Changes between Initial Version and Version 1 of Ticket #6121


Ignore:
Timestamp:
Feb 9, 2022, 10:43:33 AM (4 years ago)
Author:
pett
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #6121

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

  • Ticket #6121 – Description

    initial v1  
    15931593 
    15941594
    1595 > open
    1596 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
    1597 
    1598 Summary of feedback from opening
    1599 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb 
    1600 --- 
    1601 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    1602 THR A 20 1 14 
    1603 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    1604 17 
    1605 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    1606 15 
    1607 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    1608 13 
    1609 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    1610 53 
    1611 10570 messages similar to the above omitted 
    1612  
    1613 Chain information for hNup358_1_CRinner.pdb #15 
    1614 --- 
    1615 Chain | Description 
    1616 0 | No description available 
    1617  
    1618 
    1619 > open
    1620 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
    1621 
    1622 Summary of feedback from opening
    1623 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb 
    1624 --- 
    1625 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    1626 THR A 20 1 14 
    1627 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    1628 17 
    1629 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    1630 15 
    1631 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    1632 13 
    1633 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    1634 53 
    1635 10570 messages similar to the above omitted 
    1636  
    1637 Chain information for hNup358_2_CRinner.pdb #16 
    1638 --- 
    1639 Chain | Description 
    1640 0 | No description available 
    1641  
    1642 
    1643 > open
    1644 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
    1645 
    1646 Summary of feedback from opening
    1647 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb 
    1648 --- 
    1649 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    1650 THR A 20 1 14 
    1651 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    1652 17 
    1653 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    1654 15 
    1655 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    1656 13 
    1657 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    1658 53 
    1659 10570 messages similar to the above omitted 
    1660  
    1661 Chain information for hNup358_CRmiddle.pdb #17 
    1662 --- 
    1663 Chain | Description 
    1664 0 | No description available 
    1665  
    1666 
    1667 > open
    1668 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
    1669 
    1670 Summary of feedback from opening
    1671 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb 
    1672 --- 
    1673 warnings | Duplicate atom serial number found: 272408 
    1674 Duplicate atom serial number found: 272409 
    1675 Duplicate atom serial number found: 272410 
    1676 Duplicate atom serial number found: 272411 
    1677 Duplicate atom serial number found: 272412 
    1678 70 messages similar to the above omitted 
    1679  
    1680 Chain information for IRcyt_outer.pdb #18 
    1681 --- 
    1682 Chain | Description 
    1683 4 | No description available 
    1684 A | No description available 
    1685 B | No description available 
    1686 D | No description available 
    1687 E | No description available 
    1688 F | No description available 
    1689 H | No description available 
    1690 I | No description available 
    1691 J | No description available 
    1692 U | No description available 
    1693  
    1694 
    1695 > open
    1696 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
    1697 
    1698 Summary of feedback from opening
    1699 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb 
    1700 --- 
    1701 warnings | Duplicate atom serial number found: 616953 
    1702 Duplicate atom serial number found: 616954 
    1703 Duplicate atom serial number found: 616955 
    1704 Duplicate atom serial number found: 616956 
    1705 Duplicate atom serial number found: 616957 
    1706 130 messages similar to the above omitted 
    1707  
    1708 Chain information for IRcyt_inner.pdb #19 
    1709 --- 
    1710 Chain | Description 
    1711 A | No description available 
    1712 C | No description available 
    1713 D | No description available 
    1714 F | No description available 
    1715 H | No description available 
    1716 I | No description available 
    1717 J | No description available 
    1718 U | No description available 
    1719  
    1720 
    1721 > open
    1722 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
    1723 
    1724 Summary of feedback from opening
    1725 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb 
    1726 --- 
    1727 warnings | Duplicate atom serial number found: 652149 
    1728 Duplicate atom serial number found: 652150 
    1729 Duplicate atom serial number found: 652151 
    1730 Duplicate atom serial number found: 652152 
    1731 Duplicate atom serial number found: 652153 
