    9530 
    9531 > clip model #7 false
    9532 
    9533 > clip front 0.4 position #17:NA
    9534 
    9535 > color ##name="cap front" black target s
    9536 
    9537 > clip model #7 true
    9538 
    9539 > ~clip
    9540 
    9541 > combine #7 name NhaA-nd-6F9-K_BTPpH75_plugged_split
    9542 
    9543 > delete #26/B,C
    9544 
    9545 > hide #!7 models
    9546 
    9547 > split #26 stoms :1-10
    9548 
    9549 Expected a keyword 
    9550 
    9551 > split #26 atoms :1-10
    9552 
    9553 Split NhaA-nd-6F9-K_BTPpH75_plugged_split (#26) into 2 models 
    9554 Chain information for NhaA-nd-6F9-K_BTPpH75_plugged_split 1 #26.1 
    9555 --- 
    9556 Chain | Description 
    9557 A | No description available 
    9558  
    9559 Chain information for NhaA-nd-6F9-K_BTPpH75_plugged_split 2 #26.2 
    9560 --- 
    9561 Chain | Description 
    9562 A | No description available 
    9563  
    9564 
    9565 > coulombic #26.1-2
    9566 
    9567 Using Amber 20 recommended default charges and atom types for standard
    9568 residues 
    9569 [Repeated 1 time(s)]Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged_split
    9570 1_A SES surface #26.1.1: minimum, -4.18, mean 3.47, maximum 11.04 
    9571 Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface
    9572 #26.2.1: minimum, -15.57, mean -0.06, maximum 14.74 
    9573 To also show corresponding color key, enter the above coulombic command and
    9574 add key true 
    9575 
    9576 > hide #26 target ac
    9577 
    9578 > clip front 0.4 position #17:NA
    9579 
    9580 > color ##name="cap front" black target s
    9581 
    9582 > select #26.1.1.1
    9583 
    9584 1 model selected 
    9585 
    9586 > color sel orchid target s
    9587 
    9588 > select clear
    9589 
    9590 > ~clip
    9591 
    9592 > clip front 0.4 position #17:NA
    9593 
    9594 > color ##name="cap front" black target s
    9595 
    9596 > select #26.1.1.1
    9597 
    9598 1 model selected 
    9599 
    9600 > select up
    9601 
    9602 90 atoms, 10 residues, 3 models selected 
    9603 
    9604 > select down
    9605 
    9606 1 model selected 
    9607 
    9608 > select up
    9609 
    9610 90 atoms, 10 residues, 3 models selected 
    9611 
    9612 > color sel orchid target s
    9613 
    9614 > select clear
    9615 
    9616 > coulombic #!26.1-2
    9617 
    9618 Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged_split 1_A SES surface
    9619 #26.1.1: minimum, -4.18, mean 3.47, maximum 11.04 
    9620 Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface
    9621 #26.2.1: minimum, -15.57, mean -0.06, maximum 14.74 
    9622 To also show corresponding color key, enter the above coulombic command and
    9623 add key true 
    9624 
    9625 > clip front 0.4 position #17:NA
    9626 
    9627 > color ##name="cap front" black target s
    9628 
    9629 > select #26.1.1.1
    9630 
    9631 1 model selected 
    9632 
    9633 > color sel orchid target s
    9634 
    9635 > select clear
    9636 
    9637 > lighting soft multiShadow 1024
    9638 
    9639 > select #26.1.1.1
    9640 
    9641 1 model selected 
    9642 
    9643 > transparency sel 1 target s
    9644 
    9645 > select clear
    9646 
    9647 > save NhaA-K-pH75-plugged_cutaway.png supersample 3 transparentBackground
    9648 > true
    9649 
    9650 > transparency 70 target s
    9651 
    9652 > color ##name="cap front" white transparency 100 target s
    9653 
    9654 > select #26.1.1.1
    9655 
    9656 1 model selected 
    9657 
    9658 > transparency sel 0 target s
    9659 
    9660 > color sel orchid target s
    9661 
    9662 > transparency sel 1 target s
    9663 
    9664 > select clear
    9665 
    9666 > save NhaA-K-pH75-plugged_cutaway_surf.png supersample 3
    9667 > transparentBackground true
    9668 
    9669 > hide #!26 models
    9670 
    9671 > show #!7 models
    9672 
    9673 > hide #!7 cartoons
    9674 
    9675 > hide #!7 surfaces
    9676 
    9677 > hide #!7 atoms
    9678 
    9679 > show /A:163,164&sidechain target a
    9680 
    9681 > color /A:NA,163,164 byhetero target a
    9682 
    9683 > size stickRadius 0.5
    9684 
    9685 Changed 61174 bond radii 
    9686 
    9687 > graphics silhouettes width 5
    9688 
    9689 > ~clip
    9690 
    9691 > hide sel
    9692 
    9693 > select clear
    9694 
    9695 > show /A:163,164&sidechain target a
    9696 
    9697 > color /A:NA,163,164 byhetero target a
    9698 
    9699 > size stickRadius 0.5
    9700 
    9701 Changed 61174 bond radii 
    9702 
    9703 > graphics silhouettes width 2
    9704 
    9705 > lighting full
    9706 
    9707 > show /A:163,164&sidechain target a
    9708 
    9709 > color /A:NA,163,164 byhetero target a
    9710 
    9711 > size stickRadius 0.5
    9712 
    9713 Changed 61174 bond radii 
    9714 
    9715 > graphics silhouettes width 3
    9716 
    9717 > show /A:163,164&sidechain target a
    9718 
    9719 > color /A:NA,163,164 byhetero target a
    9720 
    9721 > size stickRadius 0.5
    9722 
    9723 Changed 61174 bond radii 
    9724 
    9725 > graphics silhouettes width 2
    9726 
    9727 > lighting simple
    9728 
    9729 > lighting full
    9730 
    9731 > lighting simple
    9732 
    9733 > lighting full
    9734 
    9735 > save NhaA-K-pH75-plugged_cutaway_res.png supersample 3 transparentBackground
    9736 > true
    9737 
    9738 > show #!9 models
    9739 
    9740 > hide #!9 models
    9741 
    9742 > show #3 models
    9743 
    9744 > hide #!7 models
    9745 
    9746 > hide #3 cartoons
    9747 
    9748 > hide #!3 atoms
    9749 
    9750 > show /A:163,164&sidechain target a
    9751 
    9752 > color /A:NA,163,164 byhetero target a
    9753 
    9754 > size stickRadius 0.5
    9755 
    9756 Changed 61174 bond radii 
    9757 
    9758 > graphics silhouettes width 2
    9759 
    9760 > hide sel
    9761 
    9762 > lighting shadows false
    9763 
    9764 > select clear
    9765 
    9766 > save NhaA-K-pH63-plugged_cutaway_res.png supersample 3 transparentBackground
    9767 > true
    9768 
    9769 > hide #!3 models
    9770 
    9771 > show #1 models
    9772 
    9773 > hide #1 atoms
    9774 
    9775 > hide #1 cartoons
    9776 
    9777 > show /A:163,164&sidechain target a
    9778 
    9779 > color /A:NA,163,164 byhetero target a
    9780 
    9781 > size stickRadius 0.5
    9782 
    9783 Changed 61174 bond radii 
    9784 
    9785 > graphics silhouettes width 2
    9786 
    9787 > select up
    9788 
    9789 4707 atoms, 4810 bonds, 1 pseudobond, 611 residues, 2 models selected 
    9790 
    9791 > select down
    9792 
    9793 1 pseudobond, 1 model selected 
    9794 
    9795 > hide sel
    9796 
    9797 > save NhaA-K-pH55-plugged_cutaway_res.png supersample 3 transparentBackground
    9798 > true
    9799 
    9800 > hide #!1 models
    9801 
    9802 > show #!11 models
    9803 
    9804 > hide #!11 atoms
    9805 
    9806 > hide #!11 cartoons
    9807 
    9808 > show /A:163,164&sidechain target a
    9809 
    9810 > color /A:NA,163,164 byhetero target a
    9811 
    9812 > size stickRadius 0.5
    9813 
    9814 Changed 61174 bond radii 
    9815 
    9816 > graphics silhouettes width 2
    9817 
    9818 > hide sel
    9819 
    9820 > select clear
    9821 
    9822 > save NhaA-K-pH85-state1-plugged_cutaway_res.png supersample 3
    9823 > transparentBackground true
    9824 
    9825 > hide #!11 models
    9826 
    9827 > combine #11 name NhaA-nd-6F9-K-BTPpH85_state1-plugged_split
    9828 
    9829 > delete #28/B,C
    9830 
    9831 > split #27 atoms :1-10
    9832 
    9833 Split NhaA-nd-6F9-K-BTPpH85_state1-plugged_split (#27) into 2 models 
    9834 Chain information for NhaA-nd-6F9-K-BTPpH85_state1-plugged_split 1 #27.1 
    9835 --- 
    9836 Chain | Description 
    9837 A | No description available 
    9838 B | No description available 
    9839 C | No description available 
    9840  
    9841 Chain information for NhaA-nd-6F9-K-BTPpH85_state1-plugged_split 2 #27.2 
    9842 --- 
    9843 Chain | Description 
    9844 A | No description available 
    9845 B | No description available 
    9846 C | No description available 
    9847  
    9848 
    9849 > combine #3 name NhaA-nd-6F9-K-BTPpH63_plugged_split
    9850 
    9851 > delete #28/B,C
    9852 
    9853 > delete #27/B,C
    9854 
    9855 > combine #1 name NhaA-nd-6F9-K-MESpH55_plugged_split
    9856 
    9857 > delete #29/B,C
    9858 
    9859 > split #29 atoms :1-10
    9860 
    9861 Split NhaA-nd-6F9-K-MESpH55_plugged_split (#29) into 2 models 
    9862 Chain information for NhaA-nd-6F9-K-MESpH55_plugged_split 1 #29.1 
    9863 --- 
    9864 Chain | Description 
    9865 A | No description available 
    9866  
    9867 Chain information for NhaA-nd-6F9-K-MESpH55_plugged_split 2 #29.2 
    9868 --- 
    9869 Chain | Description 
    9870 A | No description available 
    9871  
    9872 
    9873 > hide #!28 models
    9874 
    9875 > hide #!29 models
    9876 
    9877 > show #!28 models
    9878 
    9879 > show #!29 models
    9880 
    9881 > show #!26 models
    9882 
    9883 > hide #!26 models
    9884 
    9885 > hide #27.1#29.1#!28#!27.2#!29.2 atoms
    9886 
    9887 > hide #28 models
    9888 
    9889 > show #28 models
    9890 
    9891 > coulombic #28#27.1-2#29.1-2
    9892 
    9893 Using Amber 20 recommended default charges and atom types for standard
    9894 residues 
    9895 [Repeated 4 time(s)]Coulombic values for NhaA-nd-6F9-K-BTPpH63_plugged_split_A
    9896 SES surface #28.1: minimum, -17.16, mean 0.42, maximum 15.73 
    9897 Coulombic values for NhaA-nd-6F9-K-BTPpH85_state1-plugged_split 1_A SES
    9898 surface #27.1.1: minimum, -4.22, mean 2.78, maximum 9.56 
    9899 Coulombic values for NhaA-nd-6F9-K-BTPpH85_state1-plugged_split 2_A SES
    9900 surface #27.2.1: minimum, -16.15, mean -0.11, maximum 16.64 
    9901 Coulombic values for NhaA-nd-6F9-K-MESpH55_plugged_split 1_A SES surface
    9902 #29.1.1: minimum, -4.09, mean 3.18, maximum 13.24 
    9903 Coulombic values for NhaA-nd-6F9-K-MESpH55_plugged_split 2_A SES surface
    9904 #29.2.1: minimum, -15.70, mean -0.04, maximum 13.35 
    9905 To also show corresponding color key, enter the above coulombic command and
    9906 add key true 
    9907 
    9908 > hide #!28 models
    9909 
    9910 > hide #!29 models
    9911 
    9912 > lighting soft multiShadow 1024
    9913 
    9914 > clip front 0.4 position #17:NA
    9915 
    9916 > color ##name="cap front" black target s
    9917 
    9918 > select #27.1.1.1
    9919 
    9920 1 model selected 
    9921 
    9922 > color sel orchid transparency 1 target s
    9923 
    9924 > select clear
    9925 
    9926 > save NhaA-K-pH85-state1-plugged_cutaway.png supersample 3
    9927 > transparentBackground true
    9928 
    9929 > hide #!27 models
    9930 
    9931 > show #!28 models
    9932 
    9933 > select #28.1.1
    9934 
    9935 1 model selected 
    9936 
    9937 > select #28.1.1
    9938 
    9939 1 model selected 
    9940 
    9941 > select clear
    9942 
    9943 > show #!29 models
    9944 
    9945 > hide #!28 models
    9946 
    9947 > show #!28 models
    9948 
    9949 > hide #!29 models
    9950 
    9951 > split #28 atoms :1-10
    9952 
    9953 Split NhaA-nd-6F9-K-BTPpH63_plugged_split (#28) into 2 models 
    9954 Chain information for NhaA-nd-6F9-K-BTPpH63_plugged_split 1 #28.1 
    9955 --- 
    9956 Chain | Description 
    9957 A | No description available 
    9958  
    9959 Chain information for NhaA-nd-6F9-K-BTPpH63_plugged_split 2 #28.2 
    9960 --- 
    9961 Chain | Description 
    9962 A | No description available 
    9963  
    9964 
    9965 > coulombic #28.1-2
    9966 
    9967 Using Amber 20 recommended default charges and atom types for standard
    9968 residues 
    9969 [Repeated 1 time(s)]Coulombic values for NhaA-nd-6F9-K-BTPpH63_plugged_split
    9970 1_A SES surface #28.1.1: minimum, -4.62, mean 3.38, maximum 10.14 
    9971 Coulombic values for NhaA-nd-6F9-K-BTPpH63_plugged_split 2_A SES surface
    9972 #28.2.1: minimum, -17.21, mean 0.03, maximum 15.32 
    9973 To also show corresponding color key, enter the above coulombic command and
    9974 add key true 
    9975 
    9976 > clip front 0.4 position #17:NA
    9977 
    9978 > color ##name="cap front" black target s
    9979 
    9980 > select #28.1.1.1
    9981 
    9982 1 model selected 
    9983 
    9984 > color sel orchid target s
    9985 
    9986 > select clear
    9987 
    9988 > color sel orchid transparency 1 target s
    9989 
    9990 > select #28.1.1.1
    9991 
    9992 1 model selected 
    9993 
    9994 > color sel orchid transparency 1 target s
    9995 
    9996 > select clear
    9997 
    9998 > save NhaA-K-pH63-plugged_cutaway.png supersample 3 transparentBackground
    9999 > true
    10000 
    10001 > show #!29 models
    10002 
    10003 > hide #!28 models
    10004 
    10005 > clip front 0.4 position #17:NA
    10006 
    10007 > color ##name="cap front" black target s
    10008 
    10009 > color sel orchid transparency 1 target s
    10010 
    10011 > select #29.1.1.1
    10012 
    10013 1 model selected 
    10014 
    10015 > color sel orchid transparency 1 target s
    10016 
    10017 > select clear
    10018 
    10019 > save NhaA-K-pH55-plugged_cutaway.png supersample 3 transparentBackground
    10020 > true
    10021 
    10022 > hide #!29 models
    10023 
    10024 > show #!29 models
    10025 
    10026 > transparency 30 target s
    10027 
    10028 > color ##name="cap front" white transparency 100 target s
    10029 
    10030 > select #29.1.1.1
    10031 
    10032 1 model selected 
    10033 
    10034 > color sel orchid transparency 1 target s
    10035 
    10036 > select clear
    10037 
    10038 > save NhaA-K-pH55-plugged_cutaway_surf.png supersample 3
    10039 > transparentBackground true
    10040 
    10041 > show #!28 models
    10042 
    10043 > hide #!29 models
    10044 
    10045 > transparency 30 target s
    10046 
    10047 > color ##name="cap front" white transparency 100 target s
    10048 
    10049 > select #28.1.1.1
    10050 
    10051 1 model selected 
    10052 
    10053 > select up
    10054 
    10055 90 atoms, 10 residues, 3 models selected 
    10056 
    10057 > select down
    10058 
    10059 1 model selected 
    10060 
    10061 > color sel orchid transparency 1 target s
    10062 
    10063 > select clear
    10064 
    10065 > save NhaA-K-pH63-plugged_cutaway_surf.png supersample 3
    10066 > transparentBackground true
    10067 
    10068 > hide #!28 models
    10069 
    10070 > show #!27 models
    10071 
    10072 > transparency 30 target s
    10073 
    10074 > color ##name="cap front" white transparency 100 target s
    10075 
    10076 > select #27.1.1.1
    10077 
    10078 1 model selected 
    10079 
    10080 > color sel orchid transparency 1 target s
    10081 
    10082 > select clear
    10083 
    10084 > save NhaA-K-pH85-state1-plugged_cutaway_surf.png supersample 3
    10085 > transparentBackground true
    10086 
    10087 > hide #!27 models
    10088 
    10089 > show #!26 models
    10090 
    10091 > hide #!26.1-2 atoms
    10092 
    10093 > transparency 30 target s
    10094 
    10095 > color ##name="cap front" white transparency 100 target s
    10096 
    10097 > select #26.1.1.1
    10098 
    10099 1 model selected 
    10100 
    10101 > color sel orchid transparency 1 target s
    10102 
    10103 > select clear
    10104 
    10105 > save NhaA-K-pH75-plugged_cutaway_surf.png supersample 3
    10106 > transparentBackground true
    10107 
    10108 > save
    10109 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    10110 
    10111 > hide #!26 models
    10112 
    10113 > show #!1 models
    10114 
    10115 > hide #!1 models
    10116 
    10117 > show #!3 models
    10118 
    10119 > hide #!3 models
    10120 
    10121 > show #!5 models
    10122 
    10123 > open /Users/tsweng/Documents/Projects/NhaA/Structures/hole_analysis/NhaA-
    10124 > nd-6F9-K_BTPpH63_unplugged_hole_out.sph
    10125 
    10126 Unrecognized file suffix '.sph' 
    10127 
    10128 > lighting full
    10129 
    10130 > lighting shadows false
    10131 
    10132 > hide #!5 models
    10133 
    10134 > show #!20 models
    10135 
    10136 > hide #!20 models
    10137 
    10138 > show #19 models
    10139 
    10140 > hide #19 atoms
    10141 
    10142 > view list
    10143 
    10144 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    10145 dimer_view-all_front, mono_back, mono_back_, mono_front 
    10146 
    10147 > view dimer_view-all_front
    10148 
    10149 > show #19:CDL,PTY target a
    10150 
    10151 > size stickRadius 0.3
    10152 
    10153 Changed 70360 bond radii 
    10154 
    10155 > turn y -90
    10156 
    10157 > view
    10158 
    10159 > show #!21 models
    10160 
    10161 > hide #!21.5 models
    10162 
    10163 > hide #!21 models
    10164 
    10165 > show #!20 models
    10166 
    10167 > color #19/A,D:86-180,275-388 forest green
    10168 
    10169 > color #19/A,D:11-85,181-274 pale green
    10170 
    10171 > color :CDL,PTY gray target a
    10172 
    10173 > color #19/D white
    10174 
    10175 > color zone #20 near #19
    10176 
    10177 > color #19/A,D:86-180,275-388 forest green target ac
    10178 
    10179 > color #19/A,D:11-85,181-274 pale green target ac
    10180 
    10181 > color :CDL,PTY gray target a
    10182 
    10183 > color #19/D white
    10184 
    10185 > color zone #20 near #19
    10186 
    10187 > color #19/A,D:86-180,275-388 forest green target ac
    10188 
    10189 > color #19/A,D:1-85,181-274 pale green target ac
    10190 
    10191 > color :CDL,PTY gray target a
    10192 
    10193 > color #19/D white
    10194 
    10195 > color zone #20 near #19
    10196 
    10197 > volume splitbyzone #20
    10198 
    10199 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #30.1, grid
    10200 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10201 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #30.2, grid
    10202 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10203 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #30.3, grid
    10204 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10205 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #30.4, grid
    10206 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10207 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #30.5, grid
    10208 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10209 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 5 as #30.6, grid
    10210 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10211 
    10212 > hide #!30.6 models
    10213 
    10214 > hide #19/D target ac
    10215 
    10216 > surface dust #30 size 5
    10217 
    10218 > surface dust #30 size 6
    10219 
    10220 > view name dimer_interface
    10221 
    10222 > hide #!30.5 models
    10223 
    10224 > hide #!30.3 models
    10225 
    10226 > hide #!30.2 models
    10227 
    10228 > volume #30 level 0.0085
    10229 
    10230 > volume #30 level 0.009
    10231 
    10232 > volume #30 level 0.0085
    10233 
    10234 > volume #30 level 0.009
    10235 
    10236 > volume #30 level 0.01
    10237 
    10238 > view name dimer_interface2
    10239 
    10240 > volume #30 level 0.008
    10241 
    10242 > volume #30 level 0.0086
    10243 
    10244 > volume #30 level 0.0085
    10245 
    10246 > volume #30 level 0.0084
    10247 
    10248 > volume #30 level 0.008
    10249 
    10250 > transparency #30.4 50 target s
    10251 
    10252 > color #19:CDL,PTY byhetero target a
    10253 
    10254 > transparency #30.1 0 target s
    10255 
    10256 > transparency #30.4 70 target s
    10257 
    10258 > transparency #30.1 1 target s
    10259 
    10260 > view list
    10261 
    10262 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    10263 dimer_interface, dimer_interface2, dimer_view-all_front, mono_back,
    10264 mono_back_, mono_front 
    10265 
    10266 > view dimer_interface2
    10267 
    10268 > view name dimer_interface2
    10269 
    10270 > color #19/A,D:86-180,275-388 forest green
    10271 
    10272 > color #19/A,D:11-85,181-274 pale green
    10273 
    10274 > show #19/D target c
    10275 
    10276 > view list
    10277 
    10278 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    10279 dimer_interface, dimer_interface2, dimer_view-all_front, mono_back,
    10280 mono_back_, mono_front 
    10281 
    10282 > view dimer_view-all_front
    10283 
    10284 > view
    10285 
    10286 > turn x 90
    10287 
    10288 > select ~sel & ##selected
    10289 
    10290 Nothing selected 
    10291 
    10292 > select ~sel & ##selected
    10293 
    10294 Nothing selected 
    10295 
    10296 > turn x 5
    10297 
    10298 > turn x -5
    10299 
    10300 [Repeated 1 time(s)]
    10301 
    10302 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    10303 > nd-Fv6F9-K_BTPpH75_consensus-map_dimer_CDL-PGT.pdb
    10304 
    10305 Chain information for NhaA-nd-Fv6F9-K_BTPpH75_consensus-map_dimer_CDL-PGT.pdb
    10306 #31 
    10307 --- 
    10308 Chain | Description 
    10309 A D | No description available 
    10310 B E | No description available 
    10311 C F | No description available 
    10312  
    10313 
    10314 > mcopy #19 toAtoms #31 settings hsv
    10315 
    10316 > mmaker #31 to #19
    10317 
    10318 Parameters 
    10319 --- 
    10320 Chain pairing | bb 
    10321 Alignment algorithm | Needleman-Wunsch 
    10322 Similarity matrix | BLOSUM-62 
    10323 SS fraction | 0.3 
    10324 Gap open (HH/SS/other) | 18/18/6 
    10325 Gap extend | 1 
    10326 SS matrix |  |  | H | S | O 
    10327 ---|---|---|--- 
    10328 H | 6 | -9 | -6 
    10329 S |  | 6 | -6 
    10330 O |  |  | 4 
    10331 Iteration cutoff | 2 
    10332  
    10333 Matchmaker NhaA-nd-6F9-K_BTPpH75_consensus.pdb, chain A (#19) with NhaA-nd-
    10334 Fv6F9-K_BTPpH75_consensus-map_dimer_CDL-PGT.pdb, chain A (#31), sequence
    10335 alignment score = 1997.6 
    10336 RMSD between 388 pruned atom pairs is 0.000 angstroms; (across all 388 pairs:
    10337 0.000) 
    10338  
    10339 
    10340 > color #31/A,D:86-180,275-388 forest green
    10341 
    10342 > color #19/A,D:1-85,181-274 pale green
    10343 
    10344 > hide #31 target ac
    10345 
    10346 > show #31:PGT target a
    10347 
    10348 > style :PGT ball
    10349 
    10350 Changed 51 atom styles 
    10351 
    10352 > size stickRadius 0.3
    10353 
    10354 Changed 80007 bond radii 
    10355 
    10356 > hide #31 models
    10357 
    10358 > view name dimer_interface_top
    10359 
    10360 > volume #30 level 0.0084
    10361 
    10362 > surface dust #30 size 5
    10363 
    10364 > volume #30 level 0.0085
    10365 
    10366 > volume #30 level 0.0086
    10367 
    10368 > view list
    10369 
    10370 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    10371 dimer_interface, dimer_interface2, dimer_interface_top, dimer_view-all_front,
    10372 mono_back, mono_back_, mono_front 
    10373 
    10374 > view dimer_interface_top
    10375 
    10376 > volume #30 level 0.0088
    10377 
    10378 > volume #30 level 0.009
    10379 
    10380 > view dimer_interface_top
    10381 
    10382 > save
    10383 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    10384 
    10385 > volume #30 surfaceSmoothing true
    10386 
    10387 > volume #30 level 0.0086
    10388 
    10389 > view dimer_interface_top
    10390 
    10391 > view dimer_interface2
    10392 
    10393 > view dimer_interface
    10394 
    10395 > view dimer_interface_top
    10396 
    10397 > turn x 5
    10398 
    10399 > select #19/A:250
    10400 
    10401 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10402 
    10403 > select clear
    10404 
    10405 > show #19/A,D:ARG,TYR,LYS
    10406 
    10407 > show #19/A,D:ARG,TYR,LYS target a
    10408 
    10409 > style #19 stick
    10410 
    10411 Changed 9389 atom styles 
    10412 
    10413 > style :CDL,PTY,PGT ball
    10414 
    10415 Changed 1801 atom styles 
    10416 
    10417 > color #19 byhetero
    10418 
    10419 > show #19/A,D:ARG,TYR,LYS,TRP target a
    10420 
    10421 > show #19/A,D:204,245,250,258 target a
    10422 
    10423 > hide #19 atoms
    10424 
    10425 > show #19/A,D:204,245,250,258,CDL,PTY,PGT target a
    10426 
    10427 > view dimer_interface_top
    10428 
    10429 > select #30.1
    10430 
    10431 4 models selected 
    10432 
    10433 > select clear
    10434 
    10435 > close #30
    10436 
    10437 > color #19/A,D:86-180,275-388 forest green target ac
    10438 
    10439 > color #19/A,D:1-85,181-274 pale green target ac
    10440 
    10441 > color :CDL,PTY gray target a
    10442 
    10443 > color #19/D white
    10444 
    10445 > show #!20 models
    10446 
    10447 > show #!9 models
    10448 
    10449 > hide #!9 models
    10450 
    10451 > show #!7 models
    10452 
    10453 > hide #!7 models
    10454 
    10455 > show #!7 models
    10456 
    10457 > hide #!7 models
    10458 
    10459 > combine #7
    10460 
    10461 > mmaker #30 to #19/D
    10462 
    10463 Parameters 
    10464 --- 
    10465 Chain pairing | bb 
    10466 Alignment algorithm | Needleman-Wunsch 
    10467 Similarity matrix | BLOSUM-62 
    10468 SS fraction | 0.3 
    10469 Gap open (HH/SS/other) | 18/18/6 
    10470 Gap extend | 1 
    10471 SS matrix |  |  | H | S | O 
    10472 ---|---|---|--- 
    10473 H | 6 | -9 | -6 
    10474 S |  | 6 | -6 
    10475 O |  |  | 4 
    10476 Iteration cutoff | 2 
    10477  
    10478 Matchmaker NhaA-nd-6F9-K_BTPpH75_consensus.pdb, chain D (#19) with copy of
    10479 NhaA-nd-6F9-K_BTPpH75_plugged.pdb, chain A (#30), sequence alignment score =
    10480 1959.8 
    10481 RMSD between 378 pruned atom pairs is 0.151 angstroms; (across all 388 pairs:
    10482 2.825) 
    10483  
    10484 
    10485 > hide #!30 models
    10486 
    10487 > show #!30 models
    10488 
    10489 > show #30/A target c
    10490 
    10491 > combine #7,30 name pH75_dimer_plug_dummy
    10492 
    10493 Remapping chain ID 'A' in copy of NhaA-nd-6F9-K_BTPpH75_plugged.pdb #30 to 'D' 
    10494 Remapping chain ID 'B' in copy of NhaA-nd-6F9-K_BTPpH75_plugged.pdb #30 to 'E' 
    10495 Remapping chain ID 'C' in copy of NhaA-nd-6F9-K_BTPpH75_plugged.pdb #30 to 'F' 
    10496 
    10497 > hide #30 models
    10498 
    10499 > show #32/A target c
    10500 
    10501 > select #32/A,D:1-10
    10502 
    10503 180 atoms, 186 bonds, 20 residues, 1 model selected 
    10504 
    10505 > select ~sel & ##selected
    10506 
    10507 9292 atoms, 9494 bonds, 1208 residues, 1 model selected 
    10508 
    10509 > delete sel
    10510 
    10511 > color #19/A,D:86-180,275-388 forest green target ac
    10512 
    10513 > color #19/A,D:1-85,181-274 pale green target ac
    10514 
    10515 > color :CDL,PTY gray target a
    10516 
    10517 > color #19/D white
    10518 
    10519 > color #32 orchid
    10520 
    10521 > close #30
    10522 
    10523 > color zone #20 near #19,32
    10524 
    10525 > delete #32/B,C,E,F
    10526 
    10527 > color zone #20 near #19,32
    10528 
    10529 > color #19/A,D:86-180,275-388 forest green target ac
    10530 
    10531 > color #19/A,D:1-85,181-274 pale green target ac
    10532 
    10533 > color :CDL,PTY gray target a
    10534 
    10535 > color #19/D white
    10536 
    10537 > color #32 orchid
    10538 
    10539 > color #19/B,C,E,F gainsboro
    10540 
    10541 > color zone #20 near #19,32
    10542 
    10543 > volume splitbyzone #20
    10544 
    10545 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #30.1, grid
    10546 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10547 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #30.2, grid
    10548 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10549 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #30.3, grid
    10550 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10551 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #30.4, grid
    10552 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10553 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #30.5, grid
    10554 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10555 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 5 as #30.6, grid
    10556 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10557 Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 6 as #30.7, grid
    10558 size 248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32 
    10559 
    10560 > hide #19 models
    10561 
    10562 > show #19 models
    10563 
    10564 > hide #!30.6 models
    10565 
    10566 > show #!30.6 models
    10567 
    10568 > hide #!30.5 models
    10569 
    10570 > volume #30 level 0.86
    10571 
    10572 > volume #30 level 0.086
    10573 
    10574 > volume #30 level 0.0086
    10575 
    10576 > surface dust #30 size 5
    10577 
    10578 > hide #!30.3 models
    10579 
    10580 > hide #!30.2 models
    10581 
    10582 > hide #!30.6 models
    10583 
    10584 > hide #!30.7 models
    10585 
    10586 > hide #32 models
    10587 
    10588 > volume #30 surfaceSmoothing true
    10589 
    10590 > transparency #30.4 30
    10591 
    10592 > color #19 byhetero
    10593 
    10594 > transparency #30.4 60
    10595 
    10596 > show #!30.3 models
    10597 
    10598 > show #!30.2 models
    10599 
    10600 > show #!30.5 models
    10601 
    10602 > hide #!30.5 models
    10603 
    10604 > show #!30.6 models
    10605 
    10606 > lighting soft
    10607 
    10608 > hide #!30.1 models
    10609 
    10610 > show #!30.1 models
    10611 
    10612 > hide #!30.2 models
    10613 
    10614 > hide #!30.3 models
    10615 
    10616 > hide #!30.4 models
    10617 
    10618 > hide #!30.6 models
    10619 
    10620 > show #!30.4 models
    10621 
    10622 > coulombic #19
    10623 
    10624 Using Amber 20 recommended default charges and atom types for standard
    10625 residues 
    10626 Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_A SES surface #19.1:
    10627 minimum, -14.83, mean 0.05, maximum 16.17 
    10628 Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_B SES surface #19.2:
    10629 minimum, -18.31, mean -1.96, maximum 12.70 
    10630 Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_C SES surface #19.3:
    10631 minimum, -18.82, mean -1.78, maximum 9.24 
    10632 Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_D SES surface #19.4:
    10633 minimum, -19.90, mean 0.05, maximum 16.15 
    10634 Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_E SES surface #19.5:
    10635 minimum, -18.72, mean -1.97, maximum 12.71 
    10636 Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_F SES surface #19.6:
    10637 minimum, -19.23, mean -1.79, maximum 9.35 
    10638 To also show corresponding color key, enter the above coulombic command and
    10639 add key true 
    10640 
    10641 > hide #19/B,C,E,F target s
    10642 
    10643 > hide #19 target s
    10644 
    10645 > view dimer_interface_top
    10646 
    10647 > turn x 5
    10648 
    10649 > transparency #30.1 1
    10650 
    10651 > color #30.1 gray
    10652 
    10653 > lighting full
    10654 
    10655 > lighting shadows false
    10656 
    10657 > select ~sel & ##selected
    10658 
    10659 Nothing selected 
    10660 
    10661 > select ~sel & ##selected
    10662 
    10663 Nothing selected 
    10664 
    10665 > color #30.1 dark gray
    10666 
    10667 > graphics silhouettes false
    10668 
    10669 > graphics silhouettes true
    10670 
    10671 > cartoon style modeHelix default width 1.8 thickness 0.3
    10672 
    10673 > gid #19/A,D:1-10 tar c
    10674 
    10675 Unknown command: gid #19/A,D:1-10 tar c 
    10676 
    10677 > hide #19/A,D:1-10 target c
    10678 
    10679 > color #30.1 dark gray
    10680 
    10681 > color #30.1 silver
    10682 
    10683 > color #30.1 dark gray
    10684 
    10685 > color #30.4 silver
    10686 
    10687 > surface dust #30 size 6
    10688 
    10689 > surface dust #30 size 5
    10690 
    10691 > surface dust #30 size 6
    10692 
    10693 > color #19/D antique white target c
    10694 
    10695 > color #19/D antique white target ac
    10696 
    10697 > color #!19 byhetero
    10698 
    10699 > view name dimer_interface_top
    10700 
    10701 > lighting soft
    10702 
    10703 > lighting simple
    10704 
    10705 > lighting full
    10706 
    10707 > lighting shadows false
    10708 
    10709 > lighting gentle multiShadow 1024
    10710 
    10711 > lighting soft multiShadow 1024
    10712 
    10713 > lighting shadows true intensity 0.5
    10714 
    10715 > lighting shadows false
    10716 
    10717 > lighting full
    10718 
    10719 > lighting shadows false
    10720 
    10721 > color :CDL,PTY,PGT dim gray target a
    10722 
    10723 > color :CDL,PTY,PGT dark slate gray target a
    10724 
    10725 > color :CDL,PTY,PGT dim gray target a
    10726 
    10727 > color #!19 byhetero
    10728 
    10729 > save NhaA-K-pH75-consensus_interface_top.png supersample 3
    10730 > transparentBackground true
    10731 
    10732 > turn z -90
    10733 
    10734 > lighting soft multiShadow 1024
    10735 
    10736 > lighting simple
    10737 
    10738 > lighting shadows true
    10739 
    10740 > lighting shadows false
    10741 
    10742 > lighting full
    10743 
    10744 > lighting shadows false
    10745 
    10746 > view name dimer_interface_top2
    10747 
    10748 > view dimer_interface_top
    10749 
    10750 > graphics silhouettes false
    10751 
    10752 > graphics silhouettes true
    10753 
    10754 > graphics silhouettes false
    10755 
    10756 > graphics silhouettes true
    10757 
    10758 > graphics silhouettes width 2
    10759 
    10760 > hide #!30 models
    10761 
    10762 > hide #19/A,D target c
    10763 
    10764 > hide #19/A,D target ac
    10765 
    10766 > show #19/A,D(:204,245,250,258&sidechain)|(:CDL,PTY,PGT) tar a
    10767 
    10768 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    10769 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    10770 
    10771 > show #19/A,D((:204,245,250,258&sidechain)|(:CDL,PTY,PGT)) tar a
    10772 
    10773 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    10774 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    10775 
    10776 > show #19/A,D:204,245,250,258&sidechain target a
    10777 
    10778 > show #19/A,D:CDL,PTY,PGT target a
    10779 
    10780 > graphics silhouettes width 8
    10781 
    10782 > save NhaA-K-pH75-consensus_interface_top_res.png supersample 3
    10783 > transparentBackground true
    10784 
    10785 > graphics silhouettes width 2
    10786 
    10787 > show #!30 models
    10788 
    10789 > show #19/A,D target c
    10790 
    10791 > view list
    10792 
    10793 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    10794 dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
    10795 dimer_view-all_front, mono_back, mono_back_, mono_front 
    10796 
    10797 > view dimer_interface_top2
    10798 
    10799 > save NhaA-K-pH75-consensus_interface_top2.png supersample 3
    10800 > transparentBackground true
    10801 
    10802 > hide #!30 models
    10803 
    10804 > hide #19/A,D target c
    10805 
    10806 > graphics silhouettes width 6
    10807 
    10808 > save NhaA-K-pH75-consensus_interface_top2_res.png supersample 3
    10809 > transparentBackground true
    10810 
    10811 > view dimer_interface2
    10812 
    10813 > graphics silhouettes width 2
    10814 
    10815 > show #!30 models
    10816 
    10817 > show #19/A,D target c
    10818 
    10819 > surface dust #30 size 5
    10820 
    10821 > color #30.1 silver
    10822 
    10823 > view dimer_interface_top2
    10824 
    10825 > cartoon style modeHelix default width 1.0 thickness 0.3
    10826 
    10827 > save NhaA-K-pH75-consensus_interface_top2.png supersample 3
    10828 > transparentBackground true
    10829 
    10830 > view dimer_interface2
    10831 
    10832 > hide #19/D target c
    10833 
    10834 > clip #19/D:258@CA
    10835 
    10836 Expected a keyword 
    10837 
    10838 > clip front 0.1 #19/D:258@CA
    10839 
    10840 Expected a keyword 
    10841 
    10842 > clip front 0.1 position #19/D:258@CA
    10843 
    10844 > clip model #30.4 false
    10845 
    10846 > clip model #30.4 true
    10847 
    10848 > clip front 5 position #19/D:258@CA
    10849 
    10850 > clip model #19 true
    10851 
    10852 > clip model #19 false
    10853 
    10854 > clip front 0 position #19/D:258@CA
    10855 
    10856 > select #30.1
    10857 
    10858 5 models selected 
    10859 
    10860 > select clear
    10861 
    10862 > ~clip
    10863 
    10864 > clip front 0 position #19/D:258@CA
    10865 
    10866 > clip front -1 position #19/D:258@CA
    10867 
    10868 > clip front 0.5 position #19/D:258@CA
    10869 
    10870 > clip front 0.1 position #19/D:258@CA
    10871 
    10872 > size #19/A,D:204,245,250,258 stickRadius 0.4
    10873 
    10874 Changed 90 bond radii 
    10875 
    10876 > hide #19/A,D:1-10 target c
    10877 
    10878 > graphics silhouettes false
    10879 
    10880 > graphics silhouettes true
    10881 
    10882 > graphics silhouettes false
    10883 
    10884 > graphics silhouettes true
    10885 
    10886 > save NhaA-K-pH75-consensus_interface.png supersample 3 transparentBackground
    10887 > true
    10888 
    10889 > view list
    10890 
    10891 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    10892 dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
    10893 dimer_view-all_front, mono_back, mono_back_, mono_front 
    10894 
    10895 > view name dimer_interface2
    10896 
    10897 > save NhaA-K-pH75-consensus_interface.png supersample 3 transparentBackground
    10898 > true
    10899 
    10900 > hide #!30 models
    10901 
    10902 > hide #19/A target c
    10903 
    10904 > graphics silhouettes width 4
    10905 
    10906 > save NhaA-K-pH75-consensus_interface_res.png supersample 3
    10907 > transparentBackground true
    10908 
    10909 > show #31 models
    10910 
    10911 > hide #31 models
    10912 
    10913 > show #31 models
    10914 
    10915 > hide #31 models
    10916 
    10917 > show #31 models
    10918 
    10919 > select #31/A:402@C37
    10920 
    10921 1 atom, 1 residue, 1 model selected 
    10922 
    10923 > select add #31/A:402@C18
    10924 
    10925 2 atoms, 1 residue, 1 model selected 
    10926 
    10927 > select add #31/A:402@C19
    10928 
    10929 3 atoms, 1 residue, 1 model selected 
    10930 
    10931 > select add #31/A:402@C38
    10932 
    10933 4 atoms, 1 residue, 1 model selected 
    10934 
    10935 > select add #31/A:402@C39
    10936 
    10937 5 atoms, 1 residue, 1 model selected 
    10938 
    10939 > select add #31/A:402@C40
    10940 
    10941 6 atoms, 1 residue, 1 model selected 
    10942 
    10943 > select add #31/A:402@C20
    10944 
    10945 7 atoms, 1 residue, 1 model selected 
    10946 
    10947 > select add #31/A:402@C21
    10948 
    10949 8 atoms, 1 residue, 1 model selected 
    10950 
    10951 > select add #31/A:402@C41
    10952 
    10953 9 atoms, 1 residue, 1 model selected 
    10954 
    10955 > select add #31/A:402@C42
    10956 
    10957 10 atoms, 1 residue, 1 model selected 
    10958 
    10959 > select add #31/A:402@C43
    10960 
    10961 11 atoms, 1 residue, 1 model selected 
    10962 
    10963 > select add #31/A:402@C44
    10964 
    10965 12 atoms, 1 residue, 1 model selected 
    10966 
    10967 > select add #31/A:402@C45
    10968 
    10969 13 atoms, 1 residue, 1 model selected 
    10970 
    10971 > select add #31/A:402@C46
    10972 
    10973 14 atoms, 1 residue, 1 model selected 
    10974 
    10975 > select add #31/A:402@C47
    10976 
    10977 15 atoms, 1 residue, 1 model selected 
    10978 
    10979 > select add #31/A:402@C23
    10980 
    10981 16 atoms, 1 residue, 1 model selected 
    10982 
    10983 > select add #31/A:402@C22
    10984 
    10985 17 atoms, 1 residue, 1 model selected 
    10986 
    10987 > select add #31/A:402@C24
    10988 
    10989 18 atoms, 1 residue, 1 model selected 
    10990 
    10991 > select add #31/A:402@C25
    10992 
    10993 19 atoms, 1 residue, 1 model selected 
    10994 
    10995 > select add #31/A:402@C26
    10996 
    10997 20 atoms, 1 residue, 1 model selected 
    10998 
    10999 > select subtract #31/A:402@C47
    11000 
    11001 19 atoms, 1 residue, 1 model selected 
    11002 
    11003 > select add #31/A:402@C47
    11004 
    11005 20 atoms, 1 residue, 1 model selected 
    11006 
    11007 > delete sel
    11008 
    11009 > hide #31 models
    11010 
    11011 > show #31 models
    11012 
    11013 > hide #31 models
    11014 
    11015 > show #31 models
    11016 
    11017 > hide #31 models
    11018 
    11019 > show #31 models
    11020 
    11021 > hide #31:CDL
    11022 
    11023 > hide #19:PTY
    11024 
    11025 > color #31#!19 byhetero
    11026 
    11027 > save NhaA-K-pH75-consensus_interface_PGT_res.png supersample 3
    11028 > transparentBackground true
    11029 
    11030 > graphics silhouettes width 2
    11031 
    11032 > show #19/A target c
    11033 
    11034 > show #!30 models
    11035 
    11036 > save NhaA-K-pH75-consensus_interface_PGT.png supersample 3
    11037 > transparentBackground true
    11038 
    11039 > view dimer_interface2
    11040 
    11041 > view dimer_interface_top2
    11042 
    11043 > show #19/D target c
    11044 
    11045 > save NhaA-K-pH75-consensus_interface_top2_PGT.png supersample 3
    11046 > transparentBackground true
    11047 
    11048 > hide #!30 models
    11049 
    11050 > hide #19/A,D target c
    11051 
    11052 > graphics silhouettes width 4
    11053 
    11054 > save NhaA-K-pH75-consensus_interface_top2_PGT_res.png supersample 3
    11055 > transparentBackground true
    11056 
    11057 > select #31/A:402@C48
    11058 
    11059 1 atom, 1 residue, 1 model selected 
    11060 
    11061 > delete sel
    11062 
    11063 > view dimer_interface2
    11064 
    11065 > show #19/A target s
    11066 
    11067 > color #19/A pale green target s
    11068 
    11069 > hide #31#!19 atoms
    11070 
    11071 > show #19/D target s
    11072 
    11073 > color #19/D pale green target s
    11074 
    11075 > hide #19 target s
    11076 
    11077 > show #31#!19 cartoons
    11078 
    11079 > ~clip
    11080 
    11081 > hide #31 models
    11082 
    11083 > graphics silhouettes width 2
    11084 
    11085 > view dimer_interface
    11086 
    11087 > view dimer_view-all_front
    11088 
    11089 > save
    11090 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    11091 
    11092 > size #19/A,D:204,245,250,258 stickRadius 0.3
    11093 
    11094 Changed 90 bond radii 
    11095 
    11096 > show #19/A,D:204,245,250,258 target a
    11097 
    11098 > hide #!30.4 models
    11099 
    11100 > show #!30.4 models
    11101 
    11102 > hide #!30.4 models
    11103 
    11104 > show #!30.4 models
    11105 
    11106 > save
    11107 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    11108 
    11109 ——— End of log from Thu Aug 29 14:44:39 2024 ———
    11110 
    11111 opened ChimeraX session 
    11112 
    11113 > hide #!30 models
    11114 
    11115 > show #!1 models
    11116 
    11117 > hide #!1 models
    11118 
    11119 > hide #!19 models
    11120 
    11121 > show #!9 models
    11122 
    11123 > show #!15 models
    11124 
    11125 > hide #!9,15 atoms
    11126 
    11127 > show /A:GLU,ASP,LYS,HIS,ARG target a
    11128 
    11129 > show #1 models
    11130 
    11131 > hide #!9 models
    11132 
    11133 > hide #!15 models
    11134 
    11135 > show /A target c
    11136 
    11137 > show #3 models
    11138 
    11139 > hide #3 models
    11140 
    11141 > show #!5 models
    11142 
    11143 > hide #1 models
    11144 
    11145 > show #!9 models
    11146 
    11147 > show #!13 models
    11148 
    11149 > show #!16 models
    11150 
    11151 > hide #!16 models
    11152 
    11153 > show #!15 models
    11154 
    11155 > color #!5,9,13,15 byhetero
    11156 
    11157 > hide #!5 models
    11158 
    11159 > show #!5 models
    11160 
    11161 > hide #!9 models
    11162 
    11163 > hide #!13 models
    11164 
    11165 > show #!23 models
    11166 
    11167 > ui mousemode right distance
    11168 
    11169 > distance #15/A:225@NE2 #15/A:65@OD2
    11170 
    11171 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A HIS 225 NE2 and ASP 65
    11172 OD2: 3.587Å 
    11173 
    11174 > hide #!15 models
    11175 
    11176 > distance #5/A:65@OD2 #5/A:57@NZ
    11177 
    11178 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A ASP 65 OD2 and LYS
    11179 57 NZ: 1.745Å 
    11180 
    11181 > show #!15 models
    11182 
    11183 > show #!13 models
    11184 
    11185 > hide #!15 models
    11186 
    11187 > distance #13/A:65@OD1 #13/A:57@NZ
    11188 
    11189 Distance between NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A ASP 65 OD1
    11190 and LYS 57 NZ: 2.308Å 
    11191 
    11192 > show #!15 models
    11193 
    11194 > hide #!13 models
    11195 
    11196 > ~distance #13/A:65@OD1 #13/A:57@NZ
    11197 
    11198 > distance #15/A:57@NZ #15/A:65@OD1
    11199 
    11200 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A LYS 57 NZ and ASP 65
    11201 OD1: 4.109Å 
    11202 
    11203 > hide #!5 models
    11204 
    11205 > show #!5 models
    11206 
    11207 > show #!6 models
    11208 
    11209 > hide #!6 models
    11210 
    11211 > show #!16 models
    11212 
    11213 > hide #!16 models
    11214 
    11215 > show #!16 models
    11216 
    11217 > volume #16 level 0.01249
    11218 
    11219 > show #16 target s
    11220 
    11221 > transparency #16 30 target s
    11222 
    11223 > surface unzone #16
    11224 
    11225 > hide #!5 models
    11226 
    11227 > hide #!16 models
    11228 
    11229 > show #!5 models
    11230 
    11231 > distance #15/A:57@NZ #5/A:39@ND1
    11232 
    11233 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A LYS 57 NZ and NhaA-
    11234 nd-6F9-K_BTPpH63_unplugged.pdb #5/A HIS 39 ND1: 18.994Å 
    11235 
    11236 > distance #5/A:39@ND1 #5/A:43@OE2
    11237 
    11238 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A HIS 39 ND1 and GLU
    11239 43 OE2: 4.744Å 
    11240 
    11241 > hide #!5 models
    11242 
    11243 > hide #!15 models
    11244 
    11245 > show #!17 models
    11246 
    11247 > view list
    11248 
    11249 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    11250 dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
    11251 dimer_view-all_front, mono_back, mono_back_, mono_front 
    11252 
    11253 > view binding_site
    11254 
    11255 > show :HOH,NA target a
    11256 
    11257 > show #!18 models
    11258 
    11259 > view binding_site
    11260 
    11261 [Repeated 1 time(s)]
    11262 
    11263 > hide #!18 models
    11264 
    11265 > hide #!17 models
    11266 
    11267 > show #!15 models
    11268 
    11269 > show #!13 models
    11270 
    11271 > show #!11 models
    11272 
    11273 > hide #!15 models
    11274 
    11275 > hide #!13 models
    11276 
    11277 > show #!13 models
    11278 
    11279 > hide #!13 models
    11280 
    11281 > show #!13 models
    11282 
    11283 > hide #!11 models
    11284 
    11285 > show #!9 models
    11286 
    11287 > show #!5 models
    11288 
    11289 > hide #!9 models
    11290 
    11291 > hide #!13 models
    11292 
    11293 > distance #5/A:163@OD2 #5/A:300@NZ
    11294 
    11295 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A ASP 163 OD2 and LYS
    11296 300 NZ: 3.848Å 
    11297 
    11298 > show #!9 models
    11299 
    11300 > hide #!5 models
    11301 
    11302 > distance #9/A:163@OD2 #9/A:300@NZ
    11303 
    11304 Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A ASP 163 OD2 and LYS
    11305 300 NZ: 3.109Å 
    11306 
    11307 > show #!5 models
    11308 
    11309 > show #!13 models
    11310 
    11311 > hide #!9 models
    11312 
    11313 > hide #!5 models
    11314 
    11315 > distance #13/A:163@OD2 #13/A:300@NZ
    11316 
    11317 Distance between NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A ASP 163 OD2
    11318 and LYS 300 NZ: 2.957Å 
    11319 
    11320 > show #!11 models
    11321 
    11322 > hide #!11 models
    11323 
    11324 > show #!11 models
    11325 
    11326 > hide #!11 models
    11327 
    11328 > show #!9 models
    11329 
    11330 > show #!7 models
    11331 
    11332 > hide #!7 models
    11333 
    11334 > show #!7 models
    11335 
    11336 > hide #!9 models
    11337 
    11338 > show #!9 models
    11339 
    11340 > hide #!7 models
    11341 
    11342 > hide #!13 models
    11343 
    11344 > show #!13 models
    11345 
    11346 > hide #!13 models
    11347 
    11348 > show #!13 models
    11349 
    11350 > show #!5 models
    11351 
    11352 > hide #!5 models
    11353 
    11354 > show #1 models
    11355 
    11356 > hide #1 models
    11357 
    11358 > show #1 models
    11359 
    11360 > hide #1 models
    11361 
    11362 > show #3 models
    11363 
    11364 > hide #!9 models
    11365 
    11366 > hide #!13 models
    11367 
    11368 > show #!5 models
    11369 
    11370 > hide #3 models
    11371 
    11372 > hide #!5 models
    11373 
    11374 > show #!5 models
    11375 
    11376 > show #!9 models
    11377 
    11378 > show #3 models
    11379 
    11380 > show #1 models
    11381 
    11382 > hide #3 models
    11383 
    11384 > hide #!5 models
    11385 
    11386 > hide #!9 models
    11387 
    11388 > ~distance #15/A:163@OD2 #15/A:300@NZ
    11389 
    11390 > hide #!23 models
    11391 
    11392 > show #!23 models
    11393 
    11394 > ~distance #13/A:163@OD2 #13/A:300@NZ
    11395 
    11396 > distance #1/A:163@OD2 #1/A:300@NZ
    11397 
    11398 Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A ASP 163 OD2 and LYS 300 NZ:
    11399 3.533Å 
    11400 
    11401 > show #3 models
    11402 
    11403 > hide #1 models
    11404 
    11405 > show #1 models
    11406 
    11407 > hide #1 models
    11408 
    11409 > show #!5 models
    11410 
    11411 > hide #3 models
    11412 
    11413 > show #!7 models
    11414 
    11415 > hide #!5 models
    11416 
    11417 > show #!9 models
    11418 
    11419 > hide #!7 models
    11420 
    11421 > show #!11 models
    11422 
    11423 > hide #!9 models
    11424 
    11425 > show #!13 models
    11426 
    11427 > hide #!11 models
    11428 
    11429 > show #!15 models
    11430 
    11431 > hide #!13 models
    11432 
    11433 > show #!13 models
    11434 
    11435 > hide #!15 models
    11436 
    11437 > show #!14 models
    11438 
    11439 > hide #!14 models
    11440 
    11441 > show #!14 models
    11442 
    11443 > hide #!14 models
    11444 
    11445 > show #!14 models
    11446 
    11447 > hide #!14 models
    11448 
    11449 > view binding_site
    11450 
    11451 > show #!15 models
    11452 
    11453 > show #!11 models
    11454 
    11455 > hide #!11 models
    11456 
    11457 > show #!9 models
    11458 
    11459 > show #!5 models
    11460 
    11461 > style :NA stick
    11462 
    11463 Changed 2 atom styles 
    11464 
    11465 > show /A target c
    11466 
    11467 > show binding_site_res target a
    11468 
    11469 > cartoon /A:132 suppressBackboneDisplay false
    11470 
    11471 > cartoon tether /A:132 scale 0
    11472 
    11473 > graphics silhouettes width 2
    11474 
    11475 > color #!5,9,13,15 byhetero
    11476 
    11477 > hide #!5 models
    11478 
    11479 > show #!5 models
    11480 
    11481 > view binding_site
    11482 
    11483 > hide #!15 models
    11484 
    11485 > show #!15 models
    11486 
    11487 > hide #!15 models
    11488 
    11489 > show #!15 models
    11490 
    11491 > hide #!15 models
    11492 
    11493 > show #!15 models
    11494 
    11495 > show #!16 models
    11496 
    11497 > hide #!16 models
    11498 
    11499 > show #!14 models
    11500 
    11501 > hide #!15 models
    11502 
    11503 > hide #!14 models
    11504 
    11505 > show #!15 models
    11506 
    11507 > hide #!15 models
    11508 
    11509 > show #!15 models
    11510 
    11511 > hide #!15 models
    11512 
    11513 > show #!15 models
    11514 
    11515 > show #!16 models
    11516 
    11517 > hide #!16 models
    11518 
    11519 > hide #!5 models
    11520 
    11521 > hide #!9 models
    11522 
    11523 > view binding_site
    11524 
    11525 > color #15 dark cyan target ac
    11526 
    11527 > color #!13,15 byhetero
    11528 
    11529 > color #13 medium aquamarine target ac
    11530 
    11531 > color #!13,15 byhetero
    11532 
    11533 > color #13 medium seagreen target ac
    11534 
    11535 > color #13 light seagreen target ac
    11536 
    11537 > color #15 teal target ac
    11538 
    11539 > color #!13,15 byhetero
    11540 
    11541 > hide #!13,15 atoms
    11542 
    11543 > show /A:11,78,81,82,243,249,250,252,253,256 target a
    11544 
    11545 > show #!11 models
    11546 
    11547 > hide #!15 models
    11548 
    11549 > show #!15 models
    11550 
    11551 > show #!9 models
    11552 
    11553 > hide #!9 models
    11554 
    11555 > hide #!11 models
    11556 
    11557 > show #!9 models
    11558 
    11559 > show #!5 models
    11560 
    11561 > hide #!5,9,13,15 atoms
    11562 
    11563 > show /A:11,78,81,82,243,249,250,252,253,256 target a
    11564 
    11565 > hide #!15 models
    11566 
    11567 > hide #!13 models
    11568 
    11569 > hide #!9 models
    11570 
    11571 > distance #5/A:78@OE2 #5/A:256@NE2
    11572 
    11573 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A GLU 78 OE2 and HIS
    11574 256 NE2: 3.405Å 
    11575 
    11576 > show #!9 models
    11577 
    11578 > show #!13 models
    11579 
    11580 > show #!15 models
    11581 
    11582 > hide #!15 models
    11583 
    11584 > show #!15 models
    11585 
    11586 > hide #!15 models
    11587 
    11588 > hide #!13 models
    11589 
    11590 > hide #!9 models
    11591 
    11592 > coulombic #!5
    11593 
    11594 Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_A SES surface #5.1:
    11595 minimum, -15.26, mean 0.23, maximum 19.25 
    11596 Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_B SES surface #5.2:
    11597 minimum, -17.29, mean -2.01, maximum 8.10 
    11598 Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_C SES surface #5.3:
    11599 minimum, -13.33, mean -1.95, maximum 8.36 
    11600 To also show corresponding color key, enter the above coulombic command and
    11601 add key true 
    11602 
    11603 > hide /B,C target s
    11604 
    11605 > show #!7 models
    11606 
    11607 > hide #!5 models
    11608 
    11609 > show #!5 models
    11610 
    11611 > hide #!7 models
    11612 
    11613 > show #!9 models
    11614 
    11615 > hide #!5 models
    11616 
    11617 > show #!5 models
    11618 
    11619 > hide #!5 models
    11620 
    11621 > show #!5 models
    11622 
    11623 > hide #!5.1 models
    11624 
    11625 > show #5.1 models
    11626 
    11627 > hide #!5 models
    11628 
    11629 > hide #9.1 models
    11630 
    11631 > show #9.1 models
    11632 
    11633 > show #9 target s
    11634 
    11635 > coulombic #!9
    11636 
    11637 Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_A SES surface #9.1:
    11638 minimum, -15.35, mean 0.08, maximum 15.24 
    11639 Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_B SES surface #9.2:
    11640 minimum, -18.25, mean -1.97, maximum 8.02 
    11641 Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_C SES surface #9.3:
    11642 minimum, -13.57, mean -1.87, maximum 9.81 
    11643 To also show corresponding color key, enter the above coulombic command and
    11644 add key true 
    11645 
    11646 > hide #!9 models
    11647 
    11648 > show #!5 models
    11649 
    11650 > show #!9 models
    11651 
    11652 > hide #!5 models
    11653 
    11654 > hide #!9 models
    11655 
    11656 > show #!13 models
    11657 
    11658 > coulombic #!13
    11659 
    11660 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_A SES surface
    11661 #13.1: minimum, -16.52, mean 0.01, maximum 15.63 
    11662 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_B SES surface
    11663 #13.2: minimum, -19.83, mean -1.80, maximum 8.49 
    11664 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_C SES surface
    11665 #13.3: minimum, -13.89, mean -1.84, maximum 10.03 
    11666 To also show corresponding color key, enter the above coulombic command and
    11667 add key true 
    11668 
    11669 > hide /B,C target s
    11670 
    11671 > show #!9 models
    11672 
    11673 > hide #!13 models
    11674 
    11675 > show #!13 models
    11676 
    11677 > hide #!9 models
    11678 
    11679 > show #!15 models
    11680 
    11681 > hide #!13 models
    11682 
    11683 > coulombic #!15
    11684 
    11685 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_A SES surface #15.1:
    11686 minimum, -17.07, mean 0.02, maximum 20.09 
    11687 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_B SES surface #15.2:
    11688 minimum, -18.53, mean -1.82, maximum 10.93 
    11689 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_C SES surface #15.3:
    11690 minimum, -14.51, mean -2.14, maximum 12.50 
    11691 To also show corresponding color key, enter the above coulombic command and
    11692 add key true 
    11693 
    11694 > hide /B,C target s
    11695 
    11696 > show #!13 models
    11697 
    11698 > hide #!15 models
    11699 
    11700 > show #!15 models
    11701 
    11702 > hide #!13 models
    11703 
    11704 > show #!13 models
    11705 
    11706 > hide #!15 models
    11707 
    11708 > hide #!13 models
    11709 
    11710 > show #!13 models
    11711 
    11712 > hide #!13.1 models
    11713 
    11714 > hide #9.1 models
    11715 
    11716 > show #!9 models
    11717 
    11718 > show #!5 models
    11719 
    11720 > hide #!5.1 models
    11721 
    11722 > hide #!13 models
    11723 
    11724 > show #!13 models
    11725 
    11726 > hide #!13 models
    11727 
    11728 > show #!13 models
    11729 
    11730 > hide #!5 models
    11731 
    11732 > show #!5 models
    11733 
    11734 > hide #!5 models
    11735 
    11736 > show #!5 models
    11737 
    11738 > show #1 models
    11739 
    11740 > hide #1 models
    11741 
    11742 > show #!15 models
    11743 
    11744 > hide #!15.1 models
    11745 
    11746 > hide #!5,9,13,15 atoms
    11747 
    11748 > show /A:11,78,81,82,243,249,250,252,253,256 target a
    11749 
    11750 > show #3 models
    11751 
    11752 > hide #3 models
    11753 
    11754 > show #3 models
    11755 
    11756 > show /A:11,78,81,82,243,249,250,252,253,256 target a
    11757 
    11758 > hide #!5 models
    11759 
    11760 > show #!5 models
    11761 
    11762 > hide #!5 models
    11763 
    11764 > show #!5 models
    11765 
    11766 > hide #3 models
    11767 
    11768 > show #3 models
    11769 
    11770 > hide #3 models
    11771 
    11772 > show #!6 models
    11773 
    11774 > volume #6 level 0.005928
    11775 
    11776 > volume #6 level 0.008046
    11777 
    11778 > select clear
    11779 
    11780 > hide #!6 models
    11781 
    11782 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    11783 > nd-6F9-K_BTPpH63_unplugged.pdb
    11784 
    11785 Chain information for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #33 
    11786 --- 
    11787 Chain | Description 
    11788 A | No description available 
    11789 B | No description available 
    11790 C | No description available 
    11791  
    11792 
    11793 > mmaker #33 to #5
    11794 
    11795 Parameters 
    11796 --- 
    11797 Chain pairing | bb 
    11798 Alignment algorithm | Needleman-Wunsch 
    11799 Similarity matrix | BLOSUM-62 
    11800 SS fraction | 0.3 
    11801 Gap open (HH/SS/other) | 18/18/6 
    11802 Gap extend | 1 
    11803 SS matrix |  |  | H | S | O 
    11804 ---|---|---|--- 
    11805 H | 6 | -9 | -6 
    11806 S |  | 6 | -6 
    11807 O |  |  | 4 
    11808 Iteration cutoff | 2 
    11809  
    11810 Matchmaker NhaA-nd-6F9-K_BTPpH63_unplugged.pdb, chain A (#5) with NhaA-
    11811 nd-6F9-K_BTPpH63_unplugged.pdb, chain A (#33), sequence alignment score =
    11812 1998.2 
    11813 RMSD between 388 pruned atom pairs is 0.011 angstroms; (across all 388 pairs:
    11814 0.011) 
    11815  
    11816 
    11817 > mcopy #5 toAtoms #33 settings chsv
    11818 
    11819 > hide #!5 models
    11820 
    11821 > show #!5 models
    11822 
    11823 > hide #!5 models
    11824 
    11825 > show #!5 models
    11826 
    11827 > hide #!5 models
    11828 
    11829 > show #!5 models
    11830 
    11831 > hide #!5 models
    11832 
    11833 > show #!5 models
    11834 
    11835 > cartoon style modeHelix default width 1.0 thickness 0.3
    11836 
    11837 > cartoon style modeHelix default width 1.2 thickness 0.2
    11838 
    11839 > cartoon style modeHelix default width 1.0 thickness 0.3
    11840 
    11841 > size stickRadius 0.3
    11842 
    11843 Changed 85069 bond radii 
    11844 
    11845 > size stickRadius 0.2
    11846 
    11847 Changed 85069 bond radii 
    11848 
    11849 > size stickRadius 0.3
    11850 
    11851 Changed 85069 bond radii 
    11852 
    11853 > hide #33:CDL,PTY target a
    11854 
    11855 > close #5
    11856 
    11857 > rename #33 id #5
    11858 
    11859 > show #!16 models
    11860 
    11861 > show #!14 models
    11862 
    11863 > hide #!16 models
    11864 
    11865 > show #!16 models
    11866 
    11867 > hide #!16 models
    11868 
    11869 > show #!16 models
    11870 
    11871 > hide #!14 models
    11872 
    11873 > show #!14 models
    11874 
    11875 > hide #!16 models
    11876 
    11877 > hide #!14 models
    11878 
    11879 > distance #5/A:78@OE2 #5/A:256@NE2
    11880 
    11881 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A GLU 78 OE2 and HIS
    11882 256 NE2: 2.543Å 
    11883 
    11884 > show #1 models
    11885 
    11886 > hide #1 models
    11887 
    11888 > show #1 models
    11889 
    11890 > hide #1 models
    11891 
    11892 > show #1 models
    11893 
    11894 > hide #1 models
    11895 
    11896 > show #3 models
    11897 
    11898 > hide #3 models
    11899 
    11900 > show #3 models
    11901 
    11902 > hide #3 models
    11903 
    11904 > show #3 models
    11905 
    11906 > hide #3 models
    11907 
    11908 > show #!7 models
    11909 
    11910 > hide #!7 models
    11911 
    11912 > show #!11 models
    11913 
    11914 > hide #!11 models
    11915 
    11916 > save
    11917 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
    11918 
    11919 ——— End of log from Tue Sep 3 14:38:58 2024 ———