    1732 130 messages similar to the above omitted 
    1733  
    1734 Chain information for IRnuc_inner.pdb #20 
    1735 --- 
    1736 Chain | Description 
    1737 A | No description available 
    1738 C | No description available 
    1739 D | No description available 
    1740 F | No description available 
    1741 H | No description available 
    1742 I | No description available 
    1743 J | No description available 
    1744 U | No description available 
    1745  
    1746 
    1747 > open
    1748 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
    1749 
    1750 Summary of feedback from opening
    1751 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb 
    1752 --- 
    1753 warnings | Duplicate atom serial number found: 687345 
    1754 Duplicate atom serial number found: 687346 
    1755 Duplicate atom serial number found: 687347 
    1756 Duplicate atom serial number found: 687348 
    1757 Duplicate atom serial number found: 687349 
    1758 130 messages similar to the above omitted 
    1759  
    1760 Chain information for IRnuc_outer.pdb #21 
    1761 --- 
    1762 Chain | Description 
    1763 4 | No description available 
    1764 A | No description available 
    1765 B | No description available 
    1766 D | No description available 
    1767 E | No description available 
    1768 F | No description available 
    1769 H | No description available 
    1770 I | No description available 
    1771 J | No description available 
    1772 U | No description available 
    1773  
    1774 
    1775 > hide #!8 models
    1776 
    1777 > select #19/C:832@CG2
    1778 
    1779 1 atom, 1 residue, 1 model selected 
    1780 
    1781 > hide sel atoms
    1782 
    1783 > hide sel atoms
    1784 
    1785 > hide sel cartoons
    1786 
    1787 > hide sel atoms
    1788 
    1789 > hide sel atoms
    1790 
    1791 > hide atoms #13-21
    1792 
    1793 Expected ',' or a keyword 
    1794 
    1795 > hide #13-21
    1796 
    1797 > hide #9-21
    1798 
    1799 > hide #!9 models
    1800 
    1801 > show #!9 models
    1802 
    1803 > hide #!10 models
    1804 
    1805 > show #!10 models
    1806 
    1807 > hide #!14 models
    1808 
    1809 > show #!14 models
    1810 
    1811 > hide #9-21
    1812 
    1813 > ribbon #9-21
    1814 
    1815 > open
    1816 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
    1817 
    1818 Summary of feedback from opening
    1819 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb 
    1820 --- 
    1821 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    1822 THR A 20 1 14 
    1823 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    1824 17 
    1825 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    1826 15 
    1827 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    1828 13 
    1829 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    1830 53 
    1831 9610 messages similar to the above omitted 
    1832  
    1833 Chain information for hNup155_CRconnector.pdb #22 
    1834 --- 
    1835 Chain | Description 
    1836 D | No description available 
    1837 F | No description available 
    1838 U | No description available 
    1839  
    1840 
    1841 > open
    1842 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/YhNup155_NRconnector.pdb
    1843 
    1844 No such file/path:
    1845 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/YhNup155_NRconnector.pdb 
    1846 
    1847 > select #22/D:325
    1848 
    1849 6 atoms, 5 bonds, 1 residue, 1 model selected 
    1850 
    1851 > color /F/F?/F?? #b4e400
    1852 
    1853 > color /Y/Y?/Y?? #FF004A
    1854 
    1855 > color /0/0?/0?? cyan
    1856 
    1857 > color /E/E/E?? cyan
    1858 
    1859 > color /4/4?/4?? #005887
    1860 
    1861 > color /A #FF004A
    1862 
    1863 > color /C #005887
    1864 
    1865 > color /F #b4e400
    1866 
    1867 > color /B #0075BE
    1868 
    1869 > color /D #FA8072
    1870 
    1871 > color /J #CAEF00
    1872 
    1873 > color /K #0098EB
    1874 
    1875 > color /Q #0098EB
    1876 
    1877 > color /M #436495
    1878 
    1879 > color /S #981E05
    1880 
    1881 > color /T #00C9CA
    1882 
    1883 > color /U #20639B
    1884 
    1885 > color /V #ed553B
    1886 
    1887 > color /W #00A567
    1888 
    1889 > color /Z #FFA04D
    1890 
    1891 > color /2 #23c6c8
    1892 
    1893 > color /3 #FFC200
    1894 
    1895 > color /4 #dc4c77
    1896 
    1897 > color /8 #9D003D
    1898 
    1899 > color /9 #5A3389
    1900 
    1901 > color /L #FF5851
    1902 
    1903 > color /N #4CC7ED
    1904 
    1905 > color /R #FFC459
    1906 
    1907 > color /P #FF8853
    1908 
    1909 > color /O #007F7E
    1910 
    1911 > color /H #00C9CA
    1912 
    1913 > color /I #006686
    1914 
    1915 > color /G #FF937A
    1916 
    1917 > color /A? #FF004A
    1918 
    1919 > color /C? #005887
    1920 
    1921 > color /F? #b4e400
    1922 
    1923 > color /B? #0075BE
    1924 
    1925 > color /D? #FA8072
    1926 
    1927 > color /J? #CAEF00
    1928 
    1929 > color /K? #0098EB
    1930 
    1931 > color /Q? #0098EB
    1932 
    1933 > color /M? #436495
    1934 
    1935 > color /S? #981E05
    1936 
    1937 > color /T? #00C9CA
    1938 
    1939 > color /U? #20639B