    11920 
    11921 opened ChimeraX session 
    11922 
    11923 > color #5 orange target ac
    11924 
    11925 > color #9 forestgreen target ac
    11926 
    11927 > color #13 light seagreen target ac
    11928 
    11929 > color #15 teal target ac
    11930 
    11931 > color #5#!9,13,15 byhetero
    11932 
    11933 > ui mousemode right translate
    11934 
    11935 > select clear
    11936 
    11937 > hide #23.1 models
    11938 
    11939 > ui mousemode right distance
    11940 
    11941 > hide #!13 models
    11942 
    11943 > hide #!9 models
    11944 
    11945 > hide #5 models
    11946 
    11947 > distance #15/A:252@OE1 #15/A:81@NE
    11948 
    11949 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A GLU 252 OE1 and ARG 81
    11950 NE: 3.097Å 
    11951 
    11952 > show #23.1 models
    11953 
    11954 > hide #23.1 models
    11955 
    11956 > show #!9 models
    11957 
    11958 > show #!13 models
    11959 
    11960 > show #5 models
    11961 
    11962 > ui mousemode right translate
    11963 
    11964 > transparency 50 target c
    11965 
    11966 > hide #5 models
    11967 
    11968 > hide #!9 models
    11969 
    11970 > hide #!13 models
    11971 
    11972 > ui mousemode right distance
    11973 
    11974 > ~distance #1/A:81@NH2 #1/A:252@OE2
    11975 
    11976 > distance #15/A:252@OE1 #15/A:81@NH2
    11977 
    11978 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A GLU 252 OE1 and ARG 81
    11979 NH2: 3.074Å 
    11980 
    11981 > show #23.1 models
    11982 
    11983 > ui tool show Distances
    11984 
    11985 > ~distance #15/A:252@OE1 #15/A:81@NE
    11986 
    11987 > show #!13 models
    11988 
    11989 > show #!9 models
    11990 
    11991 > show #5 models
    11992 
    11993 > show #!17 models
    11994 
    11995 > hide #!17 models
    11996 
    11997 > show #!17 models
    11998 
    11999 > hide #!17 models
    12000 
    12001 > show #!17 models
    12002 
    12003 > hide #!17 models
    12004 
    12005 > show #!17 models
    12006 
    12007 > hide #!17 models
    12008 
    12009 > show #!17 models
    12010 
    12011 > hide #!17 models
    12012 
    12013 > show #!17 models
    12014 
    12015 > hide #!17 models
    12016 
    12017 > show #!17 models
    12018 
    12019 > hide #!17 models
    12020 
    12021 > show #!17 models
    12022 
    12023 > distance #17/A:11@OD2 #17/A:153@NZ
    12024 
    12025 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 11 OD2 and LYS 153 NZ:
    12026 3.741Å 
    12027 
    12028 > ui mousemode right translate
    12029 
    12030 > ui tool show Distances
    12031 
    12032 > ~distance #17/A:11@OD2 #17/A:153@NZ
    12033 
    12034 > hide #!17 models
    12035 
    12036 > hide #23.1 models
    12037 
    12038 > show #23.1 models
    12039 
    12040 > hide #23.1 models
    12041 
    12042 > transparency 70 target c
    12043 
    12044 > transparency 50 target c
    12045 
    12046 > show #23.1 models
    12047 
    12048 > hide #!15 models
    12049 
    12050 > show #!15 models
    12051 
    12052 > hide #!15 models
    12053 
    12054 > hide #5 models
    12055 
    12056 > hide #!13 models
    12057 
    12058 > ui mousemode right distance
    12059 
    12060 > distance #9/A:78@OE1 #9/A:256@ND1
    12061 
    12062 Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A GLU 78 OE1 and HIS
    12063 256 ND1: 4.195Å 
    12064 
    12065 > ui tool show Distances
    12066 
    12067 > ~distance #9/A:78@OE1 #9/A:256@ND1
    12068 
    12069 > show #!11 models
    12070 
    12071 > hide #!11 models
    12072 
    12073 > show #!13 models
    12074 
    12075 > show #!15 models
    12076 
    12077 > show #5 models
    12078 
    12079 > hide #23.1 models
    12080 
    12081 > select clear
    12082 
    12083 > ui mousemode right translate
    12084 
    12085 > select #9/A:81@NE
    12086 
    12087 1 atom, 1 residue, 1 model selected 
    12088 
    12089 > select clear
    12090 
    12091 > color sel gray target p
    12092 
    12093 > color sel dark gray target p
    12094 
    12095 > select clear
    12096 
    12097 > hide #!23 models
    12098 
    12099 > save NhaA-pH-sensing-superpose.png supersample 3 transparentBackground true
    12100 
    12101 > hide target c
    12102 
    12103 > show /A:11,78,81,82,243,249,250,252,253,256 target a
    12104 
    12105 > hide #5#!9,13,15 atoms
    12106 
    12107 > show /A:11,78,81,82,243,249,250,252,253,256&sidechain target a
    12108 
    12109 > hide sel
    12110 
    12111 > select clear
    12112 
    12113 > hide sel
    12114 
    12115 [Repeated 1 time(s)]
    12116 
    12117 > graphics silhouettes width 6
    12118 
    12119 > show #!23 models
    12120 
    12121 > graphics silhouettes width 8
    12122 
    12123 > graphics silhouettes width 6
    12124 
    12125 > save NhaA-pH-sensing-superpose_res.png supersample 3 transparentBackground
    12126 > true
    12127 
    12128 > graphics silhouettes width 2
    12129 
    12130 > hide #!23 models
    12131 
    12132 > show /A target c
    12133 
    12134 > transparency 50 target c
    12135 
    12136 > hide #!9 models
    12137 
    12138 > show #!9 models
    12139 
    12140 > hide #!9 models
    12141 
    12142 > show #!9 models
    12143 
    12144 > transparency 30 target c
    12145 
    12146 > save NhaA-pH-sensing-superpose.png supersample 3 transparentBackground true
    12147 
    12148 > hide target c
    12149 
    12150 > ui tool show "Selection Inspector"
    12151 
    12152 [Repeated 1 time(s)]
    12153 
    12154 > setattr =sel p display false
    12155 
    12156 Assigning display attribute to 9 items 
    12157 
    12158 > hide sel target p
    12159 
    12160 > select clear
    12161 
    12162 > show /A target c
    12163 
    12164 > view name pH-sensing
    12165 
    12166 > view list
    12167 
    12168 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    12169 dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
    12170 dimer_view-all_front, mono_back, mono_back_, mono_front, pH-sensing 
    12171 
    12172 > view binding_site
    12173 
    12174 > hide #5#!9,13,15 atoms
    12175 
    12176 > name pH-sensing /A:11,78,81,82,243,249,250,252,253,256
    12177 
    12178 > name list
    12179 
    12180 binding_site_res /A:132,133,163,164,300,NA,HOH 
    12181 core /A:86-180,275-388 
    12182 core_TM /A:91-116,123-144,150-174,281-313,325-350,355-383 
    12183 dimer /A:1-85,181-274 
    12184 dimer_TM /A:11-30,59-85,181-199,205-218,223-236,247-271 
    12185 pH-sensing /A:11,78,81,82,243,249,250,252,253,256 
    12186 
    12187 > show binding_site_res&sidechain target a
    12188 
    12189 > show /A:132 target a
    12190 
    12191 > show #!23 models
    12192 
    12193 > hide #!15 models
    12194 
    12195 > ui mousemode right distance
    12196 
    12197 > ~distance #17/A:164@OD1 #17/A:132@O
    12198 
    12199 > distance #13/A:132@O #13/A:164@OD2
    12200 
    12201 Distance between NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A THR 132 O
    12202 and ASP 164 OD2: 2.894Å 
    12203 
    12204 > show #23.1 models
    12205 
    12206 > show #!15 models
    12207 
    12208 > distance #15/A:300@NZ #15/A:163@OD2
    12209 
    12210 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A LYS 300 NZ and ASP 163
    12211 OD2: 3.294Å 
    12212 
    12213 > show #!16 models
    12214 
    12215 > hide #!16 models
    12216 
    12217 > show #!16 models
    12218 
    12219 > show #15/A:161 target a
    12220 
    12221 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    12222 > nd-6F9-K_BTPpH85_state2.pdb
    12223 
    12224 Chain information for NhaA-nd-6F9-K_BTPpH85_state2.pdb #33 
    12225 --- 
    12226 Chain | Description 
    12227 A | No description available 
    12228 B | No description available 
    12229 C | No description available 
    12230  
    12231 
    12232 > mmaker #33 to #15
    12233 
    12234 Parameters 
    12235 --- 
    12236 Chain pairing | bb 
    12237 Alignment algorithm | Needleman-Wunsch 
    12238 Similarity matrix | BLOSUM-62 
    12239 SS fraction | 0.3 
    12240 Gap open (HH/SS/other) | 18/18/6 
    12241 Gap extend | 1 
    12242 SS matrix |  |  | H | S | O 
    12243 ---|---|---|--- 
    12244 H | 6 | -9 | -6 
    12245 S |  | 6 | -6 
    12246 O |  |  | 4 
    12247 Iteration cutoff | 2 
    12248  
    12249 Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with NhaA-
    12250 nd-6F9-K_BTPpH85_state2.pdb, chain A (#33), sequence alignment score = 2000 
    12251 RMSD between 388 pruned atom pairs is 0.047 angstroms; (across all 388 pairs:
    12252 0.047) 
    12253  
    12254 
    12255 > mcopy #15 toAtoms #33 settings hsvc
    12256 
    12257 > hide #!16 models
    12258 
    12259 > cartoon style modeHelix default width 1.8 thickness 0.2
    12260 
    12261 > cartoon style modeHelix default width 1.0 thickness 0.3
    12262 
    12263 > hide #33 models
    12264 
    12265 > show #33 models
    12266 
    12267 > hide #33 models
    12268 
    12269 > show #33 models
    12270 
    12271 > hide #33 models
    12272 
    12273 > show #33 models
    12274 
    12275 > hide #33 models
    12276 
    12277 > show #33 models
    12278 
    12279 > hide #33 models
    12280 
    12281 > show #33 models
    12282 
    12283 > hide #33 models
    12284 
    12285 > show #33 models
    12286 
    12287 > hide #!15 models
    12288 
    12289 > show #!15 models
    12290 
    12291 > hide #!15 models
    12292 
    12293 > distance #33/A:164@OD1 #33/A:132@O
    12294 
    12295 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A ASP 164 OD1 and THR
    12296 132 O: 6.188Å 
    12297 
    12298 > distance #33/A:163@OD1 #33/A:300@NZ
    12299 
    12300 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A ASP 163 OD1 and LYS
    12301 300 NZ: 3.678Å 
    12302 
    12303 > view list
    12304 
    12305 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    12306 dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
    12307 dimer_view-all_front, mono_back, mono_back_, mono_front, pH-sensing 
    12308 
    12309 > view binding_site
    12310 
    12311 > show #!15 models
    12312 
    12313 > hide #!15 models
    12314 
    12315 > show #!15 models
    12316 
    12317 > hide #!15 models
    12318 
    12319 > show #!15 models
    12320 
    12321 > hide #!15 models
    12322 
    12323 > show #!15 models
    12324 
    12325 > hide #!15 models
    12326 
    12327 > show #!15 models
    12328 
    12329 > hide #!15 models
    12330 
    12331 > show #!15 models
    12332 
    12333 > hide #!15 models
    12334 
    12335 > show #!15 models
    12336 
    12337 > hide #!15 models
    12338 
    12339 > show #!15 models
    12340 
    12341 > hide #!15 models
    12342 
    12343 > show #!15 models
    12344 
    12345 > hide #!15 models
    12346 
    12347 > show #!15 models
    12348 
    12349 > hide #!15 models
    12350 
    12351 > show #!15 models
    12352 
    12353 > hide #!15 models
    12354 
    12355 > show #!15 models
    12356 
    12357 > hide #!15 models
    12358 
    12359 > show #!15 models
    12360 
    12361 > hide #!15 models
    12362 
    12363 > show #!17 models
    12364 
    12365 > hide #!17 models
    12366 
    12367 > show #!17 models
    12368 
    12369 > hide #!17 models
    12370 
    12371 > show #!15 models
    12372 
    12373 > hide #33 models
    12374 
    12375 > hide #!15 models
    12376 
    12377 > show #!15 models
    12378 
    12379 > hide #!15 models
    12380 
    12381 > show #!15 models
    12382 
    12383 > hide #!15 models
    12384 
    12385 > show #33 models
    12386 
    12387 > hide #5 models
    12388 
    12389 > hide #!9 models
    12390 
    12391 > hide #!13 models
    12392 
    12393 > coulombic #33
    12394 
    12395 Using Amber 20 recommended default charges and atom types for standard
    12396 residues 
    12397 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_A SES surface #33.1:
    12398 minimum, -15.50, mean 0.05, maximum 21.16 
    12399 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_B SES surface #33.2:
    12400 minimum, -18.13, mean -1.81, maximum 11.34 
    12401 Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_C SES surface #33.3:
    12402 minimum, -14.70, mean -2.15, maximum 10.81 
    12403 To also show corresponding color key, enter the above coulombic command and
    12404 add key true 
    12405 
    12406 > view list
    12407 
    12408 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    12409 dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
    12410 dimer_view-all_front, mono_back, mono_back_, mono_front, pH-sensing 
    12411 
    12412 > view cutaway
    12413 
    12414 > ~clip
    12415 
    12416 > view cutaway
    12417 
    12418 > hide #15,33/A:161 target a
    12419 
    12420 > hide /B,C target s
    12421 
    12422 > hide #!33 models
    12423 
    12424 > show #!9 models
    12425 
    12426 > hide #!9 models
    12427 
    12428 > show #!9 models
    12429 
    12430 > view cutaway
    12431 
    12432 > show #9.1 models
    12433 
    12434 > hide #!9.1 models
    12435 
    12436 > show #9.1 models
    12437 
    12438 > hide #!9.1 models
    12439 
    12440 > show #9.1 models
    12441 
    12442 > hide #!9.1 models
    12443 
    12444 > hide #!9 models
    12445 
    12446 > show #!17 models
    12447 
    12448 > hide #17.1 models
    12449 
    12450 > show #17.1 models
    12451 
    12452 > coulombic #!17
    12453 
    12454 Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_A SES surface #17.1: minimum,
    12455 -15.88, mean 0.07, maximum 15.24 
    12456 Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_B SES surface #17.2: minimum,
    12457 -20.11, mean -1.82, maximum 11.17 
    12458 Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_C SES surface #17.3: minimum,
    12459 -14.41, mean -2.05, maximum 16.84 
    12460 To also show corresponding color key, enter the above coulombic command and
    12461 add key true 
    12462 
    12463 > hide #!17.1 models
    12464 
    12465 > show #17.1 models
    12466 
    12467 > hide #!17.1 models
    12468 
    12469 > hide #!17.3 models
    12470 
    12471 > show #17.3 models
    12472 
    12473 > hide #17.4 models
    12474 
    12475 > show #17.4 models
    12476 
    12477 > hide #!17 models
    12478 
    12479 > show #!17 models
    12480 
    12481 > hide #!17 models
    12482 
    12483 > show #!11 models
    12484 
    12485 > hide #!11 models
    12486 
    12487 > show #!11 models
    12488 
    12489 > hide #!11 models
    12490 
    12491 > show #!12 models
    12492 
    12493 > hide #!12 models
    12494 
    12495 > show #!13 models
    12496 
    12497 > show #13.1 models
    12498 
    12499 > hide #!13.1 models
    12500 
    12501 > hide #!13 models
    12502 
    12503 > show #!15 models
    12504 
    12505 > show #15.1 models
    12506 
    12507 > show #!33 models
    12508 
    12509 > hide #!33 models
    12510 
    12511 > show #!33 models
    12512 
    12513 > hide #!33 models
    12514 
    12515 > show #!33 models
    12516 
    12517 > hide #!33 models
    12518 
    12519 > show #!33 models
    12520 
    12521 > hide #!33 models
    12522 
    12523 > show #!33 models
    12524 
    12525 > hide #!33 models
    12526 
    12527 > show #!33 models
    12528 
    12529 > hide #!15 models
    12530 
    12531 > show #!15 models
    12532 
    12533 > hide #!15 models
    12534 
    12535 > show #!15 models
    12536 
    12537 > hide #!15 models
    12538 
    12539 > show #!15 models
    12540 
    12541 > hide #!15 models
    12542 
    12543 > show #!15 models
    12544 
    12545 > hide #!15 models
    12546 
    12547 > show #!15 models
    12548 
    12549 > hide #!15 models
    12550 
    12551 > show #!15 models
    12552 
    12553 > hide #!15 models
    12554 
    12555 > show #!15 models
    12556 
    12557 > hide #!15 models
    12558 
    12559 > show #!15 models
    12560 
    12561 > hide #!15 models
    12562 
    12563 > show #!15 models
    12564 
    12565 > hide #!15 models
    12566 
    12567 > show #!15 models
    12568 
    12569 > hide #!15 models
    12570 
    12571 > hide #!33 models
    12572 
    12573 > show #!33 models
    12574 
    12575 > hide #!33 models
    12576 
    12577 > show #!33 models
    12578 
    12579 > hide #!33.1 models
    12580 
    12581 > view binding_site
    12582 
    12583 > show #!17 models
    12584 
    12585 > hide #!17 models
    12586 
    12587 > show #!17 models
    12588 
    12589 > hide #!17 models
    12590 
    12591 > view binding_site
    12592 
    12593 > hide #23.1 models
    12594 
    12595 > show #!15 models
    12596 
    12597 > hide #!15 models
    12598 
    12599 > show #!9 models
    12600 
    12601 > show #!7 models
    12602 
    12603 > hide #!7 models
    12604 
    12605 > show #5 models
    12606 
    12607 > show #!13 models
    12608 
    12609 > select clear
    12610 
    12611 > ui mousemode right translate
    12612 
    12613 > color sel dark gray target p
    12614 
    12615 > select clear
    12616 
    12617 > color sel teal target p
    12618 
    12619 > select clear
    12620 
    12621 [Repeated 1 time(s)]
    12622 
    12623 > show #23.1 models
    12624 
    12625 > hide #23.1 models
    12626 
    12627 > transparency 50 target c
    12628 
    12629 > hide #!23 models
    12630 
    12631 > hide /A:160-161 target c
    12632 
    12633 > show /A:160-161 target c
    12634 
    12635 > show /A:160 target c
    12636 
    12637 > hide /A:160 target c
    12638 
    12639 > view binding_site
    12640 
    12641 > select #13/A:162
    12642 
    12643 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12644 
    12645 > select clear
    12646 
    12647 > hide /A:160-161 target c
    12648 
    12649 > save NhaA-K-binding-site-superpose.png supersample 3 transparentBackground
    12650 > true
    12651 
    12652 > show #!23 models
    12653 
    12654 > hide target c
    12655 
    12656 > hide sel target p
    12657 
    12658 > select clear
    12659 
    12660 > graphics silhouettes width 6
    12661 
    12662 > save NhaA-K-binding-site-superpose_res.png supersample 3
    12663 > transparentBackground true
    12664 
    12665 > show #23.1 models
    12666 
    12667 > hide #23.1 models
    12668 
    12669 > hide sel target p
    12670 
    12671 > color sel dark gray target p
    12672 
    12673 > select clear
    12674 
    12675 > save NhaA-K-binding-site-superpose_res.png supersample 3
    12676 > transparentBackground true
    12677 
    12678 > hide #!23 models
    12679 
    12680 > show /A target c
    12681 
    12682 > hide #33/A:160-161 target c
    12683 
    12684 > hide /A:160-161 target c
    12685 
    12686 > graphics silhouettes width 2
    12687 
    12688 > graphics silhouettes false
    12689 
    12690 > transparency 100 target a
    12691 
    12692 > save NhaA-K-binding-site-superpose_rib.png supersample 3
    12693 > transparentBackground true
    12694 
    12695 > transparency 0 target a
    12696 
    12697 > show #!23 models
    12698 
    12699 > show #23.1 models
    12700 
    12701 > hide #!23 models
    12702 
    12703 > hide #!13 models
    12704 
    12705 > hide #!9 models
    12706 
    12707 > hide #5 models
    12708 
    12709 > show :HOH target a
    12710 
    12711 > show #!17 models
    12712 
    12713 > hide #!17 models
    12714 
    12715 > show #!23 models
    12716 
    12717 > hide #!23 models
    12718 
    12719 > ui mousemode right distance
    12720 
    12721 > distance #33/A:300@NZ #33/A:506@O
    12722 
    12723 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A LYS 300 NZ and HOH 506
    12724 O: 2.587Å 
    12725 
    12726 > show #!23 models
    12727 
    12728 > distance #33/A:163@OD1 #33/A:506@O
    12729 
    12730 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A ASP 163 OD1 and HOH
    12731 506 O: 2.835Å 
    12732 
    12733 > color sel dark gray target p
    12734 
    12735 > select clear
    12736 
    12737 > hide #23.1 models
    12738 
    12739 > show #!16 models
    12740 
    12741 > hide #!16 models
    12742 
    12743 > show #23.1 models
    12744 
    12745 > distance #33/A:164@OD2 #33/A:504@O
    12746 
    12747 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A ASP 164 OD2 and HOH
    12748 504 O: 4.635Å 
    12749 
    12750 > select #33/A:504@O
    12751 
    12752 1 atom, 1 residue, 1 model selected 
    12753 
    12754 > hide sel target a
    12755 
    12756 > ui mousemode right translate
    12757 
    12758 > hide #23.1 models
    12759 
    12760 > graphics silhouettes true
    12761 
    12762 > show #!16 models
    12763 
    12764 > show #25 models
    12765 
    12766 > hide #25 models
    12767 
    12768 > surface zone #16 nearAtoms #25|#33/A:132,133,163,164,300,HOH
    12769 
    12770 > transparency 0 target c
    12771 
    12772 > transparency #16 50 target s
    12773 
    12774 > transparency #16 70 target s
    12775 
    12776 > transparency #16 50 target s
    12777 
    12778 > view binding_site
    12779 
    12780 > select ~sel & ##selected
    12781 
    12782 4794 atoms, 4897 bonds, 5 pseudobonds, 615 residues, 2 models selected 
    12783 
    12784 > select up
    12785 
    12786 4795 atoms, 4897 bonds, 5 pseudobonds, 616 residues, 2 models selected 
    12787 
    12788 > select down
    12789 
    12790 4794 atoms, 4897 bonds, 5 pseudobonds, 615 residues, 5 models selected 
    12791 
    12792 > select clear
    12793 
    12794 > transparency #16 70 target s
    12795 
    12796 > lighting simple
    12797 
    12798 > lighting full
    12799 
    12800 > lighting shadows false
    12801 
    12802 > hide #!33 models
    12803 
    12804 > show #!33 models
    12805 
    12806 > hide #!23 models
    12807 
    12808 > transparency #16 50 target s
    12809 
    12810 > transparency #16 60 target s
    12811 
    12812 > save NhaA-K-pH85-binding-site_density.png supersample 3
    12813 > transparentBackground true
    12814 
    12815 > show #!23 models
    12816 
    12817 > hide #!23 models
    12818 
    12819 > graphics silhouettes false
    12820 
    12821 > graphics silhouettes true
    12822 
    12823 > hide #33 target c
    12824 
    12825 > hide #!16 models
    12826 
    12827 > hide sel
    12828 
    12829 > select clear
    12830 
    12831 > graphics silhouettes width 6
    12832 
    12833 > show #!23 models
    12834 
    12835 > save NhaA-K-pH85-binding-site_density_res.png supersample 3
    12836 > transparentBackground true
    12837 
    12838 > graphics silhouettes width 2
    12839 
    12840 > hide #!23 models
    12841 
    12842 > show #33/A target c
    12843 
    12844 > show #!16 models
    12845 
    12846 > transparency 100 target a
    12847 
    12848 > transparency 70 target c
    12849 
    12850 > graphics silhouettes false
    12851 
    12852 > save NhaA-K-pH85-binding-site_density_tra.png supersample 3
    12853 > transparentBackground true
    12854 
    12855 > show #!23 models
    12856 
    12857 > show #23.1 models
    12858 
    12859 > graphics silhouettes true
    12860 
    12861 > transparency 0 target c
    12862 
    12863 > transparency 0 target a
    12864 
    12865 > hide #!16 models
    12866 
    12867 > hide #!33 models
    12868 
    12869 > show #!13 models
    12870 
    12871 > show #!14 models
    12872 
    12873 > show #!16 models
    12874 
    12875 > volume #14 level 0.0125
    12876 
    12877 > hide #!16 models
    12878 
    12879 > show #!16 models
    12880 
    12881 > hide #!16 models
    12882 
    12883 > show #!16 models
    12884 
    12885 > hide #!16 models
    12886 
    12887 > hide #!14 models
    12888 
    12889 > hide #!13 models
    12890 
    12891 > show #!16 models
    12892 
    12893 > show #!10 models
    12894 
    12895 > volume #10 level 0.01289
    12896 
    12897 > hide #!16 models
    12898 
    12899 > show #!16 models
    12900 
    12901 > hide #!16 models
    12902 
    12903 > show #!16 models
    12904 
    12905 > hide #!16 models
    12906 
    12907 > show #!16 models
    12908 
    12909 > hide #!16 models
    12910 
    12911 > show #!16 models
    12912 
    12913 > hide #!16 models
    12914 
    12915 > show #!16 models
    12916 
    12917 > hide #!16 models
    12918 
    12919 > show #!16 models
    12920 
    12921 > hide #!16 models
    12922 
    12923 > show #!16 models
    12924 
    12925 > hide #!16 models
    12926 
    12927 > show #!16 models
    12928 
    12929 > hide #!16 models
    12930 
    12931 > show #!16 models
    12932 
    12933 > hide #!16 models
    12934 
    12935 > volume #10 level 0.01642
    12936 
    12937 > show #!16 models
    12938 
    12939 > volume #10 level 0.01289
    12940 
    12941 > transparency #10 0 target s
    12942 
    12943 > volume #10 level 0.01179
    12944 
    12945 > color #10 silver target s
    12946 
    12947 > color #10 silver transparency 0 target s
    12948 
    12949 > volume #10 level 0.01047
    12950 
    12951 > volume #10 level 0.01333
    12952 
    12953 > hide #!10 models
    12954 
    12955 > show #!10 models
    12956 
    12957 > volume #10 level 0.01289
    12958 
    12959 > volume #10 level 0.013
    12960 
    12961 > view binding_site
    12962 
    12963 > hide #!16 models
    12964 
    12965 > show #!16 models
    12966 
    12967 > transparency #10 50 target s
    12968 
    12969 > hide #!10 models
    12970 
    12971 > show #!10 models
    12972 
    12973 > hide #!16 models
    12974 
    12975 > show #!16 models
    12976 
    12977 > color #10 snow target s
    12978 
    12979 > hide #!10 models
    12980 
    12981 > show #!10 models
    12982 
    12983 > color #10 gainsboro target s
    12984 
    12985 > hide #!10 models
    12986 
    12987 > show #!10 models
    12988 
    12989 > hide #!16 models
    12990 
    12991 > show #!16 models
    12992 
    12993 > hide #!16 models
    12994 
    12995 > show #!9 models
    12996 
    12997 > surface zone #10 nearAtoms #9&binding-site-res
    12998 
    12999 Invalid "nearAtoms" argument: only initial part "#9" of atom specifier valid 
    13000 
    13001 > surface zone #10 nearAtoms #9&binding-site_res
    13002 
    13003 Invalid "nearAtoms" argument: only initial part "#9" of atom specifier valid 
    13004 
    13005 > name list
    13006 
    13007 binding_site_res /A:132,133,163,164,300,NA,HOH 
    13008 core /A:86-180,275-388 
    13009 core_TM /A:91-116,123-144,150-174,281-313,325-350,355-383 
    13010 dimer /A:1-85,181-274 
    13011 dimer_TM /A:11-30,59-85,181-199,205-218,223-236,247-271 
    13012 pH-sensing /A:11,78,81,82,243,249,250,252,253,256 
    13013 
    13014 > surface zone #10 nearAtoms #9&binding_site_res
    13015 
    13016 > show #!14 models
    13017 
    13018 > hide #!14 models
    13019 
    13020 > show #!14 models
    13021 
    13022 > hide #!14 models
    13023 
    13024 > show #!14 models
    13025 
    13026 > hide #!10 models
    13027 
    13028 > show #!10 models
    13029 
    13030 > hide #!10 models
    13031 
    13032 > show #!10 models
    13033 
    13034 > hide #!10 models
    13035 
    13036 > show #!10 models
    13037 
    13038 > hide #!14 models
    13039 
    13040 > hide #23.1 models
    13041 
    13042 > show #23.1 models
    13043 
    13044 > ui mousemode right distance
    13045 
    13046 > hide #!10 models
    13047 
    13048 > distance #9/A:164@OD2 #9/A:132@O
    13049 
    13050 Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A ASP 164 OD2 and THR
    13051 132 O: 2.815Å 
    13052 
    13053 > show #!10 models
    13054 
    13055 > color sel dark gray target p
    13056 
    13057 > select clear
    13058 
    13059 > hide #23.1 models
    13060 
    13061 > show #!17 models
    13062 
    13063 > distance #17/A:133@OD1 #17/A:504@O
    13064 
    13065 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 133 OD1 and HOH 504 O:
    13066 3.335Å 
    13067 
    13068 > show #23.1 models
    13069 
    13070 > hide #!9 models
    13071 
    13072 > show #!9 models
    13073 
    13074 > hide #!17 models
    13075 
    13076 > hide #!10 models
    13077 
    13078 > show #!11 models
    13079 
    13080 > hide #!11 models
    13081 
    13082 > show #!13 models
    13083 
    13084 > show #!15 models
    13085 
    13086 > hide #!15 models
    13087 
    13088 > show #!15 models
    13089 
    13090 > hide #!15.1 models
    13091 
    13092 > hide #!15 models
    13093 
    13094 > show #!33 models
    13095 
    13096 > show #5 models
    13097 
    13098 > hide #23.1 models
    13099 
    13100 > hide #33:HOH
    13101 
    13102 > hide sel target p
    13103 
    13104 [Repeated 1 time(s)]
    13105 
    13106 > select clear
    13107 
    13108 > hide target c
    13109 
    13110 > select up
    13111 
    13112 4643 atoms, 4 pseudobonds, 612 residues, 8 models selected 
    13113 
    13114 > select down
    13115 
    13116 4 pseudobonds, 4 models selected 
    13117 
    13118 > hide sel target p
    13119 
    13120 > select clear
    13121 
    13122 > graphics silhouettes width 6
    13123 
    13124 > save NhaA-K-binding-site-superpose_res.png supersample 3
    13125 > transparentBackground true
    13126 
    13127 > view list
    13128 
    13129 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    13130 dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
    13131 dimer_view-all_front, mono_back, mono_back_, mono_front, pH-sensing 
    13132 
    13133 > view binding_site
    13134 
    13135 > save NhaA-K-binding-site-superpose_res.png supersample 3
    13136 > transparentBackground true
    13137 
    13138 > hide #!5 models
    13139 
    13140 > hide #!9 models
    13141 
    13142 > hide #!13 models
    13143 
    13144 > show #!24 models
    13145 
    13146 > hide #!24,33 atoms
    13147 
    13148 > show /A:132,133,163,164,300&sidechain target a
    13149 
    13150 > show /A:132 target a
    13151 
    13152 > show :NA target a
    13153 
    13154 > hide :NA target a
    13155 
    13156 > hide sel
    13157 
    13158 > hide #!23 models
    13159 
    13160 > show #!23 models
    13161 
    13162 > show #23 target p
    13163 
    13164 > hide :HOH
    13165 
    13166 > distance #24/A:164@OD1 #24/A:132@O
    13167 
    13168 Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A ASP 164 OD1 and THR
    13169 132 O: 4.183Å 
    13170 
    13171 > color sel dodgerblue target p
    13172 
    13173 > select clear
    13174 
    13175 > hide sel target p
    13176 
    13177 > show #23.1 models
    13178 
    13179 > distance #33/A:164@OD2 #33/A:132@O
    13180 
    13181 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A ASP 164 OD2 and THR
    13182 132 O: 6.349Å 
    13183 
    13184 > ui tool show Distances
    13185 
    13186 > ~distance #33/A:164@OD2 #33/A:132@O
    13187 
    13188 > hide #23.1 models
    13189 
    13190 > view binding_site
    13191 
    13192 > select up
    13193 
    13194 33 pseudobonds, 1 model selected 
    13195 
    13196 > select down
    13197 
    13198 1 pseudobond, 1 model selected 
    13199 
    13200 > select clear
    13201 
    13202 > save NhaA-Na-pH85_vs_K-pH85_binding-site_sil2.png supersample 3
    13203 > transparentBackground true
    13204 
    13205 > hide #!23 models
    13206 
    13207 > show #!23 models
    13208 
    13209 > show #!15 models
    13210 
    13211 > hide #!15 models
    13212 