    1940 
    1941 > color /V? #ed553B
    1942 
    1943 > color /W? #00A567
    1944 
    1945 > color /Z? #FFA04D
    1946 
    1947 > color /2? #23c6c8
    1948 
    1949 > color /3? #FFC200
    1950 
    1951 > color /4? #dc4c77
    1952 
    1953 > color /8? #9D003D
    1954 
    1955 > color /9? #5A3389
    1956 
    1957 > color /L? #FF5851
    1958 
    1959 > color /N? #4CC7ED
    1960 
    1961 > color /R? #FFC459
    1962 
    1963 > color /P? #FF8853
    1964 
    1965 > color /O? #007F7E
    1966 
    1967 > color /H? #00C9CA
    1968 
    1969 > color /I? #006686
    1970 
    1971 > color /G? #FF937A
    1972 
    1973 > color /A?? #FF004A
    1974 
    1975 > color /C?? #005887
    1976 
    1977 > color /F?? #b4e400
    1978 
    1979 > color /B?? #0075BE
    1980 
    1981 > color /D?? #FA8072
    1982 
    1983 > color /J?? #CAEF00
    1984 
    1985 > color /K?? #0098EB
    1986 
    1987 > color /Q?? #0098EB
    1988 
    1989 > color /M?? #436495
    1990 
    1991 > color /S?? #981E05
    1992 
    1993 > color /T?? #00C9CA
    1994 
    1995 > color /U?? #20639B
    1996 
    1997 > color /V?? #ed553B
    1998 
    1999 > color /W?? #00A567
    2000 
    2001 > color /Z?? #FFA04D
    2002 
    2003 > color /2?? #23c6c8
    2004 
    2005 > color /3?? #FFC200
    2006 
    2007 > color /4?? #dc4c77
    2008 
    2009 > color /8?? #9D003D
    2010 
    2011 > color /9?? #5A3389
    2012 
    2013 > color /L?? #FF5851
    2014 
    2015 > color /N?? #4CC7ED
    2016 
    2017 > color /R?? #FFC459
    2018 
    2019 > color /P?? #FF8853
    2020 
    2021 > color /O?? #007F7E
    2022 
    2023 > color /H?? #00C9CA
    2024 
    2025 > color /I?? #006686
    2026 
    2027 > color /G?? #FF937A
    2028 
    2029 > close #9-22
    2030 
    2031 > color /G?? #FF937Aopen
    2032 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
    2033 
    2034 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    2035 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 
    2036 
    2037 > open
    2038 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
    2039 
    2040 Summary of feedback from opening
    2041 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb 
    2042 --- 
    2043 warnings | Duplicate atom serial number found: 616953 
    2044 Duplicate atom serial number found: 616954 
    2045 Duplicate atom serial number found: 616955 
    2046 Duplicate atom serial number found: 616956 
    2047 Duplicate atom serial number found: 616957 
    2048 130 messages similar to the above omitted 
    2049  
    2050 Chain information for IRcyt_inner.pdb #9 
    2051 --- 
    2052 Chain | Description 
    2053 A | No description available 
    2054 C | No description available 
    2055 D | No description available 
    2056 F | No description available 
    2057 H | No description available 
    2058 I | No description available 
    2059 J | No description available 
    2060 U | No description available 
    2061  
    2062 
    2063 > open
    2064 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
    2065 
    2066 Summary of feedback from opening
    2067 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb 
    2068 --- 
    2069 warnings | Duplicate atom serial number found: 652149 
    2070 Duplicate atom serial number found: 652150 
    2071 Duplicate atom serial number found: 652151 
    2072 Duplicate atom serial number found: 652152 
    2073 Duplicate atom serial number found: 652153 
    2074 130 messages similar to the above omitted 
    2075  
    2076 Chain information for IRnuc_inner.pdb #10 
    2077 --- 
    2078 Chain | Description 
    2079 A | No description available 
    2080 C | No description available 
    2081 D | No description available 
    2082 F | No description available 
    2083 H | No description available 
    2084 I | No description available 
    2085 J | No description available 
    2086 U | No description available 
    2087  
    2088 
    2089 > open
    2090 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
    2091 
    2092 Summary of feedback from opening
    2093 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb 
    2094 --- 
    2095 warnings | Duplicate atom serial number found: 687345 
    2096 Duplicate atom serial number found: 687346 
    2097 Duplicate atom serial number found: 687347 
    2098 Duplicate atom serial number found: 687348 
    2099 Duplicate atom serial number found: 687349 
    2100 130 messages similar to the above omitted 
    2101  
    2102 Chain information for IRnuc_outer.pdb #11 
    2103 --- 
    2104 Chain | Description 
    2105 4 | No description available 
    2106 A | No description available 
    2107 B | No description available 
    2108 D | No description available 
    2109 E | No description available 
    2110 F | No description available 
    2111 H | No description available 
    2112 I | No description available 
    2113 J | No description available 
    2114 U | No description available 
    2115  
    2116 
    2117 > open
    2118 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
    2119 
    2120 Summary of feedback from opening
    2121 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb 
    2122 --- 
    2123 warnings | Duplicate atom serial number found: 848673 
    2124 Duplicate atom serial number found: 848674 
    2125 Duplicate atom serial number found: 848675 
    2126 Duplicate atom serial number found: 848676 
    2127 Duplicate atom serial number found: 848677 
    2128 6155 messages similar to the above omitted 
    2129  
    2130 Chain information for Y.CRouter.pdb #12 
    2131 --- 
    2132 Chain | Description 
    2133 A | No description available 
    2134 C | No description available 
    2135 K | No description available 
    2136 L | No description available 
    2137 M | No description available 
    2138 N | No description available 
    2139 O | No description available 
    2140 P | No description available 
    2141 Q | No description available 
    2142 R | No description available 
    2143 S | No description available 
    2144 U | No description available 
    2145  
    2146 
    2147 > open
    2148 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
    2149 
    2150 Summary of feedback from opening
    2151 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb 
    2152 --- 
    2153 warnings | Duplicate atom serial number found: 811728 
    2154 Duplicate atom serial number found: 811729 
    2155 Duplicate atom serial number found: 811730 
    2156 Duplicate atom serial number found: 811731 
    2157 Duplicate atom serial number found: 811732 
    2158 6155 messages similar to the above omitted 
    2159  
    2160 Chain information for Y.CRinner.pdb #13 
    2161 --- 
    2162 Chain | Description 
    2163 A | No description available 
    2164 C | No description available 
    2165 K | No description available 
    2166 L | No description available 
    2167 M | No description available 
    2168 N | No description available 
    2169 O | No description available 
    2170 P | No description available 
    2171 Q | No description available 
    2172 R | No description available 
    2173 S | No description available 
    2174 U | No description available 
    2175  
    2176 
    2177 > open
    2178 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
    2179 
    2180 Summary of feedback from opening
    2181 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb 
    2182 --- 
    2183 warnings | Duplicate atom serial number found: 885606 
    2184 Duplicate atom serial number found: 885607 
    2185 Duplicate atom serial number found: 885608 
    2186 Duplicate atom serial number found: 885609 
    2187 Duplicate atom serial number found: 885610 
    2188 6155 messages similar to the above omitted 
    2189  
    2190 Chain information for Y.NRinner.pdb #14 
    2191 --- 
    2192 Chain | Description 
    2193 K | No description available 
    2194 L | No description available 
    2195 M | No description available 
    2196 N | No description available 
    2197 O | No description available 
    2198 P | No description available 
    2199 Q | No description available 
    2200 R | No description available 
    2201 S | No description available 
    2202 T | No description available 
    2203  
    2204 
    2205 > open
    2206 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
    2207 
    2208 Summary of feedback from opening
    2209 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb 
    2210 --- 
    2211 warnings | Duplicate atom serial number found: 922551 
    2212 Duplicate atom serial number found: 922552 
    2213 Duplicate atom serial number found: 922553 
    2214 Duplicate atom serial number found: 922554 
    2215 Duplicate atom serial number found: 922555 
    2216 6155 messages similar to the above omitted 
    2217  
    2218 Chain information for Y.NRouter.pdb #15 
    2219 --- 
    2220 Chain | Description 
    2221 A | No description available 
    2222 C | No description available 
    2223 F | No description available 
    2224 K | No description available 
    2225 L | No description available 
    2226 M | No description available 
    2227 N | No description available 
    2228 O | No description available 
    2229 P | No description available 
    2230 Q | No description available 
    2231 R | No description available 
    2232 S | No description available 
    2233 T | No description available 
    2234 U | No description available 
    2235  
    2236 
    2237 > open
    2238 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
    2239 
    2240 Summary of feedback from opening
    2241 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb 
    2242 --- 
    2243 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    2244 THR A 20 1 14 
    2245 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    2246 17 
    2247 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    2248 15 
    2249 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    2250 13 
    2251 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    2252 53 
    2253 10570 messages similar to the above omitted 
    2254  
    2255 Chain information for hNup358_1_CRouter.pdb #16 
    2256 --- 
    2257 Chain | Description 
    2258 0 | No description available 
    2259  
    2260 
    2261 > open
    2262 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
    2263 
    2264 Summary of feedback from opening
    2265 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb 
    2266 --- 