    13213 > hide #!33 models
    13214 
    13215 > hide sel target p
    13216 
    13217 > show :NA,HOH target a
    13218 
    13219 > show #23.1 models
    13220 
    13221 > hide #23.1 models
    13222 
    13223 > show #23 target p
    13224 
    13225 > select clear
    13226 
    13227 > show :NA,HOH target a
    13228 
    13229 > show #23 target p
    13230 
    13231 > hide sel
    13232 
    13233 > distance #24/A:505@NA #24/A:163@OD1
    13234 
    13235 Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A NA 505 NA and ASP
    13236 163 OD1: 3.219Å 
    13237 
    13238 > ~distance #17/A:505@NA #17/A:164@OD1
    13239 
    13240 > ~distance #15/A:164@OD1 #15/A:132@O
    13241 
    13242 > distance #24/A:505@NA #24/A:164@OD1
    13243 
    13244 Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A NA 505 NA and ASP
    13245 164 OD1: 2.181Å 
    13246 
    13247 > distance #24/A:505@NA #24/A:132@O
    13248 
    13249 Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A NA 505 NA and THR
    13250 132 O: 2.185Å 
    13251 
    13252 > distance #24/A:505@NA #24/A:504@O
    13253 
    13254 Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A NA 505 NA and HOH
    13255 504 O: 2.987Å 
    13256 
    13257 > distance #24/A:163@OD2 #24/A:506@O
    13258 
    13259 Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A ASP 163 OD2 and HOH
    13260 506 O: 2.645Å 
    13261 
    13262 > show #23.1 models
    13263 
    13264 > ~distance #33/A:300@NZ #33/A:506@O
    13265 
    13266 > distance #24/A:506@O #24/A:300@NZ
    13267 
    13268 Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A HOH 506 O and LYS
    13269 300 NZ: 2.344Å 
    13270 
    13271 > distance #24/A:163@OD2 #24/A:300@NZ
    13272 
    13273 Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A ASP 163 OD2 and LYS
    13274 300 NZ: 3.986Å 
    13275 
    13276 > hide #!24 models
    13277 
    13278 > show #!24 models
    13279 
    13280 > view binding_site
    13281 
    13282 > select clear
    13283 
    13284 [Repeated 5 time(s)]
    13285 
    13286 > select #24/A:504@O
    13287 
    13288 1 atom, 1 residue, 1 model selected 
    13289 
    13290 > select #24/A:504@O
    13291 
    13292 1 atom, 1 residue, 1 model selected 
    13293 
    13294 > select clear
    13295 
    13296 > select #24/A:132@O
    13297 
    13298 1 atom, 1 residue, 1 model selected 
    13299 
    13300 > select clear
    13301 
    13302 > hide sel pseudobonds
    13303 
    13304 > ~distance #24/A:163@OD2 #24/A:300@NZ
    13305 
    13306 > view binding_site
    13307 
    13308 > hide #23.1 models
    13309 
    13310 > ui mousemode right zoom
    13311 
    13312 > ui mousemode right translate
    13313 
    13314 Drag select of 1 pseudobonds 
    13315 [Repeated 5 time(s)]
    13316 
    13317 > color sel dark gray target p
    13318 
    13319 > select clear
    13320 
    13321 > view binding_site
    13322 
    13323 > save NhaA-Na-pH85_binding-site_simple_sil2.png supersample 3
    13324 > transparentBackground true
    13325 
    13326 > show #23.1 models
    13327 
    13328 > hide #23.1 models
    13329 
    13330 > show #!33 models
    13331 
    13332 > color #33&core light sea green
    13333 
    13334 > color #33&dimer cyan
    13335 
    13336 > color #!24,33 byhetero
    13337 
    13338 Drag select of 1 pseudobonds 
    13339 
    13340 > select clear
    13341 
    13342 [Repeated 1 time(s)]Drag select of 1 pseudobonds 
    13343 [Repeated 1 time(s)]
    13344 
    13345 > select clear
    13346 
    13347 > hide :HOH,NA
    13348 
    13349 > show #23 target p
    13350 
    13351 > hide :HOH,NA
    13352 
    13353 > hide #!33 models
    13354 
    13355 > ui mousemode right distance
    13356 
    13357 > distance #24/A:163@OD2 #24/A:300@NZ
    13358 
    13359 Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A ASP 163 OD2 and LYS
    13360 300 NZ: 3.986Å 
    13361 
    13362 > ui mousemode right translate
    13363 
    13364 > select clear
    13365 
    13366 Drag select of 1 pseudobonds 
    13367 
    13368 > select ~sel & ##selected
    13369 
    13370 37 pseudobonds, 1 model selected 
    13371 
    13372 > select ~sel & ##selected
    13373 
    13374 37 pseudobonds, 1 model selected 
    13375 
    13376 > select clear
    13377 
    13378 Drag select of 1 pseudobonds 
    13379 
    13380 > color sel dodgerblue target p
    13381 
    13382 > select clear
    13383 
    13384 > show #!33 models
    13385 
    13386 > select clear
    13387 
    13388 > save NhaA-Na-pH85_vs_K-pH85_binding-site2_sil.png supersample 3
    13389 > transparentBackground true
    13390 
    13391 [Repeated 1 time(s)]
    13392 
    13393 > hide #!24 models
    13394 
    13395 > show #!24 models
    13396 
    13397 > hide #!23 models
    13398 
    13399 > hide #!24 models
    13400 
    13401 > show #!24 models
    13402 
    13403 > hide #!24 models
    13404 
    13405 > show #!24 models
    13406 
    13407 > hide #!24 models
    13408 
    13409 > show #!17 models
    13410 
    13411 > show #!24 models
    13412 
    13413 > hide #!24 models
    13414 
    13415 > show /A target c
    13416 
    13417 > graphics silhouettes width 2
    13418 
    13419 > transparency 50 target c
    13420 
    13421 > save NhaA-Na-pH85_vs_K-pH85_binding-site2.png supersample 3
    13422 > transparentBackground true
    13423 
    13424 > hide #!33 models
    13425 
    13426 > show #!33 models
    13427 
    13428 > hide #!17 models
    13429 
    13430 > hide /A target c
    13431 
    13432 > hide sel
    13433 
    13434 > select clear
    13435 
    13436 > show #!23 models
    13437 
    13438 > show :HOH
    13439 
    13440 > select #33/A:504@O
    13441 
    13442 1 atom, 1 residue, 1 model selected 
    13443 
    13444 > hide sel
    13445 
    13446 > select clear
    13447 
    13448 > ui mousemode right distance
    13449 
    13450 > distance #33/A:300@NZ #33/A:506@O
    13451 
    13452 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A LYS 300 NZ and HOH 506
    13453 O: 2.587Å 
    13454 
    13455 > hide sel
    13456 
    13457 > select clear
    13458 
    13459 > color sel dark gray
    13460 
    13461 > select clear
    13462 
    13463 > graphics silhouettes width 2
    13464 
    13465 > graphics silhouettes width 6
    13466 
    13467 > color #33&core teal
    13468 
    13469 > color #!33 byhetero
    13470 
    13471 > save NhaA-K-pH85-binding-site_density_res2.png supersample 3
    13472 > transparentBackground true
    13473 
    13474 > hide #!33 models
    13475 
    13476 > show #!14 models
    13477 
    13478 > hide #!14 models
    13479 
    13480 > show #!13 models
    13481 
    13482 > show #24 target p
    13483 
    13484 > distance #13/A:163@OD2 #13/A:300@NZ
    13485 
    13486 Distance between NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A ASP 163 OD2
    13487 and LYS 300 NZ: 2.957Å 
    13488 
    13489 > show #23.1 models
    13490 
    13491 > hide ##name="chain trace"
    13492 
    13493 > select clear
    13494 
    13495 > color sel dark gray
    13496 
    13497 > select clear
    13498 
    13499 > hide #23.1 models
    13500 
    13501 > save NhaA-K-pH85-state1-unplugged-binding-site_density_res.png supersample 3
    13502 > transparentBackground true
    13503 
    13504 > hide #!13 models
    13505 
    13506 > show #!9 models
    13507 
    13508 > save NhaA-K-pH75-unplugged-binding-site_density_res.png supersample 3
    13509 > transparentBackground true
    13510 
    13511 > hide #!9 models
    13512 
    13513 > show #!5 models
    13514 
    13515 > ~distance #24/A:505@NA #24/A:164@OD1
    13516 
    13517 > ~distance #24/A:164@OD1 #24/A:132@O
    13518 
    13519 > distance #5/A:132@O #5/A:164@OD2
    13520 
    13521 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A THR 132 O and ASP
    13522 164 OD2: 2.705Å 
    13523 
    13524 > show #23.1 models
    13525 
    13526 > ~distance #33/A:300@NZ #33/A:506@O
    13527 
    13528 > ~distance #24/A:506@O #24/A:300@NZ
    13529 
    13530 > ~distance #13/A:163@OD2 #13/A:300@NZ
    13531 
    13532 > distance #5/A:163@OD2 #5/A:300@NZ
    13533 
    13534 Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A ASP 163 OD2 and LYS
    13535 300 NZ: 3.848Å 
    13536 
    13537 > show #!6 models
    13538 
    13539 > volume #6 level 0.01158
    13540 
    13541 > hide #!6 models
    13542 
    13543 > show #1 models
    13544 
    13545 > hide #!5 models
    13546 
    13547 > show #!5 models
    13548 
    13549 > hide #!5 models
    13550 
    13551 > show #!5 models
    13552 
    13553 > hide #!5 models
    13554 
    13555 > show #!5 models
    13556 
    13557 > hide #1 models
    13558 
    13559 > show #1 models
    13560 
    13561 > hide #!5 models
    13562 
    13563 > show #!2 models
    13564 
    13565 > view binding_site
    13566 
    13567 > hide #!2 models
    13568 
    13569 > show #!5 models
    13570 
    13571 > hide #!5 models
    13572 
    13573 > show #3 models
    13574 
    13575 > hide #3 models
    13576 
    13577 > show #!7 models
    13578 
    13579 > hide #!7 models
    13580 
    13581 > show #!11 models
    13582 
    13583 > hide #!11 models
    13584 
    13585 > hide #1 models
    13586 
    13587 > show #!5 models
    13588 
    13589 > show #!9 models
    13590 
    13591 > hide #!9 models
    13592 
    13593 > show #!13 models
    13594 
    13595 > hide #!5 models
    13596 
    13597 > distance #13/A:300@NZ #13/A:163@OD2
    13598 
    13599 Distance between NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A LYS 300 NZ
    13600 and ASP 163 OD2: 2.957Å 
    13601 
    13602 > show #!9 models
    13603 
    13604 > hide #!13 models
    13605 
    13606 > show #!5 models
    13607 
    13608 > hide #!9 models
    13609 
    13610 > show #!9 models
    13611 
    13612 > hide #!9 models
    13613 
    13614 > show #!9 models
    13615 
    13616 > hide #!9 models
    13617 
    13618 > show #!9 models
    13619 
    13620 > hide #!9 models
    13621 
    13622 > show #!9 models
    13623 
    13624 > show #!13 models
    13625 
    13626 > hide #!9 models
    13627 
    13628 > show #!9 models
    13629 
    13630 > hide #!13 models
    13631 
    13632 > hide #!9 models
    13633 
    13634 > hide #23.1 models
    13635 
    13636 > select clear
    13637 
    13638 Drag select of 1 pseudobonds 
    13639 
    13640 > select clear
    13641 
    13642 Drag select of 1 pseudobonds 
    13643 [Repeated 1 time(s)]
    13644 
    13645 > color sel dark gray
    13646 
    13647 > select clear
    13648 
    13649 > ui mousemode right translate
    13650 
    13651 > view binding_site
    13652 
    13653 > save NhaA-K-pH63-unplugged-binding-site_density_res.png supersample 3
    13654 > transparentBackground true
    13655 
    13656 > hide #!5 models
    13657 
    13658 > show #!5 models
    13659 
    13660 > show /A target c
    13661 
    13662 > hide /A:160-161 target c
    13663 
    13664 > graphics silhouettes width 2
    13665 
    13666 > transparency 50 target c
    13667 
    13668 > hide #!23 models
    13669 
    13670 > show #!6 models
    13671 
    13672 > color #6 gainsboro
    13673 
    13674 > transparency #6 50
    13675 
    13676 > surface zone #6 nearAtoms #5&binding_site_res
    13677 
    13678 > transparency 0 target c
    13679 
    13680 > show #!9 models
    13681 
    13682 > hide #!9 models
    13683 
    13684 > show #!10 models
    13685 
    13686 > volume #6 level 0.008222
    13687 
    13688 > transparency #10 0
    13689 
    13690 > volume #6 level 0.01034
    13691 
    13692 > hide #!10 models
    13693 
    13694 > volume #6 level 0.01
    13695 
    13696 > volume #6 level 0.01035
    13697 
    13698 > show #!10 models
    13699 
    13700 > hide #!10 models
    13701 
    13702 > volume #6 level 0.01212
    13703 
    13704 > show #!10 models
    13705 
    13706 > hide #!10 models
    13707 
    13708 > show #!10 models
    13709 
    13710 > hide #!10 models
    13711 
    13712 > volume #6 level 0.01018
    13713 
    13714 > save NhaA-K-pH63-unplugged-binding-site_density.png supersample 3
    13715 > transparentBackground true
    13716 
    13717 > hide #5 models
    13718 
    13719 > hide #!6 models
    13720 
    13721 > show #!9 models
    13722 
    13723 > show #!10 models
    13724 
    13725 > hide #!9 models
    13726 
    13727 > show #!9 models
    13728 
    13729 > show #!7 models
    13730 
    13731 > hide #!7 models
    13732 
    13733 > transparency #10 50
    13734 
    13735 > save NhaA-K-pH75-unplugged-binding-site_density.png supersample 3
    13736 > transparentBackground true
    13737 
    13738 > hide #!9 models
    13739 
    13740 > hide #!10 models
    13741 
    13742 > show #!13 models
    13743 
    13744 > show #!14 models
    13745 
    13746 > color #14 gainsboro
    13747 
    13748 > transparency #14 50
    13749 
    13750 > surface zone #14 nearAtoms #13&binding_site_res
    13751 
    13752 > show #!10 models
    13753 
    13754 > hide #!10 models
    13755 
    13756 > show #!10 models
    13757 
    13758 > hide #!10 models
    13759 
    13760 > show #!10 models
    13761 
    13762 > hide #!10 models
    13763 
    13764 > save NhaA-K-pH85-state1-unplugged-binding-site_density.png supersample 3
    13765 > transparentBackground true
    13766 
    13767 > show #!23 models
    13768 
    13769 > show #23.1 models
    13770 
    13771 > hide #!13 models
    13772 
    13773 > hide #!14 models
    13774 
    13775 > show #!9 models
    13776 
    13777 > hide #!9 models
    13778 
    13779 > show #5 models
    13780 
    13781 > hide #5 models
    13782 
    13783 > show #5 models
    13784 
    13785 > view mono_front
    13786 
    13787 > view mono_back_
    13788 
    13789 > hide #!23 models
    13790 
    13791 > hide #5 atoms
    13792 
    13793 > color #1,3,7,11&core indian red
    13794 
    13795 > color #1,3,7,11&dimer pink
    13796 
    13797 > color #5,9,13&core orange
    13798 
    13799 > color #5,9,13&dimer khaki
    13800 
    13801 > color #17&core dodger blue
    13802 
    13803 > color #17&dimer light sky blue
    13804 
    13805 > show #!7 models
    13806 
    13807 > hide #!7 models
    13808 
    13809 > show #!7 models
    13810 
    13811 > hide #5#!7 atoms
    13812 
    13813 > show #3 models
    13814 
    13815 > hide #3,5#!7 atoms
    13816 
    13817 > show #1 models
    13818 
    13819 > hide #1,3,5#!7 atoms
    13820 
    13821 > show #!9 models
    13822 
    13823 > show #!11 models
    13824 
    13825 > show #!13 models
    13826 
    13827 > show #!15 models
    13828 
    13829 > show #!17 models
    13830 
    13831 > hide #1,3,5#!7,9,11,13,15,17 atoms
    13832 
    13833 > hide /B,C target s
    13834 
    13835 > color #15&deep sky bluie;col #15&dimer light blue;
    13836 
    13837 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    13838 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    13839 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    13840 
    13841 > color #15&core deep skyblue bluie;col #15&dimer light blue;
    13842 
    13843 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    13844 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    13845 
    13846 > color #15&core deep sky blue
    13847 
    13848 > color #15&dimer light blue
    13849 
    13850 > hide #1 models
    13851 
    13852 > hide #3 models
    13853 
    13854 > hide #!7 models
    13855 
    13856 > hide #!11 models
    13857 
    13858 > hide #!17 models
    13859 
    13860 > show /A target s
    13861 
    13862 > hide /A target s
    13863 
    13864 > hide /A target c
    13865 
    13866 > show /A target c
    13867 
    13868 > show #!17 models
    13869 
    13870 > hide #!15 models
    13871 
    13872 > show #!15 models
    13873 
    13874 > hide #!17 models
    13875 
    13876 > cartoon style modeHelix default width 1.8 thickness 0.3
    13877 
    13878 > cartoon style modeHelix default width 1.6 thickness 0.3
    13879 
    13880 > color /A:1-10 orchid
    13881 
    13882 > hide #!5 models
    13883 
    13884 > hide #!9 models
    13885 
    13886 > hide #!15 models
    13887 
    13888 > hide #!13 models
    13889 
    13890 > show #!1 models
    13891 
    13892 > show #1/A:1-10 target s
    13893 
    13894 > show #!29 models
    13895 
    13896 > hide #!1#!29.1-2 atoms
    13897 
    13898 > hidhow #1/A:1-10 tar s
    13899 
    13900 Unknown command: hidhow #1/A:1-10 tar s 
    13901 
    13902 > hide #1/A:1-10 target s
    13903 
    13904 > hide #!29.2 models
    13905 
    13906 > hide #29.1.1 models
    13907 
    13908 > show #29.1.1 models
    13909 
    13910 > show #29.1 target s
    13911 
    13912 > hidow #29.1 tar c
    13913 
    13914 Unknown command: hidow #29.1 tar c 
    13915 
    13916 > hidow #29.1 tar ctra #29.1 30 tar s
    13917 
    13918 Unknown command: hidow #29.1 tar ctra #29.1 30 tar s 
    13919 
    13920 > transparency #29.1 30 target s
    13921 
    13922 > transparency #29.1 50 target s
    13923 
    13924 > view mono_back_
    13925 
    13926 > lighting soft
    13927 
    13928 > lighting full
    13929 
    13930 > lighting shadows false
    13931 
    13932 > lighting simple
    13933 
    13934 > lighting full
    13935 
    13936 > lighting shadows false
    13937 
    13938 > save NhaA-K-pH55-plugged_back.png supersample 3 transparentBackground true
    13939 
    13940 > transparency #29.1 30 target s
    13941 
    13942 > save NhaA-K-pH55-plugged_back.png supersample 3 transparentBackground true
    13943 
    13944 > color #29.1 medium purple
    13945 
    13946 > transparency #29.1 30 target s
    13947 
    13948 > save NhaA-K-pH55-plugged_back.png supersample 3 transparentBackground true
    13949 
    13950 > transparency #29.1 0 target s
    13951 
    13952 > save NhaA-K-pH55-plugged_back.png supersample 3 transparentBackground true
    13953 
    13954 > hide #!29 models
    13955 
    13956 > cartoon style #1/A:1-10 thickness 0.5
    13957 
    13958 > cartoon style #1/A:1-10 thickness 0.3
    13959 
    13960 > show #!29 models
    13961 
    13962 > hide #29.1.1 models
    13963 
    13964 > cartoon style #29.1 thickness 0.3
    13965 
    13966 > cartoon style #29.1 thickness 0.5
    13967 
    13968 > cartoon style #29.1 thickness 0.6
    13969 
    13970 > cartoon style #29.1 thickness 0.7
    13971 
    13972 > cartoon style xsection barbell
    13973 
    13974 > cartoon style xsection rectangle
    13975 
    13976 > cartoon style xsection oval
    13977 
    13978 > cartoon style strand xsection rectangle
    13979 
    13980 > cartoon style helix xsection barbell
    13981 
    13982 > cartoon style #29.1 thickness 1
    13983 
    13984 > open /Users/tsweng/Downloads/AF-P38264-F1-model_v4.pdb
    13985 
    13986 AF-P38264-F1-model_v4.pdb title: 
    13987 Alphafold monomer V2.0 prediction for SRP-independent targeting protein 3
    13988 (P38264) [more info...] 
    13989  
    13990 Chain information for AF-P38264-F1-model_v4.pdb #34 
    13991 --- 
    13992 Chain | Description | UniProt 
    13993 A | SRP-independent targeting protein 3 | PHO88_YEAST 1-188 
    13994  
    13995 
    13996 > hide #!29 models
    13997 
    13998 > hide #!1 models
    13999 
    14000 > view
    14001 
    14002 > mlp #34
    14003 
    14004 Map values for surface "AF-P38264-F1-model_v4.pdb_A SES surface": minimum
    14005 -26.94, mean -2.806, maximum 22.98 
    14006 To also show corresponding color key, enter the above mlp command and add key
    14007 true 
    14008 
    14009 > close #34
    14010 
    14011 > show #!1 models
    14012 
    14013 > view mono_back_
    14014 
    14015 > select #1/A:10
    14016 
    14017 6 atoms, 5 bonds, 1 residue, 1 model selected 
    14018 
    14019 > select add #1/A:9
    14020 
    14021 12 atoms, 10 bonds, 2 residues, 2 models selected 
    14022 
    14023 > select #1/A:1-10
    14024 
    14025 63 atoms, 65 bonds, 7 residues, 1 model selected 
    14026 
    14027 > graphics selection width 8 color black
    14028 
    14029 [Repeated 1 time(s)]
    14030 
    14031 > view mono_back_
    14032 
    14033 > select up
    14034 
    14035 2891 atoms, 2954 bonds, 385 residues, 2 models selected 
    14036 
    14037 > select up
    14038 
    14039 2982 atoms, 3043 bonds, 387 residues, 2 models selected 
    14040 
    14041 > select up
    14042 
    14043 4707 atoms, 4810 bonds, 611 residues, 2 models selected 
    14044 
    14045 > select down
    14046 
    14047 2982 atoms, 3043 bonds, 387 residues, 2 models selected 
    14048 
    14049 > select down
    14050 
    14051 2891 atoms, 2954 bonds, 385 residues, 2 models selected 
    14052 
    14053 > select down
    14054 
    14055 63 atoms, 65 bonds, 7 residues, 2 models selected 
    14056 
    14057 > save NhaA-K-pH55-plugged_back_.png supersample 3 transparentBackground true
    14058 
    14059 > graphics selection width 6 color black
    14060 
    14061 > graphics selection width 5 color black
    14062 
    14063 > save NhaA-K-pH55-plugged_back_.png supersample 3 transparentBackground true
    14064 
    14065 > graphics selection width 2 color lime
    14066 
    14067 > select clear
    14068 
    14069 > show #!29 models
    14070 
    14071 > combine #1
    14072 
    14073 > hide #!29 models
    14074 
    14075 > hide #34 target c
    14076 
    14077 > show #34/A:1-10 target c
    14078 
    14079 > cartoon style #34 thickness 1
    14080 
    14081 > cartoon style #34 thickness 1.5
    14082 
    14083 > cartoon style #34 thickness 1.2
    14084 
    14085 > show #34/A:1-11 target c
    14086 
    14087 > show #34/A:1-12 target c
    14088 
    14089 > hide #34/A:11-12 target c
    14090 
    14091 > save NhaA-K-pH55-plugged_back_.png supersample 3 transparentBackground true
    14092 
    14093 > color #34 medium purple
    14094 
    14095 > save NhaA-K-pH55-plugged_back_.png supersample 3 transparentBackground true
    14096 
    14097 > cartoon style #34 thickness 1.5
    14098 
    14099 > cartoon style #34 thickness 2
    14100 
    14101 > transparency #1 50 target c
    14102 
    14103 > save NhaA-K-pH55-plugged_back_.png supersample 3 transparentBackground true
    14104 
    14105 > transparency #1 20 target c
    14106 
    14107 > save NhaA-K-pH55-plugged_back_.png supersample 3 transparentBackground true
    14108 
    14109 > transparency #1 0 target c
    14110 
    14111 > cartoon style #34 thickness 3
    14112 
    14113 > cartoon style #34 thickness 2
    14114 
    14115 > view mono_back_
    14116 
    14117 > save NhaA-K-pH55-plugged_back_.png supersample 3 transparentBackground true
    14118 
    14119 > cartoon byattr bfactor #34
    14120 
    14121 Expected an atoms specifier or a keyword 
    14122 
    14123 > hide #!1 models
    14124 
    14125 > ui tool show "Render by Attribute"
    14126 
    14127 > save
    14128 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA2.cxs
    14129 
    14130 ——— End of log from Fri Sep 6 13:13:45 2024 ———
    14131 
    14132 opened ChimeraX session 
    14133 
    14134 > show #!1 models
    14135 
    14136 > hide #34 models
    14137 
    14138 > setattr #1 res bfactor 1 create true
    14139 
    14140 Assigning bfactor attribute to 611 items 
    14141 
    14142 > setattr #1 res bfactor 0 create true
    14143 
    14144 Assigning bfactor attribute to 611 items 
    14145 
    14146 > setattr #1/A:1-10 res bfactor 1 create true
    14147 
    14148 Assigning bfactor attribute to 7 items 
    14149 
    14150 > worm bfactor #1/A:1-10 min:0.3 max:3
    14151 
    14152 609 residues, residue bfactor range 43.1 to 220 
    14153 
    14154 > worm bfactor #1/A:1-10 min:0.15 max:3
    14155 
    14156 609 residues, residue bfactor range 43.1 to 220 
    14157 
    14158 > setattr #1 res thick_rad 0 create true
    14159 
    14160 Assigning thick_rad attribute to 611 items 
    14161 
    14162 > setattr #1/A:1-10 res thick_rad 1
    14163 
    14164 Assigning thick_rad attribute to 7 items 
    14165 
    14166 > worm thick_rad #1/A:1-10 min:0.15 max:3
    14167 
    14168 609 residues, residue thick_rad range 0 to 1 
    14169 
    14170 > worm thick_rad #1/A:1-10 min:0.15 max:1
    14171 
    14172 609 residues, residue thick_rad range 0 to 1 
    14173 
    14174 > ~worm
    14175 
    14176 > show #34 models
    14177 
    14178 > setattr #34 res thick_rad 0 create true
    14179 
    14180 Assigning thick_rad attribute to 611 items 
    14181 
    14182 > setattr #34/A:1-10 res thick_rad 1
    14183 
    14184 Assigning thick_rad attribute to 7 items 
    14185 
    14186 > worm thick_rad #34 min:0.15 max:1
    14187 
    14188 609 residues, residue thick_rad range 0 to 1 
    14189 
    14190 > show #34/A:1-11 target c
    14191 
    14192 > view list
    14193 
    14194 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    14195 dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
    14196 dimer_view-all_front, mono_back, mono_back_, mono_front, pH-sensing 
    14197 
    14198 > view mono_back_
    14199 
    14200 > setattr #34/A:10 res thick_rad 0
    14201 
    14202 Assigning thick_rad attribute to 1 item 
    14203 
    14204 > worm thick_rad #34 min:0.15 max:1
    14205 
    14206 609 residues, residue thick_rad range 0 to 1 
    14207 
    14208 > hide #34 models
    14209 
    14210 > show #34 models
    14211 
    14212 > hide #34 models
    14213 
    14214 > show #34 models
    14215 
    14216 > setattr #34/A:4,10 res thick_rad 0
    14217 
    14218 Assigning thick_rad attribute to 2 items 
    14219 
    14220 > worm thick_rad #34 min:0.15 max:1
    14221 
    14222 609 residues, residue thick_rad range 0 to 1 
    14223 
    14224 > setattr #34/A:1-4,10 res thick_rad 0
    14225 
    14226 Assigning thick_rad attribute to 2 items 
    14227 
    14228 > worm thick_rad #34 min:0.15 max:1
    14229 
    14230 609 residues, residue thick_rad range 0 to 1 
    14231 
    14232 > hide #!1 models
    14233 
    14234 > show #!1 models
    14235 
    14236 > hide #!1 models
    14237 
    14238 > show #!1 models
    14239 
    14240 > hide #!1 models
    14241 
    14242 > show #!1 models
    14243 
    14244 > setattr #34/A:1-10 res thick_rad 1
    14245 
    14246 Assigning thick_rad attribute to 7 items 
    14247 
    14248 > worm thick_rad #34 min:0.15 max:1
    14249 
    14250 609 residues, residue thick_rad range 0 to 1 
    14251 
    14252 > setattr #34/A:1-10 res thick_rad 1
    14253 
    14254 Assigning thick_rad attribute to 7 items 
    14255 
    14256 > worm thick_rad #34 min:0.15 max:1
    14257 
    14258 609 residues, residue thick_rad range 0 to 1 
    14259 
    14260 > hide #!1 models
    14261 
    14262 > show #!1 models
    14263 
    14264 > hide #!1 models
    14265 
    14266 > show #!1 models
    14267 
    14268 > hide #!1 models
    14269 
    14270 > show #!1 models
    14271 
    14272 > worm thick_rad #34 min:0.15 max:1.5
    14273 
    14274 609 residues, residue thick_rad range 0 to 1 
    14275 
    14276 > view mono_back_
    14277 
    14278 > worm thick_rad #34 min:0.15 max:1.2
    14279 
    14280 609 residues, residue thick_rad range 0 to 1 
    14281 
    14282 > worm thick_rad #34 min:0.15 max:1.
    14283 
    14284 609 residues, residue thick_rad range 0 to 1 
    14285 
    14286 > hide #!1 models
    14287 
    14288 > hide #34 models
    14289 
    14290 > show #!5 models
    14291 
    14292 > setattr #29.1/A:1-10 res thick_rad 1 create true
    14293 
    14294 Assigning thick_rad attribute to 7 items 
    14295 
    14296 > show #!29 models
    14297 
    14298 > worm thick_rad #29.1 min:0.15 max:1.
    14299 
    14300 7 residues, residue thick_rad range 1 to 1 
    14301 
    14302 > worm thick_rad #29 min:0.15 max:1.
    14303 
    14304 385 residues, residue thick_rad range 1 to 1 
    14305 
    14306 > setattr #29 res thick_rad 0 create true
    14307 
    14308 Assigning thick_rad attribute to 387 items 
    14309 
    14310 > setattr #29/A:1-10 res thick_rad 1 create true
    14311 
    14312 Assigning thick_rad attribute to 7 items 
    14313 
    14314 > worm thick_rad #29 min:0.15 max:1.
    14315 
    14316 385 residues, residue thick_rad range 0 to 1 
    14317 
    14318 > combine #5
    14319 
    14320 > hide #!29 models
    14321 
    14322 > hide #35 target c
    14323 
    14324 > show #35/A:1-10 target c
    14325 
    14326 > setattr #35 res thick_rad 0 create true
    14327 
    14328 Assigning thick_rad attribute to 614 items 
    14329 
    14330 > setattr #35/A:1-10 res thick_rad 1 create true
    14331 
    14332 Assigning thick_rad attribute to 10 items 
    14333 
    14334 > worm thick_rad #35 min:0.15 max:1.
    14335 
    14336 612 residues, residue thick_rad range 0 to 1 
    14337 
    14338 > show #35/A:1-11 target c
    14339 
    14340 > view mono_back_
    14341 
    14342 > color #35/A:1-10 medium purple
    14343 
    14344 > setattr #35/A:1 res thick_rad 0 create true
    14345 
    14346 Assigning thick_rad attribute to 1 item 
    14347 
    14348 > worm thick_rad #35 min:0.15 max:1.
    14349 
    14350 612 residues, residue thick_rad range 0 to 1 
    14351 
    14352 > setattr #35/A:1 res thick_rad 0.5 create true
    14353 
    14354 Assigning thick_rad attribute to 1 item 
    14355 
    14356 > worm thick_rad #35 min:0.15 max:1.
    14357 
    14358 612 residues, residue thick_rad range 0 to 1 
    14359 
    14360 > setattr #35/A:1 res thick_rad 0.1 create true
    14361 
    14362 Assigning thick_rad attribute to 1 item 
    14363 
    14364 > worm thick_rad #35 min:0.15 max:1.
    14365 
    14366 612 residues, residue thick_rad range 0 to 1 
    14367 
    14368 > hide #5/A:1-10 target c
    14369 
    14370 > setattr #35/A:1 res thick_rad 0.2 create true
    14371 
    14372 Assigning thick_rad attribute to 1 item 
    14373 
    14374 > worm thick_rad #35 min:0.15 max:1.
    14375 
    14376 612 residues, residue thick_rad range 0 to 1 
    14377 
    14378 > view mono_back_
    14379 
    14380 > worm thick_rad #35 min:0.5 max:1.
    14381 
    14382 612 residues, residue thick_rad range 0 to 1 
    14383 
    14384 > worm thick_rad #35 min:0.15 max:1.
    14385 
    14386 612 residues, residue thick_rad range 0 to 1 
    14387 
    14388 > setattr #35/A:1 res thick_rad 0.2 create true
    14389 
    14390 Assigning thick_rad attribute to 1 item 
    14391 
    14392 > worm thick_rad #35 min:0.15 max:1.
    14393 
    14394 612 residues, residue thick_rad range 0 to 1 
    14395 
    14396 > setattr #35/A:1 res thick_rad 0.1 create true
    14397 
    14398 Assigning thick_rad attribute to 1 item 
    14399 
    14400 > worm thick_rad #35 min:0.15 max:1.
    14401 
    14402 612 residues, residue thick_rad range 0 to 1 
    14403 
    14404 > setattr #35/A:1 res thick_rad 0.5 create true
    14405 
    14406 Assigning thick_rad attribute to 1 item 
    14407 
    14408 > worm thick_rad #35 min:0.15 max:1.
    14409 
    14410 612 residues, residue thick_rad range 0 to 1 
    14411 
    14412 > save test.png supersample 3 transparentBackground true
    14413 
    14414 > hide #!5 models
    14415 
    14416 > show #!1 models
    14417 
    14418 > hide #35 models
    14419 
    14420 > show #34 models
    14421 
    14422 > setattr #34/A:1-4 res thick_rad 0.5 create true
    14423 
    14424 Assigning thick_rad attribute to 1 item 
    14425 
    14426 > worm thick_rad #34 min:0.15 max:1.
    14427 
    14428 609 residues, residue thick_rad range 0 to 1 
    14429 
    14430 > save test.png supersample 3 transparentBackground true
    14431 
    14432 > hide #34 models
    14433 
    14434 > hide #!29.1 models
    14435 
    14436 > hide #!1 models
    14437 
    14438 > show #!15 models
    14439 
    14440 > combine #15
    14441 
    14442 > hide #36 target c
    14443 
    14444 > show #36/A:1-11 target c
    14445 
    14446 > setattr #36 res thick_rad 0 create true
    14447 
    14448 Assigning thick_rad attribute to 616 items 
    14449 
    14450 > setattr #36 res thick_rad 0 create true
    14451 
    14452 Assigning thick_rad attribute to 616 items 
    14453 
    14454 > setattr #36/A:1 res thick_rad 0.5
    14455 
    14456 Assigning thick_rad attribute to 1 item 
    14457 
    14458 > setattr #36/A:2-10 res thick_rad 1
    14459 
    14460 Assigning thick_rad attribute to 9 items 
    14461 
    14462 > worm thick_rad #36 min:0.15 max:1.
    14463 
    14464 612 residues, residue thick_rad range 0 to 1 
    14465 
    14466 > color #36/A:1-10 medium purple
    14467 
    14468 > save test.png supersample 3 transparentBackground true
    14469 
    14470 > hide #36 models
    14471 
    14472 > hide #!15 models
    14473 
    14474 > show #!17 models
    14475 
    14476 > combine #17
    14477 
    14478 > setattr #37 res thick_rad 0 create true
    14479 
    14480 Assigning thick_rad attribute to 617 items 
    14481 
    14482 > setattr #37/A:1 res thick_rad 0.5
    14483 
    14484 Assigning thick_rad attribute to 1 item 
    14485 
    14486 > setattr #37/A:2-10 res thick_rad 1
    14487 
    14488 Assigning thick_rad attribute to 9 items 
    14489 
    14490 > hide #37 target c
    14491 
    14492 > show #37/A:1-11 target c
    14493 
    14494 > worm thick_rad #37 min:0.15 max:1.
    14495 
    14496 612 residues, residue thick_rad range 0 to 1 
    14497 
    14498 > color #37/A:1-10 medium purple
    14499 
    14500 > save test.png supersample 3 transparentBackground true
    14501 
    14502 > cartoon style barScale 0.6
    14503 
    14504 > cartoon style barScale 0.8
    14505 
    14506 > cartoon style barScale 0.3
    14507 
    14508 > cartoon style barScale 0.5
    14509 
    14510 > cartoon style thickness 0.5
    14511 
    14512 > cartoon style thickness 0.3
    14513 
    14514 > cartoon style thickness 0.4
    14515 
    14516 > cartoon style thickness 0.3
    14517 
    14518 > hide #37 models
    14519 
    14520 > show #!1 models
    14521 
    14522 > hide #!17 models
    14523 
    14524 > view mono_back_
    14525 
    14526 > color #1/A:1-10 medium purple
    14527 
    14528 > show #1/A:1-10 target a
    14529 
    14530 > size stickRadius 0.5
    14531 
    14532 Changed 104582 bond radii 
    14533 
    14534 > size stickRadius 0.4
    14535 
    14536 Changed 104582 bond radii 
    14537 
    14538 > save test.png supersample 3 transparentBackground true
    14539 
    14540 > size stickRadius 0.5
    14541 
    14542 Changed 104582 bond radii 
    14543 
    14544 > save test.png supersample 3 transparentBackground true
    14545 
    14546 > show #34 models
    14547 
    14548 > hide #34 models
    14549 
    14550 > select ~sel & ##selected
    14551 
    14552 Nothing selected 
    14553 
    14554 > size stickRadius 0.3
    14555 
    14556 Changed 104582 bond radii 
    14557 
    14558 > hide #1/A:1-10 target a
    14559 
    14560 > show #29.1.1 models
    14561 
    14562 > transparency #29.1 30 target s
    14563 
    14564 > hide #29.1 30 tar c
    14565 
    14566 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    14567 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    14568 
    14569 > hide #29.1 target c
    14570 
    14571 > size atomRadius -1
    14572 
    14573 Cannot reduce atom radius to  size atomRadius -0.5
    14574 
    14575 Changed 102380 atom radii 
    14576 
    14577 > size atomRadius default
    14578 
    14579 Changed 102380 atom radii 
    14580 
    14581 > size atomRadius -0.5
    14582 
    14583 Changed 102380 atom radii 
    14584 
    14585 > close #29.1.1
    14586 
    14587 > show #29.1 target s
    14588 
    14589 > size atomRadius default
    14590 
    14591 Changed 102380 atom radii 
    14592 
    14593 > transparency #29.1 30 target s
    14594 
    14595 > hide #29.1.1 models
    14596 
    14597 > hide #!29 models
    14598 
    14599 > show #!3 models
    14600 
    14601 > hide #!1 models
    14602 
    14603 > show #!4 models
    14604 
    14605 > show #!3 atoms
    14606 
    14607 > hide #!3 atoms
    14608 
    14609 > show #!7 models
    14610 
    14611 > hide #!7 models
    14612 
    14613 > view mono_back_
    14614 
    14615 > hide #!4 models
    14616 
    14617 > show #!7 models
    14618 
    14619 > hide #!7 models
    14620 
    14621 > show #!4 models
    14622 
    14623 > show #!3 atoms
    14624 
    14625 > show #!8 models
    14626 
    14627 > hide #!4 models
    14628 
    14629 > hide #!3 models
    14630 
    14631 > show #!7 models
    14632 
    14633 > hide #!7 models
    14634 
    14635 > show #!3 models
    14636 
    14637 > hide #!3 models
    14638 
    14639 > show #!3 models
    14640 
    14641 > show #!7 models
    14642 
    14643 > hide #!7 models
    14644 
    14645 > show #!7 models
    14646 
    14647 > hide #!7 models
    14648 
    14649 > show #!4 models
    14650 
    14651 > hide #!8 models
    14652 
    14653 > view mono_back_
    14654 
    14655 > hide #!4 models
    14656 
    14657 > hide #!3 atoms
    14658 
    14659 > hide #3/A:1-3
    14660 
    14661 > hide #3/A:1-3 target c
    14662 
    14663 > combine #3
    14664 
    14665 > name cwm #38
    14666 
    14667 > hide ~cwm/A:1-10 tar c;setattr cwm res thick_rad 0 create 1;setattr
    14668 > cwm/A:1-4 res thick_rad 0.5;setattr cwm/A:5-10 res thick_rad 1;worm
    14669 > thick_rad cwm min:0.15 max:1.
    14670 
    14671 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    14672 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    14673 
    14674 > name cwm #38
    14675 
    14676 > hide ~(cwm/A:1-10) tar c;setattr cwm res thick_rad 0 create 1;setattr
    14677 > cwm/A:1-4 res thick_rad 0.5;setattr cwm/A:5-10 res thick_rad 1;worm
    14678 > thick_rad cwm min:0.15 max:1.
    14679 
    14680 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    14681 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    14682 
    14683 > name cwm #38
    14684 
    14685 > hide ~ (cwm/A:1-10) tar c;setattr cwm res thick_rad 0 create 1;setattr
    14686 > cwm/A:1-4 res thick_rad 0.5;setattr cwm/A:5-10 res thick_rad 1;worm
    14687 > thick_rad cwm min:0.15 max:1.
    14688 
    14689 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    14690 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    14691 
    14692 > name cwm #38
    14693 
    14694 > hide cwm&(~/A:1-10) target c
    14695 
    14696 > setattr cwm res thick_rad 0 create true
    14697 
    14698 Assigning thick_rad attribute to 614 items 
    14699 
    14700 > setattr cwm/A:1-4 res thick_rad 0.5;setattr cwm/A:5-10 res thick_rad 1;worm
    14701 > thick_rad cwm min:0.15 max:1.
    14702 
    14703 Expected a keyword 
    14704 
    14705 > setattr cwm/A:1-4 res thick_rad 0.5;
    14706 
    14707 Expected a keyword 
    14708 
    14709 > setattr cwm/A:1-4 res thick_rad 0.5 create 1;
    14710 
    14711 Expected a keyword 
    14712 
    14713 > setattr cwm/A:1-4 res thick_rad 0
    14714 
    14715 Expected a keyword 
    14716 
    14717 > setattr cwm res thick_rad 0
    14718 
    14719 Assigning thick_rad attribute to 614 items 
    14720 
    14721 > name cwm #38
    14722 
    14723 > hide cwm&~/A:1-10 target c
    14724 
    14725 > setattr cwm res thick_rad 0 create true
    14726 
    14727 Assigning thick_rad attribute to 614 items 
    14728 
    14729 > setattr cwm&/A:1-4 res thick_rad 0.5
    14730 
    14731 Assigning thick_rad attribute to 4 items 
    14732 
    14733 > setattr cwm&/A:5-10 res thick_rad 1
    14734 
    14735 Assigning thick_rad attribute to 6 items 
    14736 
    14737 > worm thick_rad cwm min:0.15 max:1.
    14738 
    14739 612 residues, residue thick_rad range 0 to 1 
    14740 
    14741 > show cwm&/A:11 target c
    14742 
    14743 > name cwm #38
    14744 
    14745 > hide cwm&~/A:1-11 target c
    14746 
    14747 > setattr cwm res thick_rad 0 create true
    14748 
    14749 Assigning thick_rad attribute to 614 items 
    14750 
    14751 > setattr cwm&/A:1-4 res thick_rad 0.2
    14752 
    14753 Assigning thick_rad attribute to 4 items 
    14754 
    14755 > setattr cwm&/A:5-10 res thick_rad 1
    14756 
    14757 Assigning thick_rad attribute to 6 items 
    14758 
    14759 > worm thick_rad cwm min:0.15 max:1.
    14760 
    14761 612 residues, residue thick_rad range 0 to 1 
    14762 
    14763 > name cwm #38
    14764 
    14765 > hide cwm&~/A:1-11 target c
    14766 
    14767 > setattr cwm res thick_rad 0 create true
    14768 
    14769 Assigning thick_rad attribute to 614 items 
    14770 
    14771 > setattr cwm&/A:1-4 res thick_rad 0.3
    14772 
    14773 Assigning thick_rad attribute to 4 items 
    14774 
    14775 > setattr cwm&/A:5-10 res thick_rad 1
    14776 
    14777 Assigning thick_rad attribute to 6 items 
    14778 
    14779 > worm thick_rad cwm min:0.15 max:1.
    14780 
    14781 612 residues, residue thick_rad range 0 to 1 
    14782 
    14783 > name cwm #38
    14784 
    14785 > hide cwm&~/A:1-11 target c
    14786 
    14787 > setattr cwm res thick_rad 0 create true
    14788 
    14789 Assigning thick_rad attribute to 614 items 
    14790 
    14791 > setattr cwm&/A:1-4 res thick_rad 0.5
    14792 
    14793 Assigning thick_rad attribute to 4 items 
    14794 
    14795 > setattr cwm&/A:5-10 res thick_rad 1
    14796 
    14797 Assigning thick_rad attribute to 6 items 
    14798 
    14799 > worm thick_rad cwm min:0.15 max:1.
    14800 
    14801 612 residues, residue thick_rad range 0 to 1 
    14802 
    14803 > view list
    14804 
    14805 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    14806 dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
    14807 dimer_view-all_front, mono_back, mono_back_, mono_front, pH-sensing 
    14808 
    14809 > view mono_back_
    14810 
    14811 > save NhaA-K-pH63-plugged_back_worm.png supersample 3 transparentBackground
    14812 > true
    14813 
    14814 > name cwm #38
    14815 
    14816 > color cwm&/A:1-10 premium purp tar c;hid cwm&~/A:1-11 tar c;setattr cwm res
    14817 > thick_rad 0 create 1;setattr cwm&/A:1-4 res thick_rad 0.5;setattr
    14818 > cwm&/A:5-10 res thick_rad 1;worm thick_rad cwm min:0.15 max:1.
    14819 
    14820 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    14821 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    14822 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    14823 
    14824 > name cwm #38
    14825 
    14826 > color cwm&/A:1-10 memium purp tar c;hid cwm&~/A:1-11 tar c;setattr cwm res
    14827 > thick_rad 0 create 1;setattr cwm&/A:1-4 res thick_rad 0.5;setattr
    14828 > cwm&/A:5-10 res thick_rad 1;worm thick_rad cwm min:0.15 max:1.
    14829 
    14830 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    14831 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    14832 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    14833 
    14834 > name cwm #38
    14835 
    14836 > color cwm&/A:1-10 medium purple target c
    14837 
    14838 > hide cwm&~/A:1-11 target c
    14839 
    14840 > setattr cwm res thick_rad 0 create true
    14841 
    14842 Assigning thick_rad attribute to 614 items 
    14843 
    14844 > setattr cwm&/A:1-4 res thick_rad 0.5
    14845 
    14846 Assigning thick_rad attribute to 4 items 
    14847 
    14848 > setattr cwm&/A:5-10 res thick_rad 1
    14849 
    14850 Assigning thick_rad attribute to 6 items 
    14851 
    14852 > worm thick_rad cwm min:0.15 max:1.
    14853 
    14854 612 residues, residue thick_rad range 0 to 1 
    14855 
    14856 > save NhaA-K-pH63-plugged_back_worm.png supersample 3 transparentBackground
    14857 > true
    14858 
    14859 > hide #!3 models
    14860 
    14861 > show #!7 models
    14862 
    14863 > hide #38 models
    14864 
    14865 > combine #7
    14866 
    14867 > name cwm #39
    14868 
    14869 > color cwm&/A:1-10 medium purple target c
    14870 
    14871 > hide cwm&~/A:1-11 target c
    14872 
    14873 > setattr cwm res thick_rad 0 create true
    14874 
    14875 Assigning thick_rad attribute to 614 items 
    14876 
    14877 > setattr cwm&/A:1-4 res thick_rad 0.5
    14878 
    14879 Assigning thick_rad attribute to 4 items 
    14880 
    14881 > setattr cwm&/A:5-10 res thick_rad 1
    14882 
    14883 Assigning thick_rad attribute to 6 items 
    14884 
    14885 > worm thick_rad cwm min:0.15 max:1.
    14886 
    14887 612 residues, residue thick_rad range 0 to 1 
    14888 
    14889 > name cwm #39
    14890 
    14891 > color cwm&/A:1-10 medium purple target c
    14892 
    14893 > hide cwm&~/A:1-11 target c
    14894 
    14895 > setattr cwm res thick_rad 0 create true
    14896 
    14897 Assigning thick_rad attribute to 614 items 
    14898 
    14899 > setattr cwm&/A:1 res thick_rad 0.5
    14900 
    14901 Assigning thick_rad attribute to 1 item 
    14902 
    14903 > setattr cwm&/A:2-10 res thick_rad 1
    14904 
    14905 Assigning thick_rad attribute to 9 items 
    14906 
    14907 > worm thick_rad cwm min:0.15 max:1.
    14908 
    14909 612 residues, residue thick_rad range 0 to 1 
    14910 
    14911 > name cwm #39
    14912 
    14913 > color cwm&/A:1-10 medium purple target c
    14914 
    14915 > hide cwm&~/A:1-11 target c
    14916 
    14917 > setattr cwm res thick_rad 0 create true
    14918 
    14919 Assigning thick_rad attribute to 614 items 
    14920 
    14921 > setattr cwm&/A:1-2 res thick_rad 0.5
    14922 
    14923 Assigning thick_rad attribute to 2 items 
    14924 
    14925 > setattr cwm&/A:3-10 res thick_rad 1
    14926 
    14927 Assigning thick_rad attribute to 8 items 
    14928 
    14929 > worm thick_rad cwm min:0.15 max:1.
    14930 
    14931 612 residues, residue thick_rad range 0 to 1 
    14932 
    14933 > name cwm #39
    14934 
    14935 > color cwm&/A:1-10 medium purple target c
    14936 
    14937 > hide cwm&~/A:1-11 target c
    14938 
    14939 > setattr cwm res thick_rad 0 create true
    14940 
    14941 Assigning thick_rad attribute to 614 items 
    14942 
    14943 > setattr cwm&/A:1-3 res thick_rad 0.5
    14944 
    14945 Assigning thick_rad attribute to 3 items 
    14946 
    14947 > setattr cwm&/A:4-10 res thick_rad 1
    14948 
    14949 Assigning thick_rad attribute to 7 items 
    14950 
    14951 > worm thick_rad cwm min:0.15 max:1.
    14952 
    14953 612 residues, residue thick_rad range 0 to 1 
    14954 
    14955 > save NhaA-K-pH75-plugged_back_worm.png supersample 3 transparentBackground
    14956 > true
    14957 
    14958 > hide #39 models
    14959 
    14960 > hide #!7 models
    14961 
    14962 > show #!11 models
    14963 
    14964 > combine #11
    14965 
    14966 > name cwm #40
    14967 
    14968 > color cwm&/A:1-10 medium purple target c
    14969 
    14970 > hide cwm&~/A:1-11 target c
    14971 
    14972 > setattr cwm res thick_rad 0 create true
    14973 
    14974 Assigning thick_rad attribute to 608 items 
    14975 
    14976 > setattr cwm&/A:1-3 res thick_rad 0.5
    14977 
    14978 Assigning thick_rad attribute to 0 items 
    14979 
    14980 > setattr cwm&/A:4-10 res thick_rad 1
    14981 
    14982 Assigning thick_rad attribute to 4 items 
    14983 
    14984 > worm thick_rad cwm min:0.15 max:1.
    14985 
    14986 606 residues, residue thick_rad range 0 to 1 
    14987 
    14988 > save NhaA-K-pH85-plugged_back_worm.png supersample 3 transparentBackground
    14989 > true
    14990 
    14991 > hide #40 models
    14992 
    14993 > hide #!11 models
    14994 
    14995 > show #!9 models
    14996 
    14997 > combine #9
    14998 
    14999 > name cwm #41
    15000 
    15001 > color cwm&/A:1-10 medium purple target c
    15002 
    15003 > hide cwm&~/A:1-11 target c
    15004 
    15005 > setattr cwm res thick_rad 0 create true
    15006 
    15007 Assigning thick_rad attribute to 614 items 
    15008 
    15009 > setattr cwm&/A:1-3 res thick_rad 0.5
    15010 
    15011 Assigning thick_rad attribute to 3 items 
    15012 
    15013 > setattr cwm&/A:4-10 res thick_rad 1
    15014 
    15015 Assigning thick_rad attribute to 7 items 
    15016 
    15017 > worm thick_rad cwm min:0.15 max:1.
    15018 
    15019 612 residues, residue thick_rad range 0 to 1 
    15020 
    15021 > name cwm #41
    15022 
    15023 > color cwm&/A:1-10 medium purple target c
    15024 
    15025 > hide cwm&~/A:1-11 target c
    15026 
    15027 > setattr cwm res thick_rad 0 create true
    15028 
    15029 Assigning thick_rad attribute to 614 items 
    15030 
    15031 > setattr cwm&/A:1-2 res thick_rad 0.5
    15032 
    15033 Assigning thick_rad attribute to 2 items 
    15034 
    15035 > setattr cwm&/A:3-10 res thick_rad 1
    15036 
    15037 Assigning thick_rad attribute to 8 items 
    15038 
    15039 > worm thick_rad cwm min:0.15 max:1.
    15040 
    15041 612 residues, residue thick_rad range 0 to 1 
    15042 
    15043 > name cwm #41
    15044 
    15045 > color cwm&/A:1-10 medium purple target c
    15046 
    15047 > hide cwm&~/A:1-11 target c
    15048 
    15049 > setattr cwm res thick_rad 0 create true
    15050 
    15051 Assigning thick_rad attribute to 614 items 
    15052 
    15053 > setattr cwm&/A:1-1 res thick_rad 0.5
    15054 
    15055 Assigning thick_rad attribute to 1 item 
    15056 
    15057 > setattr cwm&/A:2-10 res thick_rad 1
    15058 
    15059 Assigning thick_rad attribute to 9 items 
    15060 
    15061 > worm thick_rad cwm min:0.15 max:1.
    15062 
    15063 612 residues, residue thick_rad range 0 to 1 
    15064 
    15065 > save NhaA-K-pH75-unplugged_back_worm.png supersample 3 transparentBackground
    15066 > true
    15067 
    15068 > hide #!9 models
    15069 
    15070 > show #!13 models
    15071 
    15072 > hide #41 models
    15073 
    15074 > combine #13
    15075 
    15076 > name cwm #42
    15077 
    15078 > color cwm&/A:1-10 medium purple target c
    15079 
    15080 > hide cwm&~/A:1-11 target c
    15081 
    15082 > setattr cwm res thick_rad 0 create true
    15083 
    15084 Assigning thick_rad attribute to 614 items 
    15085 
    15086 > setattr cwm&/A:1-1 res thick_rad 0.5
    15087 
    15088 Assigning thick_rad attribute to 1 item 
    15089 
    15090 > setattr cwm&/A:2-10 res thick_rad 1
    15091 
    15092 Assigning thick_rad attribute to 9 items 
    15093 
    15094 > worm thick_rad cwm min:0.15 max:1.
    15095 
    15096 612 residues, residue thick_rad range 0 to 1 
    15097 
    15098 > save NhaA-K-pH85-unplugged_back_worm.png supersample 3 transparentBackground
    15099 > true
    15100 
    15101 > hide #42 models
    15102 
    15103 > show #!15 models
    15104 
    15105 > hide #!13 models
    15106 
    15107 > show #15:NA target a
    15108 
    15109 > hide #!15 models
    15110 
    15111 > show #!17 models
    15112 
    15113 > show #17:NA target a
    15114 
    15115 > style :NA sphere
    15116 
    15117 Changed 3 atom styles 
    15118 
    15119 > view mono_back_
    15120 
    15121 > show #37 models
    15122 
    15123 > hide #37 models
    15124 
    15125 > show #37 models
    15126 
    15127 > transparency #17,37 100 target c
    15128 
    15129 > transparency #17:NA 1 target a
    15130 
    15131 > graphics silhouettes false
    15132 
    15133 > graphics silhouettes true
    15134 
    15135 > graphics silhouettes false
    15136 
    15137 > graphics silhouettes true
    15138 
    15139 > graphics silhouettes false
    15140 
    15141 > graphics silhouettes true
    15142 
    15143 > graphics silhouettes false
    15144 
    15145 > select #17/A:505@NA
    15146 
    15147 1 atom, 1 residue, 1 model selected 
    15148 
    15149 > select #17/A:505@NA
    15150 
    15151 1 atom, 1 residue, 1 model selected 
    15152 
    15153 > select #17/A:98
    15154 
    15155 7 atoms, 6 bonds, 1 residue, 1 model selected 
    15156 
    15157 > select clear
    15158 
    15159 > graphics silhouettes true
    15160 
    15161 > save NhaA-Na-pH85_back_worm_Na.png supersample 3 transparentBackground true
    15162 
    15163 > transparency #17:NA 0 target a
    15164 
    15165 > transparency #17,37 0 target c
    15166 
    15167 > hide #37 models
    15168 
    15169 > hide #!17 models
    15170 
    15171 > show #!19 models
    15172 
    15173 > view dimer_view-all_front
    15174 
    15175 > show #19 target c
    15176 
    15177 > hide #!19 atoms
    15178 
    15179 > color #19/A,D:86-180,275-388 forest green
    15180 
    15181 > color #19/A,D:11-85,181-274 pale green
    15182 
    15183 > hide #19/A,D:1-10 target c
    15184 
    15185 > save /Users/tsweng/Desktop/image192.png supersample 3
    15186 
    15187 > save NhaA-K-pH75_consensus_front_2.png supersample 3 transparentBackground
    15188 > true
    15189 
    15190 > show :CDL,PTY target a
    15191 
    15192 > save NhaA-K-pH75_consensus_front_2_PTY.png supersample 3
    15193 > transparentBackground true
    15194 
    15195 > hide :CDL,PTY
    15196 
    15197 > show #!31 models
    15198 
    15199 > hide #31 target ac
    15200 
    15201 > show #31:CDL,PGT target a
    15202 
    15203 > hide #31:CDL target a
    15204 
    15205 > show #19:CDL target a
    15206 
    15207 > save NhaA-K-pH75_consensus_front_2_PGT.png supersample 3
    15208 > transparentBackground true
    15209 
    15210 > hide #!31 models
    15211 
    15212 > hide #!19 models
    15213 
    15214 > show #!7 models
    15215 
    15216 > hide #!7 models
    15217 
    15218 > show #!7 models
    15219 
    15220 > show #39 models
    15221 
    15222 > view N-term_density_top
    15223 
    15224 > view mono_back_
    15225 
    15226 > turn x 90
    15227 
    15228 > ui tool show "Side View"
    15229 
    15230 > select #7/A:48
    15231 
    15232 8 atoms, 7 bonds, 1 residue, 1 model selected 
    15233 
    15234 > select up
    15235 
    15236 49 atoms, 49 bonds, 6 residues, 2 models selected 
    15237 
    15238 > select up
    15239 
    15240 2918 atoms, 2982 bonds, 388 residues, 2 models selected 
    15241 
    15242 > select clear
    15243 
    15244 > save NhaA-K-pH75_plugged_top.png supersample 3 transparentBackground true
    15245 
    15246 > hide #39 models
    15247 
    15248 > show #41 models
    15249 
    15250 > hide #!7 models
    15251 
    15252 > show #!9 models
    15253 
    15254 > save NhaA-K-pH75_unplugged_top.png supersample 3 transparentBackground true
    15255 
    15256 > select #41/A:6
    15257 
    15258 11 atoms, 10 bonds, 1 residue, 1 model selected 
    15259 
    15260 > select #41/A:6
    15261 
    15262 11 atoms, 10 bonds, 1 residue, 1 model selected 
    15263 
    15264 > select clear
    15265 
    15266 > hide #!9 models
    15267 
    15268 > show #!9 models
    15269 
    15270 > hide #41 models
    15271 
    15272 > color /A:1-10 medium purple target c
    15273 
    15274 > show #!7 models
    15275 
    15276 > hide #!7 models
    15277 
    15278 > show #!5 models
    15279 
    15280 > show #!13 models
    15281 
    15282 > show #!15 models
    15283 
    15284 > ui mousemode right zoom
    15285 
    15286 > ui mousemode right translate
    15287 
    15288 > ui mousemode right zoom
    15289 
    15290 > ui mousemode right translate
    15291 
    15292 > save
    15293 > /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA2.cxs
    15294 
    15295 > color #5&core dark orange
    15296 
    15297 > color #9&core orange
    15298 
    15299 > color #13&core gold
    15300 
    15301 > color #13&core dark orange
    15302 
    15303 > color #9&core orange
    15304 
    15305 > color #5&core gold
    15306 
    15307 > cartoon style modeHelix default width 1.0 thickness 0.3
    15308 
    15309 > cartoon style modeHelix default width 1.8 thickness 0.3
    15310 
    15311 > cartoon style modeHelix default width 1.6 thickness 0.3
    15312 
    15313 > color #13 dark orange
    15314 
    15315 > color #9 orange
    15316 
    15317 > color #5 gold
    15318 
    15319 > view mono_back_
    15320 
    15321 > cartoon style modeHelix tube radius 1.8 sides 24
    15322 
    15323 > color #15 deep skyblue bluie;
    15324 
    15325 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    15326 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    15327 
    15328 > color #15 deep sky blue
    15329 
    15330 > lighting soft
    15331 
    15332 > lighting full
    15333 
    15334 > lighting shadows false
    15335 
    15336 > lighting simple
    15337 
    15338 > lighting full
    15339 
    15340 > lighting shadows false
    15341 
    15342 > lighting full multiShadow 1024
    15343 
    15344 > lighting shadows false
    15345 
    15346 > lighting full multiShadow 1024 shadows false
    15347 
    15348 > cartoon style modeHelix tube radius 1.6 sides 24
    15349 
    15350 > cartoon style modeHelix tube radius 1.4 sides 24
    15351 
    15352 > cartoon style modeHelix default width 1.8 thickness 0.3
    15353 
    15354 > cartoon style modeHelix tube radius 1.4 sides 24
    15355 
    15356 > graphics silhouettes false
    15357 
    15358 > graphics silhouettes true
    15359 
    15360 > save NhaA-pH-superpose_back.png supersample 3 transparentBackground true
    15361 
    15362 > color #5,9,13&dimer_TM snow transparency 50 target c
    15363 
    15364 > color #5,9,13,15&dimer_TM snow transparency 50 target c
    15365 
    15366 > color #5,9,13,15&(dimer&~/A:35-58) snow transparency 50 target c
    15367 
    15368 > view list
    15369 
    15370 Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
    15371 dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
    15372 dimer_view-all_front, mono_back, mono_back_, mono_front, pH-sensing 
    15373 
    15374 > view mono_back_
    15375 
    15376 > transparency 1 target c
    15377 
    15378 > color #5,9,13,15&(dimer&~/A:35-58) snow transparency 50 target c
    15379 
    15380 > save NhaA-pH-superpose_back_tra.png supersample 3 transparentBackground true
    15381 
    15382 > color #5,9,13,15&(dimer&~/A:35-58) snow transparency 20 target c
    15383 
    15384 > save NhaA-pH-superpose_back_tra.png supersample 3 transparentBackground true
    15385 
    15386 > transparency 0 target c
    15387 
    15388 > color #5&core dark orange
    15389 
    15390 > color #9&core orange
    15391 
    15392 > color #13&core gold
    15393 
    15394 > color #15 deep sky blue
    15395 
    15396 > color #5 dark orange
    15397 
    15398 > color #9 orange
    15399 
    15400 > color #13 gold
    15401 
    15402 > color #15 deep sky blue
    15403 
    15404 > turn x 90
    15405 
    15406 > turn x -5
    15407 
    15408 > cartoon style modeHelix default width 1.0 thickness 0.3 xsection oval
    15409 
    15410 > color #13 dark orange
    15411 
    15412 > color #9 orange
    15413 
    15414 > color #5 gold
    15415 
    15416 > color #15 deep sky blue
    15417 
    15418 > cartoon style strand xsection rectangle
    15419 
    15420 > ui mousemode right zoom
    15421 
    15422 > view mono_back_
    15423 
    15424 > show #5/A:1-11 target c
    15425 
    15426 > cartoon style modeHelix tube radius 1.4 sides 24
    15427 
    15428 > save NhaA-pH-superpose_back.png supersample 3 transparentBackground true
    15429 
    15430 > color #5,9,13,15&(dimer&~/A:35-58) snow transparency 20 target c
    15431 
    15432 > transparency 1 target c
    15433 
    15434 > color #5,9,13,15&(dimer&~/A:35-58) snow transparency 20 target c
    15435 
    15436 > save NhaA-pH-superpose_back_tra.png supersample 3 transparentBackground true
    15437 
    15438 > transparency 100 target c
    15439 
    15440 > color #5,9,13,15&(dimer&~/A:35-58) snow transparency 20 target c
    15441 
    15442 > save NhaA-pH-superpose_back_tra.png supersample 3 transparentBackground true
    15443 
    15444 > color #13 dark orange
    15445 
    15446 > color #9 orange
    15447 
    15448 > color #5 gold
    15449 
    15450 > color #15 deep sky blue
    15451 
    15452 > transparency 0 target c
    15453 
    15454 > hide #!5 models
    15455 
    15456 > hide #!9 models
    15457 
    15458 > hide #!13 models
    15459 
    15460 > open /Users/tsweng/Downloads/NhaA-6F9_pH85_Na_open.pdb
    15461 
    15462 Chain information for NhaA-6F9_pH85_Na_open.pdb #43 
    15463 --- 
    15464 Chain | Description 
    15465 A | No description available 
    15466  
    15467 
    15468 > lighting full
    15469 
    15470 > lighting shadows false
    15471 
    15472 > delete #43:SOL
    15473 
    15474 > delete #43:BUF
    15475 
    15476 > delete #43:CLA
    15477 
    15478 > delete #43:POPC
    15479 
    15480 > mmaker #43/A to #15/A
    15481 
    15482 Parameters 
    15483 --- 
    15484 Chain pairing | bb 
    15485 Alignment algorithm | Needleman-Wunsch 
    15486 Similarity matrix | BLOSUM-62 
    15487 SS fraction | 0.3 
    15488 Gap open (HH/SS/other) | 18/18/6 
    15489 Gap extend | 1 
    15490 SS matrix |  |  | H | S | O 
    15491 ---|---|---|--- 
    15492 H | 6 | -9 | -6 
    15493 S |  | 6 | -6 
    15494 O |  |  | 4 
    15495 Iteration cutoff | 2 
    15496  
    15497 Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
    15498 NhaA-6F9_pH85_Na_open.pdb, chain A (#43), sequence alignment score = 1621.3 
    15499 RMSD between 184 pruned atom pairs is 1.220 angstroms; (across all 379 pairs:
    15500 2.698) 
    15501  
    15502 
    15503 > cartoon style modeHelix default width 1.0 thickness 0.3
    15504 
    15505 > hide #!15 models
    15506 
    15507 > show #!15 models
    15508 
    15509 > close #43
    15510 
    15511 > open /Users/tsweng/Downloads/NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb
    15512 
    15513 Summary of feedback from opening
    15514 /Users/tsweng/Downloads/NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb 
    15515 --- 
    15516 warnings | Ignored bad PDB record found on line 1 
    15517 REMARK GENERATED BY TRJCONV 
    15518  
    15519 Ignored bad PDB record found on line 3 
    15520 REMARK THIS IS A SIMULATION BOX 
    15521  
    15522 NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb title: 
    15523 Protein t= 1174557.62500 step= 587278800 [more info...] 
    15524  
    15525 Chain information for NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb #43 
    15526 --- 
    15527 Chain | Description 
    15528 A | No description available 
    15529  
    15530 Non-standard residues in NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb #43 
    15531 --- 
    15532 ARGT — (ARGT) 
    15533 ASPT — (ASPT) 
    15534 BUF — (BUF) 
    15535 CLA — (CLA) 
    15536 GLUT — (glut) 
    15537 HSPT — (HSPT) 
    15538 LYST — (lyst) 
    15539 NA — (NA) 
    15540 POPC — (popc) 
    15541 SOD — (SOD) 
    15542 SOL — (SOL) 
    15543  
    15544 
    15545 > delete #43:POPC
    15546 
    15547 > delete #43:SOL,BUF,POPC,CLA
    15548 
    15549 > mmaker #43/A to #15/A
    15550 
    15551 Parameters 
    15552 --- 
    15553 Chain pairing | bb 
    15554 Alignment algorithm | Needleman-Wunsch 
    15555 Similarity matrix | BLOSUM-62 
    15556 SS fraction | 0.3 
    15557 Gap open (HH/SS/other) | 18/18/6 
    15558 Gap extend | 1 
    15559 SS matrix |  |  | H | S | O 
    15560 ---|---|---|--- 
    15561 H | 6 | -9 | -6 
    15562 S |  | 6 | -6 
    15563 O |  |  | 4 
    15564 Iteration cutoff | 2 
    15565  
    15566 Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
    15567 NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb, chain A (#43), sequence alignment score
    15568 = 1627.6 
    15569 RMSD between 231 pruned atom pairs is 1.276 angstroms; (across all 388 pairs:
    15570 2.521) 
    15571  
    15572 
    15573 > show #43 target a
    15574 
    15575 > delete #43@H
    15576 
    15577 > delete #43@H*
    15578 
    15579 > open /Users/tsweng/Downloads/NhaA-6F9_pH85_Na_open.pdb
    15580 
    15581 Chain information for NhaA-6F9_pH85_Na_open.pdb #44 
    15582 --- 
    15583 Chain | Description 
    15584 A | No description available 
    15585  
    15586 
    15587 > open /Users/tsweng/Downloads/NhaA-6F9_pH40_Na_closed.pdb
    15588 
    15589 Chain information for NhaA-6F9_pH40_Na_closed.pdb #45 
    15590 --- 
    15591 Chain | Description 
    15592 A | No description available 
    15593  
    15594 
    15595 > delete #44,45:SOL,BUF,POPC,CLA
    15596 
    15597 > delete #44,45@H*
    15598 
    15599 > mmaker #44,45/A to #15/A
    15600 
    15601 Parameters 
    15602 --- 
    15603 Chain pairing | bb 
    15604 Alignment algorithm | Needleman-Wunsch 
    15605 Similarity matrix | BLOSUM-62 
    15606 SS fraction | 0.3 
    15607 Gap open (HH/SS/other) | 18/18/6 
    15608 Gap extend | 1 
    15609 SS matrix |  |  | H | S | O 
    15610 ---|---|---|--- 
    15611 H | 6 | -9 | -6 
    15612 S |  | 6 | -6 
    15613 O |  |  | 4 
    15614 Iteration cutoff | 2 
    15615  
    15616 Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
    15617 NhaA-6F9_pH85_Na_open.pdb, chain A (#44), sequence alignment score = 1621.3 
    15618 RMSD between 184 pruned atom pairs is 1.220 angstroms; (across all 379 pairs:
    15619 2.698) 
    15620  
    15621 Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
    15622 NhaA-6F9_pH40_Na_closed.pdb, chain A (#45), sequence alignment score = 1632.1 
    15623 RMSD between 278 pruned atom pairs is 1.152 angstroms; (across all 379 pairs:
    15624 2.025) 
    15625  
    15626 
    15627 > hide #43 models
    15628 
    15629 > hide #44 models
    15630 
    15631 > show #44 models
    15632 
    15633 > hide #45 models
    15634 
    15635 > mmaker #44,45/A to #15&dimer_TM
    15636 
    15637 Parameters 
    15638 --- 
    15639 Chain pairing | bb 
    15640 Alignment algorithm | Needleman-Wunsch 
    15641 Similarity matrix | BLOSUM-62 
    15642 SS fraction | 0.3 
    15643 Gap open (HH/SS/other) | 18/18/6 
    15644 Gap extend | 1 
    15645 SS matrix |  |  | H | S | O 
    15646 ---|---|---|--- 
    15647 H | 6 | -9 | -6 
    15648 S |  | 6 | -6 
    15649 O |  |  | 4 
    15650 Iteration cutoff | 2 
    15651  
    15652 Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
    15653 NhaA-6F9_pH85_Na_open.pdb, chain A (#44), sequence alignment score = 548 
    15654 RMSD between 84 pruned atom pairs is 1.025 angstroms; (across all 119 pairs:
    15655 1.894) 
    15656  
    15657 Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
    15658 NhaA-6F9_pH40_Na_closed.pdb, chain A (#45), sequence alignment score = 555.2 
    15659 RMSD between 111 pruned atom pairs is 0.935 angstroms; (across all 119 pairs:
    15660 1.258) 
    15661  
    15662 
    15663 > show #45 models
    15664 
    15665 > hide #44 models
    15666 
    15667 > show #!13 models
    15668 
    15669 > hide #!15 models
    15670 
    15671 > show #!15 models
    15672 
    15673 > hide #!15 models
    15674 
    15675 > show #!15 models
    15676 
    15677 > hide #!15 models
    15678 
    15679 > show #!15 models
    15680 
    15681 > hide #!15 models
    15682 
    15683 > show #!15 models
    15684 
    15685 > hide #!15 models
    15686 
    15687 > show #!15 models
    15688 
    15689 > hide #!15 models
    15690 
    15691 > show #!15 models
    15692 
    15693 > hide #!15 models
    15694 
    15695 > show #44 models
    15696 
    15697 > hide #44 models
    15698 
    15699 > show #44 models
    15700 
    15701 > hide target a
    15702 
    15703 > cartoon style modeHelix default width 1.0 thickness 0.3
    15704 
    15705 > show #!15 models
    15706 
    15707 > hide #!13 models
    15708 
    15709 > show #!17 models
    15710 
    15711 > hide #!17 models
    15712 
    15713 > show #!17 models
    15714 
    15715 > hide #!17 models
    15716 
    15717 > show #!17 models
    15718 
    15719 > hide #!15 models
    15720 
    15721 > show #!15 models
    15722 
    15723 > hide #!17 models
    15724 
    15725 > show #!13 models
    15726 
    15727 > hide #!13 models
    15728 
    15729 > show #!13 models
    15730 
    15731 > hide #!13 models
    15732 
    15733 > hide #44 models
    15734 
    15735 > hide #45 models
    15736 
    15737 > view binding_site
    15738 
    15739 > view mono_back_
    15740 
    15741 > turn y 90
    15742 
    15743 > show #!13 models
    15744 
    15745 > show #!9 models
    15746 
    15747 > show #!5 models
    15748 
    15749 > hide #!9 models
    15750 
    15751 > show #!9 models
    15752 
    15753 > hide #!9 models
    15754 
    15755 > show #!9 models
    15756 
    15757 > hide #!9 models
    15758 
    15759 > show #!9 models
    15760 
    15761 > hide dimer target c
    15762 
    15763 > view core_inner_side
    15764 
    15765 > view name core_inner_side2
    15766 
    15767 > select /A:150-174,130-144,338-350
    15768 
    15769 11252 atoms, 11339 bonds, 6 pseudobonds, 1537 residues, 30 models selected 
    15770 
    15771 > grs sel col black wid 6
    15772 
    15773 Unknown command: grs sel col black wid 6 
    15774 
    15775 > grs sel col black wid 6
    15776 
    15777 Unknown command: grs sel col black wid 6 
    15778 
    15779 > graphics selection color black width 6
    15780 
    15781 > graphics selection color black width 5
    15782 
    15783 > graphics selection color black width 4
    15784 
    15785 > transparency 1 target c
    15786 
    15787 > tar ~/A:150-174,130-144,338-350 30 tar c
    15788 
    15789 Unknown command: tar ~/A:150-174,130-144,338-350 30 tar c 
    15790 
    15791 > transparency ~/A:150-174,130-144,338-350 30 target c
    15792 
    15793 > transparency 0 target c
    15794 
    15795 > transparency ~/A:150-174,130-144,338-350 30 target c
    15796 
    15797 > save NhaA-pH-superpose_core_inner_side.png supersample 3
    15798 > transparentBackground true
    15799 
    15800 > select clear
    15801 
    15802 > transparency 0 target c
    15803 
    15804 > turn x 90
    15805 
    15806 > view mono_back_
    15807 
    15808 > turn x 90
    15809 
    15810 > turn x -10
    15811 
    15812 > turn x -5
    15813 
    15814 > show /A target c
    15815 
    15816 > turn x -5
    15817 
    15818 > transparency dimer 30 target c
    15819 
    15820 > transparency dimer 50 target c
    15821 
    15822 > transparency dimer 70 target c
    15823 
    15824 > turn x -5
    15825 
    15826 > ui mousemode right translate
    15827 
    15828 > select #15/A:150-174,130-144,338-350
    15829 
    15830 388 atoms, 391 bonds, 53 residues, 1 model selected 
    15831 
    15832 > select #15&core
    15833 
    15834 1552 atoms, 1583 bonds, 1 pseudobond, 209 residues, 2 models selected 
    15835 
    15836 > select clear
    15837 
    15838 > save NhaA-pH-superpose_core_top.png supersample 3 transparentBackground true
    15839 
    15840 > transparency 1 target c
    15841 
    15842 > transparency dimer 70 target c
    15843 
    15844 > save NhaA-pH-superpose_core_top2.png supersample 3 transparentBackground
    15845 > true
    15846 
    15847 > transparency 0 target c
    15848 
    15849 > transparency dimer 70 target c
    15850 
    15851 > ui mousemode right zoom
    15852 
    15853 > ui mousemode right translate
    15854 
    15855 > view list
    15856 
    15857 Named views: N-term_density_top, binding_site, core_inner_side,
    15858 core_inner_side2, cutaway, dimer_interface, dimer_interface2,
    15859 dimer_interface_top, dimer_interface_top2, dimer_view-all_front, mono_back,
    15860 mono_back_, mono_front, pH-sensing 
    15861 
    15862 > view name core_top
    15863 
    15864 > show /A:11,78,81,82,243,248,250,252,253,256 target a
    15865 
    15866 > color #!5,9,13,15 byhetero
    15867 
    15868 > select /A:11,78,81,82,243,248,250,252,253,256 tar a
    15869 
    15870 Expected a keyword 
    15871 
    15872 > select /A:11,78,81,82,243,248,250,252,253,256
    15873 
    15874 2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 30 models selected 
    15875 
    15876 > select up
    15877 
    15878 14979 atoms, 15284 bonds, 7 pseudobonds, 1858 residues, 47 models selected 
    15879 
    15880 > select up
    15881 
    15882 83928 atoms, 85754 bonds, 7 pseudobonds, 11176 residues, 47 models selected 
    15883 
    15884 > select down
    15885 
    15886 14979 atoms, 15284 bonds, 7 pseudobonds, 1858 residues, 47 models selected 
    15887 
    15888 > select down
    15889 
    15890 2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 47 models selected 
    15891 
    15892 > select down
    15893 
    15894 2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 47 models selected 
    15895 
    15896 > select down
    15897 
    15898 2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 47 models selected 
    15899 
    15900 > select down
    15901 
    15902 2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 47 models selected 
    15903 
    15904 > select down
    15905 
    15906 2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 47 models selected 
    15907 
    15908 > select clear
    15909 
    15910 > select /A:11,78,81,82,243,248,250,252,253,256&sidechain
    15911 
    15912 1798 atoms, 1595 bonds, 7 pseudobonds, 290 residues, 30 models selected 
    15913 
    15914 > select clear
    15915 
    15916 > select #15/A:11@OD2
    15917 
    15918 1 atom, 1 residue, 1 model selected 
    15919 
    15920 > select clear
    15921 
    15922 > select /A:11,78,81,82,243,248,250,252,253,256&sidechain
    15923 
    15924 1798 atoms, 1595 bonds, 7 pseudobonds, 290 residues, 30 models selected 
    15925 
    15926 > select clear
    15927 
    15928 > hide #!5,9,13,15 atoms
    15929 
    15930 > show /A:11,78,81,82,243,249,250,252,253,256 target a
    15931 
    15932 > hide #!5,9,13,15 atoms
    15933 
    15934 > show /A:11,78,81,82,243,249,250,252,253,256&sidechain target a
    15935 
    15936 > transparency 30 target c
    15937 
    15938 > transparency 0 target a
    15939 
    15940 > transparency 1000 target a
    15941 
    15942 > transparency core 70 target c
    15943 
    15944 > transparency core 80 target c
    15945 
    15946 > transparency core 70 target c
    15947 
    15948 > save NhaA-pH-superpose_pH-sensing_top.png supersample 3
    15949 > transparentBackground true
    15950 
    15951 > hide target c
    15952 
    15953 > transparency 0 target a
    15954 
    15955 > graphics silhouettes width 6
    15956 
    15957 > hide target c
    15958 
    15959 > transparency 0 target a
    15960 
    15961 > graphics silhouettes width 6
    15962 
    15963 > hide ##="chain trace";
    15964 
    15965 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    15966 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    15967 
    15968 > hide target c
    15969 
    15970 > transparency 0 target a
    15971 
    15972 > graphics silhouettes width 6
    15973 
    15974 > hide ##name="chain trace"
    15975 
    15976 > save NhaA-pH-superpose_pH-sensing_top_res.png supersample 3
    15977 > transparentBackground true
    15978 
    15979 > show /A target c
    15980 
    15981 > transparency 0 target a
    15982 
    15983 > graphics silhouettes width 2
    15984 
    15985 > view list
    15986 
    15987 Named views: N-term_density_top, binding_site, core_inner_side,
    15988 core_inner_side2, core_top, cutaway, dimer_interface, dimer_interface2,
    15989 dimer_interface_top, dimer_interface_top2, dimer_view-all_front, mono_back,
    15990 mono_back_, mono_front, pH-sensing 
    15991 
    15992 > view core_top
    15993 
    15994 > hide target a
    15995 
    15996 > transparency 0 target c
    15997 
    15998 > transparency dimer 70 target c
    15999 
    16000 > save NhaA-pH-superpose_core_top2.png supersample 3 transparentBackground
    16001 > true
    16002 
    16003 > transparency 0 target c
    16004 
    16005 > view binding_site
    16006 
    16007 > show binding_site_res&sidechain target a
    16008 
    16009 > show /A:132 target a
    16010 
    16011 > hide #!15 models
    16012 
    16013 > hide #!9 models
    16014 
    16015 > show #!9 models
    16016 
    16017 > hide #!5 models
    16018 
    16019 > hide #!13 models
    16020 
    16021 > show #!13 models
    16022 
    16023 > show #!5 models
    16024 
    16025 > show #!17 models
    16026 
    16027 > color #!5,9,13,17 byhetero
    16028 
    16029 > hide /A:160-161 target c
    16030 
    16031 > show #!23 models
    16032 
    16033 > hide #23.1 models
    16034 
    16035 > hide sel
    16036 
    16037 > select clear
    16038 
    16039 > hide sel
    16040 
    16041 > color sel dark gray
    16042 
    16043 > select clear
    16044 
    16045 > transparency 30 target c
    16046 
    16047 > hide #!23 models
    16048 
    16049 > transparency 0 target a
    16050 
    16051 > transparency 100 target a
    16052 
    16053 > save NhaA-pH-superpose_binding_site.png supersample 3 transparentBackground
    16054 > true
    16055 
    16056 > transparency 0 target a
    16057 
    16058 > hide target c
    16059 
    16060 > hide ##name="chain trace"
    16061 
    16062 > graphics silhouettes 6
    16063 
    16064 Expected true or false or a keyword 
    16065 
    16066 > transparency 0 target a
    16067 
    16068 > hide target c
    16069 
    16070 > hide ##name="chain trace"
    16071 
    16072 > graphics silhouettes width 6
    16073 
    16074 > show #23.1 models
    16075 
    16076 > hide #23.1 models
    16077 
    16078 > save NhaA-pH-superpose_binding_site_res.png supersample 3
    16079 > transparentBackground true
    16080 
    16081 > hide #!17 models
    16082 
    16083 > show #!15 models
    16084 
    16085 > save NhaA-pH-superpose_binding_site_res.png supersample 3
    16086 > transparentBackground true
    16087 
    16088 > transparency 100 target a
    16089 
    16090 > show /A target c
    16091 
    16092 > graphics silhouettes width 2
    16093 
    16094 > hide #!15 models
    16095 
    16096 > show #!15 models
    16097 
    16098 > hide #!23 models
    16099 
    16100 > save NhaA-pH-superpose_binding_site.png supersample 3 transparentBackground
    16101 > true
    16102 
    16103 > show #!33 models
    16104 
    16105 > mcopy #15 toAtoms #33 settings c
    16106 
    16107 > hide #!15 models
    16108 
    16109 > hide /A:160-161 target c
    16110 
    16111 > save NhaA-pH-superpose_binding_site.png supersample 3 transparentBackground
    16112 > true
    16113 
    16114 > transparency 0 target a
    16115 
    16116 > hide target c
    16117 
    16118 > hide ##name="chain trace"
    16119 
    16120 > graphics silhouettes width 6
    16121 
    16122 > transparency 0 target a
    16123 
    16124 > hide target c
    16125 
    16126 > hide ##name="chain trace"
    16127 
    16128 > graphics silhouettes width 6
    16129 
    16130 > save NhaA-pH-superpose_binding_site_res.png supersample 3
    16131 > transparentBackground true
    16132 
    16133 > show #!23 models
    16134 
    16135 > hide #!23 models
    16136 
    16137 > show #!23 models
    16138 
    16139 > show #23 target p
    16140 
    16141 > hide :HOH target a
    16142 
    16143 > hide sel
    16144 
    16145 > select clear
    16146 
    16147 > hide sel
    16148 
    16149 > select clear
    16150 
    16151 > hide sel
    16152 
    16153 > select clear
    16154 
    16155 > hide sel
    16156 
    16157 > select #33/A:300@NZ
    16158 
    16159 1 atom, 1 residue, 1 model selected 
    16160 
    16161 > select #33/A:300@NZ
    16162 
    16163 1 atom, 1 residue, 1 model selected 
    16164 
    16165 > select clear
    16166 
    16167 > color sel drak gra
    16168 
    16169 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    16170 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    16171 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    16172 
    16173 > color sel dark gray
    16174 
    16175 > select clear
    16176 
    16177 > select #33/A:164@CB
    16178 
    16179 1 atom, 1 residue, 1 model selected 
    16180 
    16181 > select up
    16182 
    16183 8 atoms, 7 bonds, 1 residue, 2 models selected 
    16184 
    16185 > select clear
    16186 
    16187 > save NhaA-pH-superpose_binding_site_res.png supersample 3
    16188 > transparentBackground true
    16189 
    16190 > hide #!23 models
    16191 
    16192 > hide #!5 models
    16193 
    16194 > hide #!9 models
    16195 
    16196 > hide #!13 models
    16197 
    16198 > show #33:HOH
    16199 
    16200 > select #33/A:504@O
    16201 
    16202 1 atom, 1 residue, 1 model selected 
    16203 
    16204 > hide sel target a
    16205 
    16206 > select clear
    16207 
    16208 > show #!23 models
    16209 
    16210 > show #23 target p
    16211 
    16212 > select clear
    16213 
    16214 > select #33/A:504@O
    16215 
    16216 1 atom, 1 residue, 1 model selected 
    16217 
    16218 > select up
    16219 
    16220 3070 atoms, 3130 bonds, 392 residues, 1 model selected 
    16221 
    16222 > select down
    16223 
    16224 1 atom, 1 residue, 2 models selected 
    16225 
    16226 > hide sel target a
    16227 
    16228 > hide sel target p
    16229 
    16230 > ui mousemode right distance
    16231 
    16232 > distance #33/A:506@O #33/A:300@NZ
    16233 
    16234 Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A HOH 506 O and LYS 300
    16235 NZ: 2.587Å 
    16236 
    16237 > select clear
    16238 
    16239 > color sel dark gray
    16240 
    16241 > select clear
    16242 
    16243 > save NhaA-K-pH85-open_binding_site_res.png supersample 3
    16244 > transparentBackground true
    16245 
    16246 > hide #!23 models
    16247 
    16248 > show #!16 models
    16249 
    16250 > graphics silhouettes 2
    16251 
    16252 Expected true or false or a keyword 
    16253 
    16254 > graphics silhouettes width 2
    16255 
    16256 > show #31/A target c
    16257 
    16258 > show #33/A target c
    16259 
    16260 > transparency 0 target c
    16261 
    16262 > transparency #33 100 target a
    16263 
    16264 > transparency #33 0 target a
    16265 
    16266 > transparency #33 100 target a
    16267 
    16268 > save NhaA-K-pH85-open_binding_site_density.png supersample 3
    16269 > transparentBackground true
    16270 
    16271 > transparency #33 0 target a
    16272 
    16273 > save NhaA-K-pH85-open_binding_site_density.png supersample 3
    16274 > transparentBackground true
    16275 
    16276 > show #!33 atoms
    16277 
    16278 > hide #!33 atoms
    16279 
    16280 > show #!13 models
    16281 
    16282 > show #!9 models
    16283 
    16284 > show #!5 models
    16285 
    16286 > hide #!16 models
    16287 
    16288 > show #!15 models
    16289 
    16290 > hide #!5,9,13,15,33 atoms
    16291 
    16292 > show /A target c
    16293 
    16294 > view list
    16295 
    16296 Named views: N-term_density_top, binding_site, core_inner_side,
    16297 core_inner_side2, core_top, cutaway, dimer_interface, dimer_interface2,
    16298 dimer_interface_top, dimer_interface_top2, dimer_view-all_front, mono_back,
    16299 mono_back_, mono_front, pH-sensing 
    16300 
    16301 > view core_top
    16302 
    16303 > hide #!33 models
    16304 
    16305 > show #!17 models
    16306 
    16307 > hide #!17 models
    16308 
    16309 > show #!17 models
    16310 
    16311 > hide #!17 models
    16312 
    16313 > show #!17 models
    16314 
    16315 > hide #!17 models
    16316 
    16317 > show #!33 models
    16318 
    16319 > hide #!33 models
    16320 
    16321 > show #!33 models
    16322 
    16323 > hide #!33 models
    16324 
    16325 > show #!33 models
    16326 
    16327 > hide #!33 models
    16328 
    16329 > show #!33 models
    16330 
    16331 > hide #!33 models
    16332 
    16333 > show #!33 models
    16334 
    16335 > hide #!33 models
    16336 
    16337 > show #!33 models
    16338 
    16339 > hide #!33 models
    16340 
    16341 > show #!33 models
    16342 
    16343 > hide #!33 models
    16344 
    16345 > show /A:11,78,81,82,243,249,250,252,253,256&sidechain target a
    16346 
    16347 > show #!23 models
    16348 
    16349 > color sel dark gray
    16350 
    16351 > select clear
    16352 
    16353 > view core_top
    16354 
    16355 > show #23.1 models
    16356 
    16357 > hide #23.1 models
    16358 
    16359 > show #23.1 models
    16360 
    16361 > hide #23.1 models
    16362 
    16363 > hide target c
    16364 
    16365 > transparency 0 target a
    16366 
    16367 > graphics silhouettes width 6
    16368 
    16369 > hide ##name="chain trace"
    16370 
    16371 > hide target c
    16372 
    16373 > transparency 0 target a
    16374 
    16375 > graphics silhouettes width 6
    16376 
    16377 > hide ##name="chain trace"
    16378 
    16379 > save NhaA-pH-superpose_pH-sensing_top_res2.png supersample 3
    16380 > transparentBackground true
    16381 
    16382 > graphics silhouettes width 2
    16383 
    16384 > show /A target c
    16385 
    16386 > hide #!23 models
    16387 
    16388 > hide #!5,9,13,15 atoms
    16389 
    16390 > view mono_back_
    16391 
    16392 > show #45 models
    16393 
    16394 > hide #45 models
    16395 
    16396 > show #45 models
    16397 
    16398 > hide #45 models
    16399 
    16400 > show #44 models
    16401 
    16402 > hide #44 models
    16403 
    16404 > show #44 models
    16405 
    16406 > show #43 models
    16407 
    16408 > hide #44 models
    16409 
    16410 > show #44 models
    16411 
    16412 > hide #44 models
    16413 
    16414 > show #44 models
    16415 
    16416 > hide #44 models
    16417 
    16418 > show #44 models
    16419 
    16420 > hide #44 models
    16421 
    16422 > show #44 models
    16423 
    16424 > show #45 models
    16425 
    16426 > hide #43-45#!5,9,13,15 atoms
    16427 
    16428 > show /A:GLU,ASP,HIS,LYS,ARG target a
    16429 
    16430 > hide #!15 models
    16431 
    16432 > hide #!13 models
    16433 
    16434 > hide #!9 models
    16435 
    16436 > hide #!5 models
    16437 
    16438 > show #!5 models
    16439 
    16440 > show /A:GLUT,ASPT,HIST,LYST,ARGT target a
    16441 
    16442 > show /A:GLUT,ASPT,HSPT,LYST,ARGT target a
    16443 
    16444 > hide #!5 models
    16445 
    16446 > show #!15 models
    16447 
    16448 > show #!5 models
    16449 
    16450 > hide #43 models
    16451 
    16452 > hide #44 models
    16453 
    16454 > hide #45 models
    16455 
    16456 > show #!6 models
    16457 
    16458 > hide #!6 models
    16459 
    16460 > show #!20 models
    16461 
    16462 > hide #!20 models
    16463 
    16464 > show #!21 models
    16465 
    16466 > hide #!5 models
    16467 
    16468 > show #!5 models
    16469 
    16470 > hide #!15 models
    16471 
    16472 > lighting full
    16473 
    16474 > lighting simple
    16475 
    16476 > hide #!21 models
    16477 
    16478 > show #!20 models
    16479 
    16480 > hide #!20 models
    16481 
    16482 > show #!20 models
    16483 
    16484 > volume #20 level 0.007186
    16485 
    16486 > hide #!20 models
    16487 
    16488 > show #!20 models
    16489 
    16490 > hide #!20 models
    16491 
    16492 > show #!20 models
    16493 
    16494 > volume #20 level 0.0081
    16495 
    16496 > hide #!20 models
    16497 
    16498 > show #!15 models
    16499 
    16500 > show #!17 models
    16501 
    16502 > hide #!17 models
    16503 
    16504 > show #!17 models
    16505 
    16506 > hide #!17 models
    16507 
    16508 > show #!17 models
    16509 
    16510 > hide #!17 models
    16511 
    16512 > show #23.1 models
    16513 
    16514 > show #!5,15 atoms
    16515 
    16516 > hide #!5,15 atoms
    16517 
    16518 > show /A:GLU,ASP,HIS,LYS,ARG target a
    16519 
    16520 > view mono_back_
    16521 
    16522 > show #43 models
    16523 
    16524 > show #45 models
    16525 
    16526 > hide #43 models
    16527 
    16528 > show #43 models
    16529 
    16530 > hide #45 models
    16531 
    16532 > show #44 models
    16533 
    16534 > hide #43 models
    16535 
    16536 > hide #44 models
    16537 
    16538 > show #43 models
    16539 
    16540 > show #44 models
    16541 
    16542 > show #45 models
    16543 
    16544 > hide #43 models
    16545 
    16546 > hide #44 models
    16547 
    16548 > hide #45 models
    16549 
    16550 > open /Users/tsweng/Downloads/NhaA-6F9_pH40_no-sodium.pdb
    16551 
    16552 Chain information for NhaA-6F9_pH40_no-sodium.pdb #46 
    16553 --- 
    16554 Chain | Description 
    16555 A | No description available 
    16556  
    16557 
    16558 > open /Users/tsweng/Downloads/NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb
    16559 
    16560 Summary of feedback from opening
    16561 /Users/tsweng/Downloads/NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb 
    16562 --- 
    16563 warnings | Ignored bad PDB record found on line 1 
    16564 REMARK GENERATED BY TRJCONV 
    16565  
    16566 Ignored bad PDB record found on line 3 
    16567 REMARK THIS IS A SIMULATION BOX 
    16568  
    16569 NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb title: 
    16570 Protein t= 1193217.37500 step= 596608700 [more info...] 
    16571  
    16572 Chain information for NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb #47 
    16573 --- 
    16574 Chain | Description 
    16575 A | No description available 
    16576  
    16577 Non-standard residues in NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb #47 
    16578 --- 
    16579 ARGT — (ARGT) 
    16580 ASPT — (ASPT) 
    16581 BUF — (BUF) 
    16582 CL — (CL) 
    16583 CLA — (CLA) 
    16584 GLUT — (glut) 
    16585 HSPT — (HSPT) 
    16586 LYST — (lyst) 
    16587 POPC — (popc) 
    16588 SOD — (SOD) 
    16589 SOL — (SOL) 
    16590  
    16591 
    16592 > hide :POPC
    16593 
    16594 > delete :SOL,CLA
    16595 
    16596 > delete :SOL,CLA,BUF
    16597 
    16598 > hide :SOD
    16599 
    16600 > select ~sel & ##selected
    16601 
    16602 Nothing selected 
    16603 
    16604 > hide :CL
    16605 
    16606 > mmaker #46,47/A to #15&dimer_TM
    16607 
    16608 Parameters 
    16609 --- 
    16610 Chain pairing | bb 
    16611 Alignment algorithm | Needleman-Wunsch 
    16612 Similarity matrix | BLOSUM-62 
    16613 SS fraction | 0.3 
    16614 Gap open (HH/SS/other) | 18/18/6 
    16615 Gap extend | 1 
    16616 SS matrix |  |  | H | S | O 
    16617 ---|---|---|--- 
    16618 H | 6 | -9 | -6 
    16619 S |  | 6 | -6 
    16620 O |  |  | 4 
    16621 Iteration cutoff | 2 
    16622  
    16623 Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
    16624 NhaA-6F9_pH40_no-sodium.pdb, chain A (#46), sequence alignment score = 558.2 
    16625 RMSD between 108 pruned atom pairs is 0.891 angstroms; (across all 119 pairs:
    16626 1.334) 
    16627  
    16628 Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
    16629 NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb, chain A (#47), sequence alignment score
    16630 = 544.4 
    16631 RMSD between 109 pruned atom pairs is 0.990 angstroms; (across all 119 pairs:
    16632 1.303) 
    16633  
    16634 
    16635 > hide #!23 models
    16636 
    16637 > show #!23 models
    16638 
    16639 > hide #!15 models
    16640 
    16641 > hide #!5 models
    16642 
    16643 > hide #46-47 atoms
    16644 
    16645 > show /A:GLUT,ASPT,HSPT,LYST,ARGT target a
    16646 
    16647 > delete #46,47@H*
    16648 
    16649 > show #!15 models
    16650 
    16651 > show #!5 models
    16652 
    16653 > hide #46 models
    16654 
    16655 > hide #47 models
    16656 
    16657 > hide #!5,15 cartoons
    16658 
    16659 > show /A target c
    16660 
    16661 > hide #!5,15 atoms
    16662 
    16663 > hide #!5 models
    16664 
    16665 > hide #!15 models
    16666 
    16667 > show #!7 models
    16668 
    16669 > show #!9 models
    16670 
    16671 > hide #!7,9 atoms
    16672 
    16673 > color /A:1-10 medium purple
    16674 
    16675 > color #5,9,13&core orange
    16676 
    16677 > color #5,9,13&dimer khaki
    16678 
    16679 > color /A:1-10 medium purple
    16680 
    16681 > hide #!9 models
    16682 
    16683 > show #!9 models
    16684 
    16685 > select #9/A:10
    16686 
    16687 6 atoms, 5 bonds, 1 residue, 1 model selected 
    16688 
    16689 > select add #9/A:9
    16690 
    16691 12 atoms, 10 bonds, 2 residues, 2 models selected 
    16692 
    16693 > select add #9/A:8
    16694 
    16695 23 atoms, 21 bonds, 3 residues, 2 models selected 
    16696 
    16697 > select clear
    16698 
    16699 > select #9/A:1-10
    16700 
    16701 90 atoms, 93 bonds, 10 residues, 1 model selected 
    16702 
    16703 > mlp sel
    16704 
    16705 Map values for surface "NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_A SES surface":
    16706 minimum -27.5, mean 0.3038, maximum 23.58 
    16707 To also show corresponding color key, enter the above mlp command and add key
    16708 true 
    16709 
    16710 > select clear
    16711 
    16712 > hide #9.1 models
    16713 
    16714 > show #9.1 models
    16715 
    16716 > hide #9.1 models
    16717 
    16718 > show #9.1 models
    16719 
    16720 > hide #9.1 models
    16721 
    16722 > show #9.1 models
    16723 
    16724 > hide #9.1 models
    16725 
    16726 > show #41 models
    16727 
    16728 > hide #41 models
    16729 
    16730 > show #9.1 models
    16731 
    16732 > transparency #9.1 30
    16733 
    16734 > transparency #9.1 50
    16735 
    16736 > transparency #9.1 30
    16737 
    16738 > combine #9
    16739 
    16740 > split #9 atoms /A:1-10
    16741 
    16742 Split NhaA-nd-6F9-K_BTPpH75_unplugged.pdb (#9) into 2 models 
    16743 Chain information for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 1 #9.1 
    16744 --- 
    16745 Chain | Description 
    16746 A | No description available 
    16747  
    16748 Chain information for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 2 #9.2 
    16749 --- 
    16750 Chain | Description 
    16751 A | No description available 
    16752 B | No description available 
    16753 C | No description available 
    16754  
    16755 
    16756 > hide #48 models
    16757 
    16758 > show #48 models
    16759 
    16760 > hide #48 models
    16761 
    16762 > show #48 models
    16763 
    16764 > hide #48 models
    16765 
    16766 > show #48 models
    16767 
    16768 > open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
    16769 > nd-6F9-K_BTPpH75_unplugged.pdb
    16770 
    16771 Chain information for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #49 
    16772 --- 
    16773 Chain | Description 
    16774 A | No description available 
    16775 B | No description available 
    16776 C | No description available 
    16777  
    16778 
    16779 > mmaker #49 to #48
    16780 
    16781 Parameters 
    16782 --- 
    16783 Chain pairing | bb 
    16784 Alignment algorithm | Needleman-Wunsch 
    16785 Similarity matrix | BLOSUM-62 
    16786 SS fraction | 0.3 
    16787 Gap open (HH/SS/other) | 18/18/6 
    16788 Gap extend | 1 
    16789 SS matrix |  |  | H | S | O 
    16790 ---|---|---|--- 
    16791 H | 6 | -9 | -6 
    16792 S |  | 6 | -6 
    16793 O |  |  | 4 
    16794 Iteration cutoff | 2 
    16795  
    16796 Matchmaker copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#48) with
    16797 NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#49), sequence alignment score =
    16798 1999.4 
    16799 RMSD between 388 pruned atom pairs is 0.000 angstroms; (across all 388 pairs:
    16800 0.000) 
    16801  
    16802 
    16803 > mcopy #13 toAtoms #49 settings hc
    16804 
    16805 > hide #48 models
    16806 
    16807 > hide #!9 models
    16808 
    16809 > show #!9 models
    16810 
    16811 > hide #!9 models
    16812 
    16813 > mcopy #13 toAtoms #49 settings v
    16814 
    16815 > show #49 target c
    16816 
    16817 > show #49 models
    16818 
    16819 > mcopy #13 toAtoms #49 settings s
    16820 
    16821 > cartoon style modeHelix default width 1.1 thickness 0.2
    16822 
    16823 > cartoon style modeHelix default width 1.0 thickness 0.3
    16824 
    16825 > hide #49#!7 atoms
    16826 
    16827 > hide /B,C
    16828 
    16829 > hide /B,C target c
    16830 
    16831 > show #!9 models
    16832 
    16833 > hide #!9 models
    16834 
    16835 > show #!9 models
    16836 
    16837 > hide #!9 models
    16838 
    16839 > show #!9 models
    16840 
    16841 > hide #!9 models
    16842 
    16843 > close #9
    16844 
    16845 > rename #49 #9
    16846 
    16847 No name or id option specified for renaming 
    16848 
    16849 > rename #49 id #9
    16850 
    16851 > split #48 atoms /A:1-10
    16852 
    16853 Split copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb (#48) into 2 models 
    16854 Chain information for copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 1 #48.1 
    16855 --- 
    16856 Chain | Description 
    16857 A | No description available 
    16858  
    16859 Chain information for copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 2 #48.2 
    16860 --- 
    16861 Chain | Description 
    16862 A | No description available 
    16863 B | No description available 
    16864 C | No description available 
    16865  
    16866 
    16867 > hide #!48 models
    16868 
    16869 > show #!48 models
    16870 
    16871 > show #48.1 models
    16872 
    16873 > select add #48.1
    16874 
    16875 90 atoms, 93 bonds, 10 residues, 1 model selected 
    16876 
    16877 > mlp sel
    16878 
    16879 Map values for surface "copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 1_A SES
    16880 surface": minimum -21.99, mean -0.3689, maximum 22.72 
    16881 To also show corresponding color key, enter the above mlp command and add key
    16882 true 
    16883 
    16884 > select clear
    16885 
    16886 > hide #48 target c
    16887 
    16888 > transparency #48 30
    16889 
    16890 > transparency #48 40
    16891 
    16892 > show #9/A:2-9 target a
    16893 
    16894 > hide #!48 models
    16895 
    16896 > color #9#!7 byhetero
    16897 
    16898 > show #!48 models
    16899 
    16900 > lighting full multiShadow 1024
    16901 
    16902 > lighting full multiShadow 1024 shadows false
    16903 
    16904 > transparency #48 30
    16905 
    16906 > transparency #48 20
    16907 
    16908 > lighting simple
    16909 
    16910 > lighting full multiShadow 1024 shadows false
    16911 
    16912 > transparency #48 10
    16913 
    16914 > transparency #48 0
    16915 
    16916 > transparency #48 10
    16917 
    16918 > transparency #48 20
    16919 
    16920 > transparency #48 30
    16921 
    16922 > hide #!48 models
    16923 
    16924 > select #9/A:9
    16925 
    16926 6 atoms, 5 bonds, 1 residue, 1 model selected 
    16927 
    16928 > show #!48 models
    16929 
    16930 > hide #!48 models
    16931 
    16932 > select #9/A:1-10
    16933 
    16934 90 atoms, 93 bonds, 10 residues, 1 model selected 
    16935 
    16936 > show #!48 models
    16937 
    16938 > select clear
    16939 
    16940 > select #9/A:1-10
    16941 
    16942 90 atoms, 93 bonds, 10 residues, 1 model selected 
    16943 
    16944 > select clear
    16945 
    16946 > transparency #48 30
    16947 
    16948 > transparency #48 50
    16949 
    16950 > select #9/A:1-10
    16951 
    16952 90 atoms, 93 bonds, 10 residues, 1 model selected 
    16953 
    16954 > transparency #48 50
    16955 
    16956 > transparency #48 80
    16957 
    16958 > hide #!7 models
    16959 
    16960 > ui mousemode right translate
    16961 
    16962 > ui mousemode right zoom
    16963 
    16964 > ui mousemode right translate
    16965 
    16966 > show #!7 models
    16967 
    16968 > select up
    16969 
    16970 2918 atoms, 2982 bonds, 388 residues, 1 model selected 
    16971 
    16972 > select up
    16973 
    16974 3012 atoms, 3074 bonds, 390 residues, 1 model selected 
    16975 
    16976 > select down
    16977 
    16978 2918 atoms, 2982 bonds, 388 residues, 1 model selected 
    16979 
    16980 > select down
    16981 
    16982 90 atoms, 93 bonds, 10 residues, 1 model selected 
    16983 
    16984 > show /A:1-10 target a
    16985 
    16986 > hide #48 target a
    16987 
    16988 > show #7/A:1-10,78,81,82,252,253,256 target a
    16989 
    16990 > ui mousemode right zoom
    16991 
    16992 > ui mousemode right translate
    16993 
    16994 > view name plug_side
    16995 
    16996 > hide sel atoms
    16997 
    16998 > select clear
    16999 
    17000 > hide #!7 models
    17001 
    17002 > show /A:2-9 target a
    17003 
    17004 > hide #48 target a
    17005 
    17006 > save test.png supersample 3 transparentBackground true
    17007 
    17008 > hide #9 models
    17009 
    17010 > transparency #48 0
    17011 
    17012 > save test2.png supersample 3 transparentBackground true
    17013 
    17014 > hide #!48 models
    17015 
    17016 > show #!48 models
    17017 
    17018 > transparency #48 80
    17019 
    17020 > show #9 models
    17021 
    17022 > select #9/A:1-10
    17023 
    17024 90 atoms, 93 bonds, 10 residues, 1 model selected 
    17025 
    17026 > save test.png supersample 3 transparentBackground true
    17027 
    17028 > select clear
    17029 
    17030 > hide #9 models
    17031 
    17032 > hide #!48 models
    17033 
    17034 > show #!5 models
    17035 
    17036 > hide #!5 models
    17037 
    17038 > show #!7 models
    17039 
    17040 > transparency #7&core 0 target c
    17041 
    17042 > transparency #7&core 100 target c
    17043 
    17044 > transparency #7&core 80 target c
    17045 
    17046 > transparency #7&core 100 target c
    17047 
    17048 > transparency #7&dimer 1 target c
    17049 
    17050 > transparency #7 0 target c
    17051 
    17052 > view list
    17053 
    17054 Named views: N-term_density_top, binding_site, core_inner_side,
    17055 core_inner_side2, core_top, cutaway, dimer_interface, dimer_interface2,
    17056 dimer_interface_top, dimer_interface_top2, dimer_view-all_front, mono_back,
    17057 mono_back_, mono_front, pH-sensing, plug_side 
    17058 
    17059 > view mono_back_
    17060 
    17061 > hide #!7 atoms
    17062 
    17063 > show #9 models
    17064 
    17065 > hide #9#!7 atoms
    17066 
    17067 > show #39 models
    17068 
    17069 > show #41 models
    17070 
    17071 > hide #9,39,41#!7 atoms
    17072 
    17073 > hide #41 models
    17074 
    17075 > hide #39 models
    17076 
    17077 > cartoon style modeHelix tube radius 1.4 sides 24
    17078 
    17079 > color #9 orange
    17080 
    17081 > color #7 indianred
    17082 
    17083 > color /A:1-10 medium purple
    17084 
    17085 > select #7,9/A:1-10
    17086 
    17087 180 atoms, 186 bonds, 20 residues, 2 models selected 
    17088 
    17089 > color #9 orange
    17090 
    17091 > color #7 indianred
    17092 
    17093 > graphics selection color medium purple
    17094 
    17095 > graphics selection color medium purple width 6
    17096 
    17097 > graphics selection color medium purple width 8
    17098 
    17099 > graphics selection color medium purple width 6
    17100 
    17101 > graphics selection color medium purple width 4
    17102 
    17103 > graphics selection color black width 4
    17104 
    17105 > graphics selection color black width 8
    17106 
    17107 > select clear
    17108 
    17109 > save NhaA-pH75-plug-superpose.png supersample 3 transparentBackground true
    17110 
    17111 > select #7,9/A:1-10
    17112 
    17113 180 atoms, 186 bonds, 20 residues, 2 models selected 
    17114 
    17115 > select up
    17116 
    17117 188 atoms, 194 bonds, 21 residues, 3 models selected 
    17118 
    17119 > select down
    17120 
    17121 180 atoms, 186 bonds, 20 residues, 3 models selected 
    17122 
    17123 > save NhaA-pH75-plug-superpose.png supersample 3 transparentBackground true
    17124 
    17125 > graphics selection color black width 6
    17126 
    17127 > graphics selection color black width 4
    17128 
    17129 > save NhaA-pH75-plug-superpose.png supersample 3 transparentBackground true
    17130 
    17131 > transparency 80 target c
    17132 
    17133 > transparency sel 1 target c
    17134 
    17135 > select clear
    17136 
    17137 > save NhaA-pH75-plug-superpose_tra.png supersample 3 transparentBackground
    17138 > true
    17139 
    17140 > transparency 50 target c
    17141 
    17142 > transparency #7,9/A:1-10 1 target c
    17143 
    17144 > save NhaA-pH75-plug-superpose_tra.png supersample 3 transparentBackground
    17145 > true
    17146 
    17147 > transparency 30 target c
    17148 
    17149 > transparency #7,9/A:1-10 1 target c
    17150 
    17151 > save NhaA-pH75-plug-superpose_tra.png supersample 3 transparentBackground
    17152 > true
    17153 
    17154 > select #7,9/A:1-10
    17155 
    17156 180 atoms, 186 bonds, 20 residues, 2 models selected 
    17157 
    17158 > select #9/A:1-10|#7/A:1-7,9
    17159 
    17160 163 atoms, 167 bonds, 18 residues, 2 models selected 
    17161 
    17162 > select #9/A:1-10|#7/A:1-6,8-9
    17163 
    17164 163 atoms, 167 bonds, 18 residues, 2 models selected 
    17165 
    17166 > select clear
    17167 
    17168 > color ~#7,9/A:1-10 snow
    17169 
    17170 > save NhaA-pH75-plug-superpose_tra.png supersample 3 transparentBackground
    17171 > true
    17172 
    17173 > select #9/A:1-10|#7/A:1-6,8-9
    17174 
    17175 163 atoms, 167 bonds, 18 residues, 2 models selected 
    17176 
    17177 > select clear
    17178 
    17179 > color #9 orange
    17180 
    17181 > color #7 indianred
    17182 
    17183 > transparency 0 target c
    17184 
    17185 > cartoon style modeHelix default width 1.0 thickness 0.3
    17186 
    17187 > turn y -90
    17188 
    17189 > hide core target c
    17190 
    17191 > hide #9 models
    17192 
    17193 > hide #!7 models
    17194 
    17195 > show #9 models
    17196 
    17197 > color #7,9/A:1-10 medium purple
    17198 
    17199 > show #!48 models
    17200 
    17201 > select add #48
    17202 
    17203 4737 atoms, 4840 bonds, 614 residues, 3 models selected 
    17204 
    17205 > mlp sel & #!48.1
    17206 
    17207 Map values for surface "copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 1_A SES
    17208 surface": minimum -21.99, mean -0.3689, maximum 22.72 
    17209 To also show corresponding color key, enter the above mlp command and add key
    17210 true 
    17211 
    17212 > select clear
    17213 
    17214 > hide #!48.1 models
    17215 
    17216 > show #!48.1 models
    17217 
    17218 > hide #!48 models
    17219 
    17220 > show #!48 models
    17221 
    17222 > hide #9 models
    17223 
    17224 > hide #!48 models
    17225 
    17226 > show #!7 models
    17227 
    17228 > show #7/A:1-10,78,81,82,252,253,256 target a
    17229 
    17230 > color #!7 byhetero
    17231 
    17232 > show #9 models
    17233 
    17234 > show #9/A:2-9 target a
    17235 
    17236 > color #9#!7 byhetero
    17237 
    17238 > view mono_back_
    17239 
    17240 > turn y -90
    17241 
    17242 > show #!48 models
    17243 
    17244 > hide #!48 models
    17245 
    17246 > hide #!48.1 models
    17247 
    17248 > show #!48.1 models
    17249 
    17250 > hide #!48 models
    17251 
    17252 > show /A target c
    17253 
    17254 > view mono_back_
    17255 
    17256 > turn x 50
    17257 
    17258 > lighting simple
    17259 
    17260 > show #39 models
    17261 
    17262 > hide #39 models
    17263 
    17264 > show #39 models
    17265 
    17266 > hide #39 models
    17267 
    17268 > show #!26 models
    17269 
    17270 > hide #!26.1 models
    17271 
    17272 > show #!26.1 models
    17273 
    17274 > hide #!26.1 models
    17275 
    17276 > hide #!26.2 models
    17277 
    17278 > select add #26.2.1
    17279 
    17280 2828 atoms, 378 residues, 1 model selected 
    17281 
    17282 > select subtract #26.2.1
    17283 
    17284 1 model selected 
    17285 
    17286 > select add #26.2
    17287 
    17288 2921 atoms, 2979 bonds, 380 residues, 1 model selected 
    17289 
    17290 > mlp #9#!7
    17291 
    17292 Map values for surface "NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_A SES surface":
    17293 minimum -27.5, mean 0.3038, maximum 23.58 
    17294 Map values for surface "NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_B SES surface":
    17295 minimum -24.66, mean -5.522, maximum 22.07 
    17296 Map values for surface "NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_C SES surface":
    17297 minimum -26.11, mean -5.396, maximum 23.67 
    17298 Map values for surface "NhaA-nd-6F9-K_BTPpH75_plugged.pdb_A SES surface":
    17299 minimum -27.56, mean 0.1673, maximum 23.61 
    17300 Map values for surface "NhaA-nd-6F9-K_BTPpH75_plugged.pdb_B SES surface":
    17301 minimum -26.83, mean -5.72, maximum 22.56 
    17302 Map values for surface "NhaA-nd-6F9-K_BTPpH75_plugged.pdb_C SES surface":
    17303 minimum -25.35, mean -5.769, maximum 23.24 
    17304 To also show corresponding color key, enter the above mlp command and add key
    17305 true 
    17306 
    17307 > select subtract #26.2
    17308 
    17309 1 model selected 
    17310 
    17311 > hide #26.2.1 models
    17312 
    17313 > show #26.2.1 models
    17314 
    17315 > hide #!26 models
    17316 
    17317 > show #!26 models
    17318 
    17319 > hide #7,9 target s
    17320 
    17321 > select add #26
    17322 
    17323 3011 atoms, 3072 bonds, 390 residues, 3 models selected 
    17324 
    17325 > mlp sel & #!26.2
    17326 
    17327 Map values for surface "NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface":
    17328 minimum -27.17, mean 0.3244, maximum 23.52 
    17329 To also show corresponding color key, enter the above mlp command and add key
    17330 true 
    17331 
    17332 > select add #26
    17333 
    17334 3011 atoms, 3072 bonds, 390 residues, 7 models selected 
    17335 
    17336 > select subtract #26
    17337 
    17338 2 models selected 
    17339 
    17340 > hide #!26.2 models
    17341 
    17342 > show #!26.2 models
    17343 
    17344 > hide /B,C target s
    17345 
    17346 > hide #26 target a
    17347 
    17348 > hide #!26 models
    17349 
    17350 > hide #!9 models
    17351 
    17352 > hide #7/A:1-10
    17353 
    17354 > show #7/A:4-9
    17355 
    17356 > hide #23.1 models
    17357 
    17358 > show #!26 models
    17359 
    17360 > hide #!26 models
    17361 
    17362 > show #!26 models
    17363 
    17364 > hide #!26 models
    17365 
    17366 > show #!26 models
    17367 
    17368 > hide #!26 models
    17369 
    17370 > show #!26 models
    17371 
    17372 > hide #!26 models
    17373 
    17374 > show #!26 models
    17375 
    17376 > select #26.2/A:81@CG
    17377 
    17378 1 atom, 1 residue, 1 model selected 
    17379 
    17380 > select #26.2/A:82@OE1
    17381 
    17382 1 atom, 1 residue, 1 model selected 
    17383 
    17384 > select add #26.2/A:81@CG
    17385 
    17386 2 atoms, 2 residues, 2 models selected 
    17387 
    17388 > select add #26.2/A:81@NE
    17389 
    17390 3 atoms, 2 residues, 2 models selected 
    17391 
    17392 > select add #26.2/A:81@NH2
    17393 
    17394 4 atoms, 2 residues, 2 models selected 
    17395 
    17396 > select add #26.2/A:81@NH1
    17397 
    17398 5 atoms, 2 residues, 2 models selected 
    17399 
    17400 > select add #26.2/A:252@CB
    17401 
    17402 6 atoms, 3 residues, 2 models selected 
    17403 
    17404 > select add #26.2/A:253@CB
    17405 
    17406 7 atoms, 4 residues, 2 models selected 
    17407 
    17408 > select add #26.2/A:249@O
    17409 
    17410 8 atoms, 5 residues, 2 models selected 
    17411 
    17412 > select add #26.2/A:253@CA
    17413 
    17414 9 atoms, 5 residues, 2 models selected 
    17415 
    17416 > select clear
    17417 
    17418 > hide #!7 models
    17419 
    17420 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 18801 of
    17421 299176 triangles, cap far, 2104 of 9688 triangles, cap near, 285 of 2384
    17422 triangles, 39 residues 
    17423 
    17424 > select subtract #26.2/A:258@CZ2
    17425 
    17426 290 atoms, 39 residues, 4 models selected 
    17427 
    17428 > select subtract #26.2/A:258@CH2
    17429 
    17430 289 atoms, 39 residues, 4 models selected 
    17431 
    17432 > select subtract #26.2/A:258@CZ3
    17433 
    17434 288 atoms, 39 residues, 4 models selected 
    17435 
    17436 > select subtract #26.2/A:258@NE1
    17437 
    17438 287 atoms, 39 residues, 4 models selected 
    17439 
    17440 > select subtract #26.2/A:258@CD2
    17441 
    17442 286 atoms, 39 residues, 4 models selected 
    17443 
    17444 > select subtract #26.2/A:258@CD1
    17445 
    17446 285 atoms, 39 residues, 4 models selected 
    17447 
    17448 > select subtract #26.2/A:258@CE2
    17449 
    17450 284 atoms, 39 residues, 4 models selected 
    17451 
    17452 > select subtract #26.2/A:258@CE3
    17453 
    17454 283 atoms, 39 residues, 4 models selected 
    17455 
    17456 > select subtract #26.2/A:258@CG
    17457 
    17458 282 atoms, 39 residues, 4 models selected 
    17459 
    17460 > select subtract #26.2/A:258@CA
    17461 
    17462 281 atoms, 39 residues, 4 models selected 
    17463 
    17464 > select subtract #26.2/A:257@CG
    17465 
    17466 280 atoms, 39 residues, 4 models selected 
    17467 
    17468 > select subtract #26.2/A:257@CB
    17469 
    17470 279 atoms, 39 residues, 4 models selected 
    17471 
    17472 > select subtract #26.2/A:257@O
    17473 
    17474 278 atoms, 39 residues, 4 models selected 
    17475 
    17476 > select subtract #26.2/A:258@N
    17477 
    17478 277 atoms, 39 residues, 4 models selected 
    17479 
    17480 > select subtract #26.2/A:257@C
    17481 
    17482 276 atoms, 39 residues, 4 models selected 
    17483 
    17484 > select add #26.2/A:142@CB
    17485 
    17486 277 atoms, 40 residues, 4 models selected 
    17487 
    17488 > select subtract #26.2/A:12@CB
    17489 
    17490 276 atoms, 40 residues, 4 models selected 
    17491 
    17492 > select subtract #26.2/A:12@C
    17493 
    17494 275 atoms, 40 residues, 4 models selected 
    17495 
    17496 > show #!7 models
    17497 
    17498 > select subtract #26.2/A:257@CD
    17499 
    17500 274 atoms, 40 residues, 4 models selected 
    17501 
    17502 > select add #26.2/A:257@CD
    17503 
    17504 275 atoms, 40 residues, 4 models selected 
    17505 
    17506 > select add #26.2/A:253@O
    17507 
    17508 276 atoms, 41 residues, 4 models selected 
    17509 
    17510 > select add #26.2/A:253@CD2
    17511 
    17512 277 atoms, 41 residues, 4 models selected 
    17513 
    17514 > select add #26.2/A:253@NE2
    17515 
    17516 278 atoms, 41 residues, 4 models selected 
    17517 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 8 of
    17518 299176 triangles 
    17519 
    17520 > hide #!7 models
    17521 
    17522 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 18787 of
    17523 299176 triangles, cap far, 2367 of 10109 triangles, cap near, 58 of 2444
    17524 triangles, 42 residues 
    17525 
    17526 > select subtract #26.2/A:255@CD2
    17527 
    17528 312 atoms, 42 residues, 4 models selected 
    17529 
    17530 > select subtract #26.2/A:255@CD1
    17531 
    17532 311 atoms, 42 residues, 4 models selected 
    17533 
    17534 > select subtract #26.2/A:255@CG
    17535 
    17536 310 atoms, 42 residues, 4 models selected 
    17537 
    17538 > select subtract #26.2/A:70@CA
    17539 
    17540 309 atoms, 42 residues, 4 models selected 
    17541 
    17542 > select subtract #26.2/A:70@N
    17543 
    17544 308 atoms, 42 residues, 4 models selected 
    17545 
    17546 > select subtract #26.2/A:70@CG2
    17547 
    17548 307 atoms, 42 residues, 4 models selected 
    17549 
    17550 > select add #26.2/A:70@CG2
    17551 
    17552 308 atoms, 42 residues, 4 models selected 
    17553 
    17554 > select subtract #26.2/A:70@CG2
    17555 
    17556 307 atoms, 42 residues, 4 models selected 
    17557 
    17558 > select subtract #26.2/A:70@CG1
    17559 
    17560 306 atoms, 42 residues, 4 models selected 
    17561 
    17562 > select subtract #26.2/A:263@CD1
    17563 
    17564 305 atoms, 42 residues, 4 models selected 
    17565 
    17566 > select subtract #26.2/A:263@CG1
    17567 
    17568 304 atoms, 42 residues, 4 models selected 
    17569 
    17570 > select subtract #26.2/A:258@CB
    17571 
    17572 303 atoms, 42 residues, 4 models selected 
    17573 
    17574 > select subtract #26.2/A:258@CD1
    17575 
    17576 302 atoms, 42 residues, 4 models selected 
    17577 
    17578 > select subtract #26.2/A:255@CA
    17579 
    17580 301 atoms, 42 residues, 4 models selected 
    17581 
    17582 > select subtract #26.2/A:258@NE1
    17583 
    17584 300 atoms, 42 residues, 4 models selected 
    17585 
    17586 > select subtract #26.2/A:258@CG
    17587 
    17588 299 atoms, 42 residues, 4 models selected 
    17589 
    17590 > select subtract #26.2/A:258@CZ3
    17591 
    17592 298 atoms, 42 residues, 4 models selected 
    17593 
    17594 > select subtract #26.2/A:258@CE3
    17595 
    17596 297 atoms, 42 residues, 4 models selected 
    17597 
    17598 > select subtract #26.2/A:258@CD2
    17599 
    17600 296 atoms, 42 residues, 4 models selected 
    17601 
    17602 > select subtract #26.2/A:258@CE2
    17603 
    17604 295 atoms, 42 residues, 4 models selected 
    17605 
    17606 > select subtract #26.2/A:258@CH2
    17607 
    17608 294 atoms, 42 residues, 4 models selected 
    17609 
    17610 > select subtract #26.2/A:258@CZ2
    17611 
    17612 293 atoms, 42 residues, 4 models selected 
    17613 
    17614 > select subtract #26.2/A:258@CA
    17615 
    17616 292 atoms, 42 residues, 4 models selected 
    17617 
    17618 > select subtract #26.2/A:257@O
    17619 
    17620 291 atoms, 42 residues, 4 models selected 
    17621 
    17622 > select subtract #26.2/A:257@C
    17623 
    17624 290 atoms, 42 residues, 4 models selected 
    17625 
    17626 > select subtract #26.2/A:258@N
    17627 
    17628 289 atoms, 42 residues, 4 models selected 
    17629 
    17630 > show #!7 models
    17631 
    17632 > select subtract #26.2/A:265@CB
    17633 
    17634 288 atoms, 42 residues, 4 models selected 
    17635 
    17636 > select subtract #26.2/A:265@CG
    17637 
    17638 287 atoms, 42 residues, 4 models selected 
    17639 
    17640 > select subtract #26.2/A:265@O
    17641 
    17642 286 atoms, 42 residues, 4 models selected 
    17643 
    17644 > select subtract #26.2/A:265@C
    17645 
    17646 285 atoms, 42 residues, 4 models selected 
    17647 
    17648 > select subtract #26.2/A:136@CE2
    17649 
    17650 284 atoms, 42 residues, 4 models selected 
    17651 
    17652 > select subtract #26.2/A:136@CZ
    17653 
    17654 283 atoms, 42 residues, 4 models selected 
    17655 
    17656 > select subtract #26.2/A:136@CE1
    17657 
    17658 282 atoms, 42 residues, 4 models selected 
    17659 
    17660 > select subtract #26.2/A:136@CD1
    17661 
    17662 281 atoms, 42 residues, 4 models selected 
    17663 
    17664 > select subtract #26.2/A:16@CG2
    17665 
    17666 280 atoms, 42 residues, 4 models selected 
    17667 
    17668 > select subtract #26.2/A:16@CA
    17669 
    17670 279 atoms, 42 residues, 4 models selected 
    17671 
    17672 > select subtract #26.2/A:16@O
    17673 
    17674 278 atoms, 42 residues, 4 models selected 
    17675 
    17676 > select subtract #26.2/A:15@CA
    17677 
    17678 277 atoms, 42 residues, 4 models selected 
    17679 
    17680 > select subtract #26.2/A:139@CA
    17681 
    17682 276 atoms, 42 residues, 4 models selected 
    17683 
    17684 > select subtract #26.2/A:15@C
    17685 
    17686 275 atoms, 42 residues, 4 models selected 
    17687 
    17688 > select subtract #26.2/A:16@CG1
    17689 
    17690 274 atoms, 42 residues, 4 models selected 
    17691 
    17692 > select subtract #26.2/A:16@CD1
    17693 
    17694 273 atoms, 42 residues, 4 models selected 
    17695 
    17696 > select subtract #26.2/A:13@O
    17697 
    17698 272 atoms, 42 residues, 4 models selected 
    17699 
    17700 > select subtract #26.2/A:16@CB
    17701 
    17702 271 atoms, 42 residues, 4 models selected 
    17703 
    17704 > select subtract #26.2/A:13@CA
    17705 
    17706 270 atoms, 42 residues, 4 models selected 
    17707 
    17708 > select subtract #26.2/A:13@CB
    17709 
    17710 269 atoms, 42 residues, 4 models selected 
    17711 
    17712 > select subtract #26.2/A:12@CB
    17713 
    17714 268 atoms, 42 residues, 4 models selected 
    17715 
    17716 > select subtract #26.2/A:13@N
    17717 
    17718 267 atoms, 42 residues, 4 models selected 
    17719 
    17720 > select subtract #26.2/A:12@N
    17721 
    17722 266 atoms, 42 residues, 4 models selected 
    17723 
    17724 > select subtract #26.2/A:12@C
    17725 
    17726 265 atoms, 42 residues, 4 models selected 
    17727 
    17728 > select subtract #26.2/A:13@OG
    17729 
    17730 264 atoms, 42 residues, 4 models selected 
    17731 
    17732 > select add #26.2/A:139@CA
    17733 
    17734 265 atoms, 42 residues, 4 models selected 
    17735 
    17736 > select add #26.2/A:15@CA
    17737 
    17738 266 atoms, 42 residues, 4 models selected 
    17739 
    17740 > select subtract #26.2/A:151@CB
    17741 
    17742 265 atoms, 42 residues, 4 models selected 
    17743 
    17744 > select subtract #26.2/A:158@CB
    17745 
    17746 264 atoms, 42 residues, 4 models selected 
    17747 
    17748 > select subtract #26.2/A:154@CG2
    17749 
    17750 263 atoms, 42 residues, 4 models selected 
    17751 
    17752 > select add #26.2/A:82@OE1
    17753 
    17754 264 atoms, 43 residues, 4 models selected 
    17755 
    17756 > select add #26.2/A:82@CD
    17757 
    17758 265 atoms, 43 residues, 4 models selected 
    17759 
    17760 > select add #26.2/A:81@CG
    17761 
    17762 266 atoms, 44 residues, 4 models selected 
    17763 
    17764 > select add #26.2/A:81@CB
    17765 
    17766 267 atoms, 44 residues, 4 models selected 
    17767 
    17768 > select add #26.2/A:82@CG
    17769 
    17770 268 atoms, 1 pseudobond, 44 residues, 5 models selected 
    17771 
    17772 > select add #26.2/A:81@CD
    17773 
    17774 269 atoms, 1 pseudobond, 44 residues, 5 models selected 
    17775 
    17776 > select add #26.2/A:81@NH1
    17777 
    17778 270 atoms, 1 pseudobond, 44 residues, 5 models selected 
    17779 
    17780 > select add #26.2/A:81@NH2
    17781 
    17782 271 atoms, 1 pseudobond, 44 residues, 5 models selected 
    17783 
    17784 > select add #26.2/A:81@NE
    17785 
    17786 272 atoms, 1 pseudobond, 44 residues, 5 models selected 
    17787 
    17788 > select add #26.2/A:81@CZ
    17789 
    17790 273 atoms, 1 pseudobond, 44 residues, 5 models selected 
    17791 
    17792 > select add #26.2/A:249@O
    17793 
    17794 274 atoms, 1 pseudobond, 45 residues, 5 models selected 
    17795 
    17796 > select subtract #26.2/A:151@CA
    17797 
    17798 273 atoms, 1 pseudobond, 45 residues, 5 models selected 
    17799 
    17800 > select subtract #26.2/A:151@N
    17801 
    17802 272 atoms, 1 pseudobond, 45 residues, 5 models selected 
    17803 
    17804 > select subtract #26.2/A:150@N
    17805 
    17806 271 atoms, 1 pseudobond, 45 residues, 5 models selected 
    17807 
    17808 > select add #26.2/A:142@CB
    17809 
    17810 272 atoms, 1 pseudobond, 46 residues, 5 models selected 
    17811 
    17812 > select add #26.2/A:142@CA
    17813 
    17814 273 atoms, 1 pseudobond, 46 residues, 5 models selected 
    17815 
    17816 > select add #26.2/A:154@CG2
    17817 
    17818 274 atoms, 1 pseudobond, 46 residues, 5 models selected 
    17819 
    17820 > select subtract #26.2/A:154@CG2
    17821 
    17822 273 atoms, 1 pseudobond, 46 residues, 5 models selected 
    17823 
    17824 > select add #26.2/A:154@CG2
    17825 
    17826 274 atoms, 1 pseudobond, 46 residues, 5 models selected 
    17827 
    17828 > select add #26.2/A:82@OE2
    17829 
    17830 275 atoms, 1 pseudobond, 46 residues, 5 models selected 
    17831 
    17832 > name sel pH-75-plugged-entrance
    17833 
    17834 "sel" is reserved and cannot be redefined 
    17835 
    17836 > name pH-75-plugged-entrance sel
    17837 
    17838 > select clear
    17839 
    17840 > hide #26 target s
    17841 
    17842 > name list
    17843 
    17844 binding_site_res /A:132,133,163,164,300,NA,HOH 
    17845 core /A:86-180,275-388 
    17846 cwm #42 
    17847 dimer /A:1-85,181-274 
    17848 dimer_TM /A:11-30,59-85,181-199,205-218,223-236,247-271 
    17849 pH-75-plugged-entrance sel 
    17850 pH-sensing /A:11,78,81,82,243,249,250,252,253,256 
    17851 
    17852 > show pH-75-plugged-entrance target s
    17853 
    17854 > hide #26 target c
    17855 
    17856 > show #26.1/A target s
    17857 
    17858 > select add #26
    17859 
    17860 3011 atoms, 3072 bonds, 390 residues, 5 models selected 
    17861 
    17862 > mlp sel & #!26.2
    17863 
    17864 Map values for surface "NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface":
    17865 minimum -27.17, mean 0.3244, maximum 23.52 
    17866 To also show corresponding color key, enter the above mlp command and add key
    17867 true 
    17868 
    17869 > select clear
    17870 
    17871 > hide #!7 models
    17872 
    17873 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 16068 of
    17874 299176 triangles, cap far, 1824 of 10660 triangles 
    17875 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 19002 of
    17876 299176 triangles, cap far, 1748 of 10880 triangles, cap near, 229 of 3002
    17877 triangles 
    17878 
    17879 > select #26.2/A:153@NZ
    17880 
    17881 1 atom, 1 residue, 1 model selected 
    17882 
    17883 > select clear
    17884 
    17885 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 22916 of
    17886 299176 triangles, cap far, 1943 of 10880 triangles, cap near, 267 of 3002
    17887 triangles 
    17888 
    17889 > select clear
    17890 
    17891 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 1491 of
    17892 299176 triangles, cap far, 239 of 10832 triangles 
    17893 
    17894 > select clear
    17895 
    17896 > show #26.1 target c
    17897 
    17898 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 14598 of
    17899 299176 triangles, cap far, 1196 of 10832 triangles 
    17900 
    17901 > select clear
    17902 
    17903 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 2963 of
    17904 299176 triangles, cap far, 319 of 10832 triangles 
    17905 
    17906 > select clear
    17907 
    17908 > select #26.2/A:134@CG2
    17909 
    17910 1 atom, 1 residue, 1 model selected 
    17911 
    17912 > select #26.2/A:134@CB
    17913 
    17914 1 atom, 1 residue, 1 model selected 
    17915 
    17916 > select #26.2/A:135@CA
    17917 
    17918 1 atom, 1 residue, 1 model selected 
    17919 
    17920 > select #26.2/A:134@CG2
    17921 
    17922 1 atom, 1 residue, 1 model selected 
    17923 
    17924 > select clear
    17925 
    17926 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 6962 of
    17927 299176 triangles, cap far, 754 of 11866 triangles 
    17928 
    17929 > select clear
    17930 
    17931 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 32887 of
    17932 299176 triangles 
    17933 
    17934 > select clear
    17935 
    17936 > select #26.2/A:256@ND1
    17937 
    17938 1 atom, 1 residue, 1 model selected 
    17939 
    17940 > select add #26.2/A:256@CE1
    17941 
    17942 2 atoms, 1 residue, 2 models selected 
    17943 
    17944 > select add #26.2/A:78@OE2
    17945 
    17946 3 atoms, 2 residues, 2 models selected 
    17947 
    17948 > select clear
    17949 
    17950 > select #26.2/A:256@CE1
    17951 
    17952 1 atom, 1 residue, 1 model selected 
    17953 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 23532 of
    17954 299176 triangles 
    17955 
    17956 > select clear
    17957 
    17958 > select #26.2/A:256@ND1
    17959 
    17960 1 atom, 1 residue, 1 model selected 
    17961 
    17962 > select add #26.2/A:256@CE1
    17963 
    17964 2 atoms, 1 residue, 2 models selected 
    17965 
    17966 > select add #26.2/A:260@CB
    17967 
    17968 3 atoms, 2 residues, 2 models selected 
    17969 
    17970 > select add #26.2/A:256@O
    17971 
    17972 4 atoms, 2 residues, 2 models selected 
    17973 
    17974 > select add #26.2/A:256@CB
    17975 
    17976 5 atoms, 2 residues, 2 models selected 
    17977 
    17978 > select add #26.2/A:256@CD2
    17979 
    17980 6 atoms, 2 residues, 2 models selected 
    17981 
    17982 > select add #26.2/A:256@CG
    17983 
    17984 7 atoms, 2 residues, 2 models selected 
    17985 
    17986 > select add #26.2/A:256@NE2
    17987 
    17988 8 atoms, 2 residues, 2 models selected 
    17989 
    17990 > select add #26.2/A:78@OE2
    17991 
    17992 9 atoms, 3 residues, 2 models selected 
    17993 
    17994 > select add #26.2/A:78@CD
    17995 
    17996 10 atoms, 3 residues, 2 models selected 
    17997 
    17998 > select add #26.2/A:157@SD
    17999 
    18000 11 atoms, 4 residues, 2 models selected 
    18001 
    18002 > select add #26.2/A:157@CB
    18003 
    18004 12 atoms, 4 residues, 2 models selected 
    18005 
    18006 > select add #26.2/A:138@CD1
    18007 
    18008 13 atoms, 5 residues, 2 models selected 
    18009 
    18010 > select add #26.2/A:157@CG
    18011 
    18012 14 atoms, 5 residues, 2 models selected 
    18013 
    18014 > select add #26.2/A:161@CD1
    18015 
    18016 15 atoms, 6 residues, 2 models selected 
    18017 
    18018 > select add #26.2/A:78@CB
    18019 
    18020 16 atoms, 6 residues, 2 models selected 
    18021 
    18022 > select add #26.2/A:78@CG
    18023 
    18024 17 atoms, 6 residues, 2 models selected 
    18025 
    18026 > select add #26.2/A:75@CA
    18027 
    18028 18 atoms, 7 residues, 2 models selected 
    18029 
    18030 > select add #26.2/A:75@N
    18031 
    18032 19 atoms, 7 residues, 2 models selected 
    18033 
    18034 > select add #26.2/A:74@C
    18035 
    18036 20 atoms, 8 residues, 2 models selected 
    18037 
    18038 > select add #26.2/A:74@CG
    18039 
    18040 21 atoms, 8 residues, 2 models selected 
    18041 
    18042 > select add #26.2/A:74@CB
    18043 
    18044 22 atoms, 8 residues, 2 models selected 
    18045 
    18046 > select add #26.2/A:75@CG2
    18047 
    18048 23 atoms, 8 residues, 2 models selected 
    18049 
    18050 > select subtract #26.2/A:75@CG2
    18051 
    18052 22 atoms, 8 residues, 2 models selected 
    18053 
    18054 > select add #26.2/A:75@CG2
    18055 
    18056 23 atoms, 8 residues, 2 models selected 
    18057 
    18058 > select add #26.2/A:71@CE1
    18059 
    18060 24 atoms, 9 residues, 2 models selected 
    18061 
    18062 > select add #26.2/A:71@CZ
    18063 
    18064 25 atoms, 9 residues, 2 models selected 
    18065 
    18066 > select add #26.2/A:134@CD1
    18067 
    18068 26 atoms, 10 residues, 2 models selected 
    18069 
    18070 > select add #26.2/A:161@CG1
    18071 
    18072 27 atoms, 10 residues, 2 models selected 
    18073 
    18074 > select add #26.2/A:134@CG2
    18075 
    18076 28 atoms, 10 residues, 2 models selected 
    18077 
    18078 > select add #26.2/A:134@CB
    18079 
    18080 29 atoms, 10 residues, 2 models selected 
    18081 
    18082 > select add #26.2/A:135@CA
    18083 
    18084 30 atoms, 11 residues, 2 models selected 
    18085 
    18086 > select add #26.2/A:135@N
    18087 
    18088 31 atoms, 11 residues, 2 models selected 
    18089 
    18090 > select add #26.2/A:134@O
    18091 
    18092 32 atoms, 11 residues, 2 models selected 
    18093 
    18094 > select add #26.2/A:135@CB
    18095 
    18096 33 atoms, 11 residues, 2 models selected 
    18097 
    18098 > select add #26.2/A:264@CD1
    18099 
    18100 34 atoms, 12 residues, 2 models selected 
    18101 
    18102 > select add #26.2/A:259@CG1
    18103 
    18104 35 atoms, 13 residues, 2 models selected 
    18105 
    18106 > select add #26.2/A:74@CD2
    18107 
    18108 36 atoms, 13 residues, 2 models selected 
    18109 
    18110 > select add #26.2/A:259@CB
    18111 
    18112 37 atoms, 13 residues, 2 models selected 
    18113 
    18114 > select add #26.2/A:256@CA
    18115 
    18116 38 atoms, 13 residues, 2 models selected 
    18117 
    18118 > select add #26.2/A:260@CA
    18119 
    18120 39 atoms, 13 residues, 2 models selected 
    18121 
    18122 > select add #26.2/A:260@N
    18123 
    18124 40 atoms, 13 residues, 2 models selected 
    18125 
    18126 > select add #26.2/A:135@O
    18127 
    18128 41 atoms, 13 residues, 2 models selected 
    18129 
    18130 > select add #26.2/A:139@N
    18131 
    18132 42 atoms, 14 residues, 2 models selected 
    18133 
    18134 > select add #26.2/A:14@C
    18135 
    18136 43 atoms, 15 residues, 2 models selected 
    18137 
    18138 > select add #26.2/A:14@CA
    18139 
    18140 44 atoms, 15 residues, 2 models selected 
    18141 
    18142 > select add #26.2/A:18@CD1
    18143 
    18144 45 atoms, 16 residues, 2 models selected 
    18145 
    18146 > select add #26.2/A:264@CB
    18147 
    18148 46 atoms, 16 residues, 2 models selected 
    18149 
    18150 > select add #26.2/A:18@CB
    18151 
    18152 47 atoms, 16 residues, 2 models selected 
    18153 
    18154 > select add #26.2/A:18@CD2
    18155 
    18156 48 atoms, 16 residues, 2 models selected 
    18157 
    18158 > select add #26.2/A:18@CG
    18159 
    18160 49 atoms, 16 residues, 2 models selected 
    18161 
    18162 > select add #26.2/A:14@O
    18163 
    18164 50 atoms, 16 residues, 2 models selected 
    18165 
    18166 > select add #26.2/A:265@CD
    18167 
    18168 51 atoms, 17 residues, 2 models selected 
    18169 
    18170 > select add #26.2/A:260@O
    18171 
    18172 52 atoms, 17 residues, 2 models selected 
    18173 
    18174 > select add #26.2/A:265@CG
    18175 
    18176 53 atoms, 17 residues, 2 models selected 
    18177 
    18178 > select add #26.2/A:138@CB
    18179 
    18180 54 atoms, 17 residues, 2 models selected 
    18181 
    18182 > select add #26.2/A:15@N
    18183 
    18184 55 atoms, 18 residues, 2 models selected 
    18185 
    18186 > select add #26.2/A:139@CA
    18187 
    18188 56 atoms, 18 residues, 2 models selected 
    18189 
    18190 > select add #26.2/A:15@CA
    18191 
    18192 57 atoms, 18 residues, 2 models selected 
    18193 
    18194 > select add #26.2/A:138@C
    18195 
    18196 58 atoms, 18 residues, 2 models selected 
    18197 
    18198 > select add #26.2/A:138@O
    18199 
    18200 59 atoms, 18 residues, 2 models selected 
    18201 
    18202 > select add #26.2/A:142@CB
    18203 
    18204 60 atoms, 19 residues, 2 models selected 
    18205 
    18206 > select add #26.2/A:11@CA
    18207 
    18208 61 atoms, 20 residues, 2 models selected 
    18209 
    18210 > select add #26.2/A:11@O
    18211 
    18212 62 atoms, 20 residues, 2 models selected 
    18213 
    18214 > select add #26.2/A:11@C
    18215 
    18216 63 atoms, 20 residues, 2 models selected 
    18217 
    18218 > select add #26.2/A:11@N
    18219 
    18220 64 atoms, 20 residues, 2 models selected 
    18221 
    18222 > select add #26.2/A:11@OD2
    18223 
    18224 65 atoms, 20 residues, 2 models selected 
    18225 
    18226 > select add #26.2/A:14@N
    18227 
    18228 66 atoms, 20 residues, 2 models selected 
    18229 
    18230 > select add #26.2/A:13@OG
    18231 
    18232 67 atoms, 21 residues, 2 models selected 
    18233 
    18234 > select add #26.2/A:11@CG
    18235 
    18236 68 atoms, 21 residues, 2 models selected 
    18237 
    18238 > select add #26.2/A:11@CB
    18239 
    18240 69 atoms, 21 residues, 2 models selected 
    18241 
    18242 > select add #26.2/A:261@CZ
    18243 
    18244 70 atoms, 22 residues, 2 models selected 
    18245 
    18246 > select add #26.2/A:261@CE1
    18247 
    18248 71 atoms, 22 residues, 2 models selected 
    18249 
    18250 > select add #26.2/A:261@OH
    18251 
    18252 72 atoms, 22 residues, 2 models selected 
    18253 
    18254 > select subtract #26.2/A:261@CE1
    18255 
    18256 71 atoms, 22 residues, 2 models selected 
    18257 
    18258 > show #!7 models
    18259 
    18260 > hide #!7 models
    18261 
    18262 > select add #26.2/A:257@CD
    18263 
    18264 72 atoms, 23 residues, 2 models selected 
    18265 
    18266 > select add #26.2/A:257@N
    18267 
    18268 73 atoms, 23 residues, 2 models selected 
    18269 
    18270 > select add #26.2/A:256@C
    18271 
    18272 74 atoms, 23 residues, 2 models selected 
    18273 
    18274 > select add #26.2/A:257@CA
    18275 
    18276 75 atoms, 23 residues, 2 models selected 
    18277 
    18278 > select add #26.2/A:261@CE2
    18279 
    18280 76 atoms, 23 residues, 2 models selected 
    18281 
    18282 > select add #26.2/A:257@CB
    18283 
    18284 77 atoms, 23 residues, 2 models selected 
    18285 
    18286 > select add #26.2/A:257@CG
    18287 
    18288 78 atoms, 23 residues, 2 models selected 
    18289 
    18290 > select add #26.2/A:261@CE1
    18291 
    18292 79 atoms, 23 residues, 2 models selected 
    18293 
    18294 > select add #26.2/A:253@NE2
    18295 
    18296 80 atoms, 24 residues, 2 models selected 
    18297 
    18298 > select add #26.2/A:253@O
    18299 
    18300 81 atoms, 24 residues, 2 models selected 
    18301 
    18302 > select add #26.2/A:253@CD2
    18303 
    18304 82 atoms, 24 residues, 2 models selected 
    18305 
    18306 > select add #26.2/A:252@CG
    18307 
    18308 83 atoms, 25 residues, 2 models selected 
    18309 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 41 of
    18310 299176 triangles 
    18311 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 12439 of
    18312 299176 triangles 
    18313 
    18314 > select clear
    18315 
    18316 > ui mousemode right select
    18317 
    18318 > ui mousemode right translate
    18319 
    18320 > hide #26.2.1 models
    18321 
    18322 > show #26.2 target c
    18323 
    18324 > show #26.2.1 models
    18325 
    18326 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 27437 of
    18327 299176 triangles, 71 residues 
    18328 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 24490 of
    18329 299176 triangles, 45 residues 
    18330 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 4712 of
    18331 299176 triangles, 13 residues 
    18332 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 2203 of
    18333 299176 triangles, 14 residues 
    18334 
    18335 > select add #26.2/A:71@CE1
    18336 
    18337 708 atoms, 96 residues, 2 models selected 
    18338 
    18339 > select add #26.2/A:75@CG2
    18340 
    18341 709 atoms, 97 residues, 2 models selected 
    18342 
    18343 > select add #26.2/A:264@CD1
    18344 
    18345 710 atoms, 98 residues, 2 models selected 
    18346 
    18347 > select add #26.2/A:71@CZ
    18348 
    18349 711 atoms, 98 residues, 2 models selected 
    18350 
    18351 > select add #26.2/A:18@CD1
    18352 
    18353 712 atoms, 99 residues, 2 models selected 
    18354 
    18355 > select add #26.2/A:264@CB
    18356 
    18357 713 atoms, 99 residues, 2 models selected 
    18358 
    18359 > select add #26.2/A:18@CB
    18360 
    18361 714 atoms, 99 residues, 2 models selected 
    18362 
    18363 > select add #26.2/A:18@CD2
    18364 
    18365 715 atoms, 99 residues, 2 models selected 
    18366 
    18367 > select add #26.2/A:18@CG
    18368 
    18369 716 atoms, 99 residues, 2 models selected 
    18370 
    18371 > select add #26.2/A:11@OD2
    18372 
    18373 717 atoms, 100 residues, 2 models selected 
    18374 
    18375 > select add #26.2/A:11@OD1
    18376 
    18377 718 atoms, 100 residues, 2 models selected 
    18378 
    18379 > select add #26.2/A:11@CB
    18380 
    18381 719 atoms, 100 residues, 2 models selected 
    18382 
    18383 > select add #26.2/A:11@CG
    18384 
    18385 720 atoms, 100 residues, 2 models selected 
    18386 
    18387 > select add #26.2/A:11@N
    18388 
    18389 721 atoms, 100 residues, 2 models selected 
    18390 
    18391 > select add #26.2/A:11@CA
    18392 
    18393 722 atoms, 100 residues, 2 models selected 
    18394 
    18395 > select add #26.2/A:142@CB
    18396 
    18397 723 atoms, 101 residues, 2 models selected 
    18398 
    18399 > select subtract #26.2/A:363@CD2
    18400 
    18401 722 atoms, 101 residues, 2 models selected 
    18402 
    18403 > select subtract #26.2/A:363@CA
    18404 
    18405 721 atoms, 101 residues, 2 models selected 
    18406 
    18407 > select subtract #26.2/A:339@CE2
    18408 
    18409 720 atoms, 101 residues, 2 models selected 
    18410 
    18411 > select subtract #26.2/A:339@CD2
    18412 
    18413 719 atoms, 101 residues, 2 models selected 
    18414 
    18415 > select subtract #26.2/A:339@CZ
    18416 
    18417 718 atoms, 101 residues, 2 models selected 
    18418 
    18419 > select subtract #26.2/A:136@CZ
    18420 
    18421 717 atoms, 101 residues, 2 models selected 
    18422 
    18423 > select subtract #26.2/A:136@CE2
    18424 
    18425 716 atoms, 101 residues, 2 models selected 
    18426 
    18427 > select subtract #26.2/A:339@CE1
    18428 
    18429 715 atoms, 101 residues, 2 models selected 
    18430 
    18431 > select subtract #26.2/A:339@CB
    18432 
    18433 714 atoms, 101 residues, 2 models selected 
    18434 
    18435 > select subtract #26.2/A:136@CE1
    18436 
    18437 713 atoms, 101 residues, 2 models selected 
    18438 
    18439 > select subtract #26.2/A:136@CD1
    18440 
    18441 712 atoms, 101 residues, 2 models selected 
    18442 
    18443 > select subtract #26.2/A:139@CA
    18444 
    18445 711 atoms, 101 residues, 2 models selected 
    18446 
    18447 > select subtract #26.2/A:16@CA
    18448 
    18449 710 atoms, 101 residues, 2 models selected 
    18450 
    18451 > select subtract #26.2/A:16@CG2
    18452 
    18453 709 atoms, 101 residues, 2 models selected 
    18454 
    18455 > select subtract #26.2/A:16@O
    18456 
    18457 708 atoms, 101 residues, 2 models selected 
    18458 
    18459 > select subtract #26.2/A:16@CG1
    18460 
    18461 707 atoms, 101 residues, 2 models selected 
    18462 
    18463 > select add #26.2/A:16@CG1
    18464 
    18465 708 atoms, 101 residues, 2 models selected 
    18466 
    18467 > select subtract #26.2/A:16@CG1
    18468 
    18469 707 atoms, 101 residues, 2 models selected 
    18470 
    18471 > select subtract #26.2/A:15@CA
    18472 
    18473 706 atoms, 101 residues, 2 models selected 
    18474 
    18475 > select subtract #26.2/A:139@C
    18476 
    18477 705 atoms, 101 residues, 2 models selected 
    18478 
    18479 > select subtract #26.2/A:15@C
    18480 
    18481 704 atoms, 101 residues, 2 models selected 
    18482 
    18483 > select subtract #26.2/A:16@CD1
    18484 
    18485 703 atoms, 101 residues, 2 models selected 
    18486 
    18487 > select subtract #26.2/A:12@CB
    18488 
    18489 702 atoms, 101 residues, 2 models selected 
    18490 
    18491 > select subtract #26.2/A:13@CA
    18492 
    18493 701 atoms, 101 residues, 2 models selected 
    18494 
    18495 > select subtract #26.2/A:13@O
    18496 
    18497 700 atoms, 101 residues, 2 models selected 
    18498 
    18499 > select subtract #26.2/A:16@CB
    18500 
    18501 699 atoms, 101 residues, 2 models selected 
    18502 
    18503 > select subtract #26.2/A:265@O
    18504 
    18505 698 atoms, 101 residues, 2 models selected 
    18506 
    18507 > select subtract #26.2/A:265@CB
    18508 
    18509 697 atoms, 101 residues, 2 models selected 
    18510 
    18511 > select subtract #26.2/A:265@C
    18512 
    18513 696 atoms, 101 residues, 2 models selected 
    18514 
    18515 > select subtract #26.2/A:261@O
    18516 
    18517 695 atoms, 101 residues, 2 models selected 
    18518 
    18519 > select subtract #26.2/A:265@CG
    18520 
    18521 694 atoms, 101 residues, 2 models selected 
    18522 
    18523 > select subtract #26.2/A:261@CB
    18524 
    18525 693 atoms, 101 residues, 2 models selected 
    18526 
    18527 > select subtract #26.2/A:261@CA
    18528 
    18529 692 atoms, 101 residues, 2 models selected 
    18530 
    18531 > select subtract #26.2/A:261@C
    18532 
    18533 691 atoms, 101 residues, 2 models selected 
    18534 
    18535 > select subtract #26.2/A:258@CB
    18536 
    18537 690 atoms, 101 residues, 2 models selected 
    18538 
    18539 > select subtract #26.2/A:258@NE1
    18540 
    18541 689 atoms, 101 residues, 2 models selected 
    18542 
    18543 > select subtract #26.2/A:258@CZ2
    18544 
    18545 688 atoms, 101 residues, 2 models selected 
    18546 
    18547 > select subtract #26.2/A:258@CH2
    18548 
    18549 687 atoms, 101 residues, 2 models selected 
    18550 
    18551 > select subtract #26.2/A:258@CZ3
    18552 
    18553 686 atoms, 101 residues, 2 models selected 
    18554 
    18555 > select subtract #26.2/A:258@CD2
    18556 
    18557 685 atoms, 101 residues, 2 models selected 
    18558 
    18559 > select subtract #26.2/A:258@CE3
    18560 
    18561 684 atoms, 101 residues, 2 models selected 
    18562 
    18563 > select add #26.2/A:258@CD2
    18564 
    18565 685 atoms, 101 residues, 2 models selected 
    18566 
    18567 > select subtract #26.2/A:258@CG
    18568 
    18569 684 atoms, 101 residues, 2 models selected 
    18570 
    18571 > select subtract #26.2/A:258@CE2
    18572 
    18573 683 atoms, 101 residues, 2 models selected 
    18574 
    18575 > select subtract #26.2/A:258@CD2
    18576 
    18577 682 atoms, 101 residues, 2 models selected 
    18578 
    18579 > select subtract #26.2/A:258@CD1
    18580 
    18581 681 atoms, 101 residues, 2 models selected 
    18582 
    18583 > select subtract #26.2/A:258@CA
    18584 
    18585 680 atoms, 101 residues, 2 models selected 
    18586 
    18587 > show #!7 models
    18588 
    18589 > select add #26.2/A:252@OE2
    18590 
    18591 681 atoms, 102 residues, 2 models selected 
    18592 
    18593 > select add #26.2/A:252@CG
    18594 
    18595 682 atoms, 102 residues, 2 models selected 
    18596 
    18597 > select add #26.2/A:252@CD
    18598 
    18599 683 atoms, 102 residues, 2 models selected 
    18600 
    18601 > select add #26.2/A:81@CD
    18602 
    18603 684 atoms, 103 residues, 2 models selected 
    18604 
    18605 > select add #26.2/A:81@NH2
    18606 
    18607 685 atoms, 103 residues, 2 models selected 
    18608 
    18609 > select add #26.2/A:81@NE
    18610 
    18611 686 atoms, 103 residues, 2 models selected 
    18612 
    18613 > select add #26.2/A:81@NH1
    18614 
    18615 687 atoms, 103 residues, 2 models selected 
    18616 
    18617 > select add #26.2/A:81@CZ
    18618 
    18619 688 atoms, 103 residues, 2 models selected 
    18620 
    18621 > select add #26.2/A:249@O
    18622 
    18623 689 atoms, 104 residues, 2 models selected 
    18624 
    18625 > select add #26.2/A:252@CB
    18626 
    18627 690 atoms, 104 residues, 2 models selected 
    18628 
    18629 > select add #26.2/A:253@CA
    18630 
    18631 691 atoms, 105 residues, 2 models selected 
    18632 
    18633 > select add #26.2/A:253@N
    18634 
    18635 692 atoms, 105 residues, 2 models selected 
    18636 
    18637 > select add #26.2/A:252@C
    18638 
    18639 693 atoms, 105 residues, 2 models selected 
    18640 
    18641 > select add #26.2/A:252@O
    18642 
    18643 694 atoms, 105 residues, 2 models selected 
    18644 
    18645 > select add #26.2/A:253@O
    18646 
    18647 695 atoms, 105 residues, 2 models selected 
    18648 
    18649 > select add #26.2/A:253@NE2
    18650 
    18651 696 atoms, 105 residues, 2 models selected 
    18652 
    18653 > select add #26.2/A:253@CD2
    18654 
    18655 697 atoms, 105 residues, 2 models selected 
    18656 
    18657 > select add #26.2/A:253@CE1
    18658 
    18659 698 atoms, 105 residues, 2 models selected 
    18660 
    18661 > select add #26.2/A:253@CB
    18662 
    18663 699 atoms, 105 residues, 2 models selected 
    18664 
    18665 > select add #26.2/A:253@ND1
    18666 
    18667 700 atoms, 105 residues, 2 models selected 
    18668 
    18669 > select add #26.2/A:253@CG
    18670 
    18671 701 atoms, 105 residues, 2 models selected 
    18672 
    18673 > select add #26.2/A:81@CG
    18674 
    18675 702 atoms, 105 residues, 2 models selected 
    18676 
    18677 > select add #26.2/A:82@OE1
    18678 
    18679 703 atoms, 106 residues, 2 models selected 
    18680 
    18681 > select add #26.2/A:81@CB
    18682 
    18683 704 atoms, 106 residues, 2 models selected 
    18684 
    18685 > select add #26.2/A:82@CD
    18686 
    18687 705 atoms, 106 residues, 2 models selected 
    18688 
    18689 > select add #26.2/A:82@CG
    18690 
    18691 706 atoms, 1 pseudobond, 106 residues, 3 models selected 
    18692 
    18693 > select add #26.2/A:154@CG2
    18694 
    18695 707 atoms, 1 pseudobond, 107 residues, 3 models selected 
    18696 
    18697 > select add #26.2/A:82@OE2
    18698 
    18699 708 atoms, 1 pseudobond, 107 residues, 3 models selected 
    18700 
    18701 > select add #26.2/A:154@CA
    18702 
    18703 709 atoms, 1 pseudobond, 107 residues, 3 models selected 
    18704 
    18705 > select add #26.2/A:154@CD1
    18706 
    18707 710 atoms, 1 pseudobond, 107 residues, 3 models selected 
    18708 
    18709 > select add #26.2/A:154@CG1
    18710 
    18711 711 atoms, 1 pseudobond, 107 residues, 3 models selected 
    18712 
    18713 > select add #26.2/A:154@N
    18714 
    18715 712 atoms, 1 pseudobond, 107 residues, 3 models selected 
    18716 
    18717 > select add #26.2/A:150@CD1
    18718 
    18719 713 atoms, 1 pseudobond, 108 residues, 3 models selected 
    18720 
    18721 > select add #26.2/A:150@CD2
    18722 
    18723 714 atoms, 1 pseudobond, 108 residues, 3 models selected 
    18724 
    18725 > select add #26.2/A:150@CB
    18726 
    18727 715 atoms, 1 pseudobond, 108 residues, 3 models selected 
    18728 
    18729 > select add #26.2/A:150@CG
    18730 
    18731 716 atoms, 1 pseudobond, 108 residues, 3 models selected 
    18732 
    18733 > select add #26.2/A:150@CA
    18734 
    18735 717 atoms, 1 pseudobond, 108 residues, 3 models selected 
    18736 
    18737 > hide #26.2&~sel target s
    18738 
    18739 > show #26.2&~sel target s
    18740 
    18741 > select add #26.2/A:139@CA
    18742 
    18743 718 atoms, 1 pseudobond, 108 residues, 3 models selected 
    18744 
    18745 > select add #26.2/A:15@CA
    18746 
    18747 719 atoms, 1 pseudobond, 108 residues, 3 models selected 
    18748 
    18749 > select add #26.2/A:265@CG
    18750 
    18751 720 atoms, 1 pseudobond, 108 residues, 3 models selected 
    18752 
    18753 > select add #26.2/A:11@O
    18754 
    18755 721 atoms, 1 pseudobond, 108 residues, 3 models selected 
    18756 
    18757 > select add #26.2/A:11@C
    18758 
    18759 722 atoms, 1 pseudobond, 108 residues, 3 models selected 
    18760 
    18761 > select add #26.2/A:267@CE1
    18762 
    18763 723 atoms, 1 pseudobond, 109 residues, 3 models selected 
    18764 
    18765 > select add #26.2/A:68@SD
    18766 
    18767 724 atoms, 1 pseudobond, 110 residues, 3 models selected 
    18768 
    18769 > select add #26.2/A:267@CZ
    18770 
    18771 725 atoms, 1 pseudobond, 110 residues, 3 models selected 
    18772 
    18773 > select add #26.2/A:267@CD1
    18774 
    18775 726 atoms, 1 pseudobond, 110 residues, 3 models selected 
    18776 
    18777 > select add #26.2/A:264@CD2
    18778 
    18779 727 atoms, 1 pseudobond, 110 residues, 3 models selected 
    18780 
    18781 > select add #26.2/A:68@CE
    18782 
    18783 728 atoms, 1 pseudobond, 110 residues, 3 models selected 
    18784 
    18785 > select add #26.2/A:71@CE2
    18786 
    18787 729 atoms, 1 pseudobond, 110 residues, 3 models selected 
    18788 Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 8669 of
    18789 299176 triangles, 20 residues 
    18790 
    18791 > hide #26.2&~sel target s
    18792 
    18793 > select subtract #26.2/A:113@CB
    18794 
    18795 736 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18796 
    18797 > select subtract #26.2/A:113@O
    18798 
    18799 735 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18800 
    18801 > select subtract #26.2/A:113@C
    18802 
    18803 734 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18804 
    18805 > select subtract #26.2/A:113@CD2
    18806 
    18807 733 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18808 
    18809 > select subtract #26.2/A:113@CD1
    18810 
    18811 732 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18812 
    18813 > select subtract #26.2/A:126@CD1
    18814 
    18815 731 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18816 
    18817 > select subtract #26.2/A:126@CG
    18818 
    18819 730 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18820 
    18821 > select subtract #26.2/A:126@NE1
    18822 
    18823 729 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18824 
    18825 > select subtract #26.2/A:126@CZ2
    18826 
    18827 728 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18828 
    18829 > select subtract #26.2/A:126@CH2
    18830 
    18831 727 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18832 
    18833 > select subtract #26.2/A:126@CZ3
    18834 
    18835 726 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18836 
    18837 > select subtract #26.2/A:126@CD2
    18838 
    18839 725 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18840 
    18841 > select subtract #26.2/A:126@CE3
    18842 
    18843 724 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18844 
    18845 > select subtract #26.2/A:126@CE2
    18846 
    18847 723 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18848 
    18849 > select subtract #26.2/A:126@CB
    18850 
    18851 722 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18852 
    18853 > select subtract #26.2/A:161@CD1
    18854 
    18855 721 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18856 
    18857 > select subtract #26.2/A:157@CE
    18858 
    18859 720 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18860 
    18861 > select subtract #26.2/A:82@CG
    18862 
    18863 719 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18864 
    18865 > select add #26.2/A:82@CG
    18866 
    18867 720 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18868 
    18869 > select add #26.2/A:157@CE
    18870 
    18871 721 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18872 
    18873 > select add #26.2/A:161@CD1
    18874 
    18875 722 atoms, 1 pseudobond, 112 residues, 5 models selected 
    18876 
    18877 > show #26.2&~sel target s
    18878 
    18879 > select add #26.2/A:74@CD2
    18880 
    18881 723 atoms, 1 pseudobond, 113 residues, 5 models selected 
    18882 
    18883 > select add #26.2/A:74@CB
    18884 
    18885 724 atoms, 1 pseudobond, 113 residues, 5 models selected 
    18886 
    18887 > select add #26.2/A:74@CG
    18888 
    18889 725 atoms, 1 pseudobond, 113 residues, 5 models selected 
    18890 
    18891 > select add #26.2/A:75@N
    18892 
    18893 726 atoms, 1 pseudobond, 113 residues, 5 models selected 
    18894 
    18895 > select add #26.2/A:75@CA
    18896 
    18897 727 atoms, 1 pseudobond, 113 residues, 5 models selected 
     1217[deleted to fit within ticket limits]
    188981218
    188991219> select add #26.2/A:74@C