    2267 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    2268 THR A 20 1 14 
    2269 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    2270 17 
    2271 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    2272 15 
    2273 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    2274 13 
    2275 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    2276 53 
    2277 10570 messages similar to the above omitted 
    2278  
    2279 Chain information for hNup358_2_CRouter.pdb #17 
    2280 --- 
    2281 Chain | Description 
    2282 0 | No description available 
    2283  
    2284 
    2285 > open
    2286 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
    2287 
    2288 Summary of feedback from opening
    2289 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb 
    2290 --- 
    2291 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    2292 THR A 20 1 14 
    2293 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    2294 17 
    2295 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    2296 15 
    2297 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    2298 13 
    2299 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    2300 53 
    2301 10570 messages similar to the above omitted 
    2302  
    2303 Chain information for hNup358_1_CRinner.pdb #18 
    2304 --- 
    2305 Chain | Description 
    2306 0 | No description available 
    2307  
    2308 
    2309 > open
    2310 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
    2311 
    2312 Summary of feedback from opening
    2313 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb 
    2314 --- 
    2315 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    2316 THR A 20 1 14 
    2317 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    2318 17 
    2319 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    2320 15 
    2321 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    2322 13 
    2323 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    2324 53 
    2325 10570 messages similar to the above omitted 
    2326  
    2327 Chain information for hNup358_2_CRinner.pdb #19 
    2328 --- 
    2329 Chain | Description 
    2330 0 | No description available 
    2331  
    2332 
    2333 > open
    2334 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
    2335 
    2336 Summary of feedback from opening
    2337 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb 
    2338 --- 
    2339 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    2340 THR A 20 1 14 
    2341 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    2342 17 
    2343 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    2344 15 
    2345 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    2346 13 
    2347 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    2348 53 
    2349 10570 messages similar to the above omitted 
    2350  
    2351 Chain information for hNup358_CRmiddle.pdb #20 
    2352 --- 
    2353 Chain | Description 
    2354 0 | No description available 
    2355  
    2356 
    2357 > open
    2358 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
    2359 
    2360 Summary of feedback from opening
    2361 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb 
    2362 --- 
    2363 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    2364 THR A 20 1 14 
    2365 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    2366 17 
    2367 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    2368 15 
    2369 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    2370 13 
    2371 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    2372 53 
    2373 9610 messages similar to the above omitted 
    2374  
    2375 Chain information for hNup155_CRconnector.pdb #21 
    2376 --- 
    2377 Chain | Description 
    2378 D | No description available 
    2379 F | No description available 
    2380 U | No description available 
    2381  
    2382 
    2383 > open
    2384 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/YhNup155_NRconnector.pdb
    2385 
    2386 No such file/path:
    2387 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/YhNup155_NRconnector.pdb 
    2388 
    2389 > open
    2390 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
    2391 
    2392 Summary of feedback from opening
    2393 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb 
    2394 --- 
    2395 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    2396 THR A 20 1 14 
    2397 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    2398 17 
    2399 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    2400 15 
    2401 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    2402 13 
    2403 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    2404 53 
    2405 9610 messages similar to the above omitted 
    2406  
    2407 Chain information for hNup155_NRconnector.pdb #22 
    2408 --- 
    2409 Chain | Description 
    2410 D | No description available 
    2411 F | No description available 
    2412 U | No description available 
    2413  
    2414 
    2415 > hide #9-22
    2416 
    2417 > hide #9-22
    2418 
    2419 > ribbon #9-22
    2420 
    2421 > color /F/F?/F?? #b4e400
    2422 
    2423 > color /Y/Y?/Y?? #FF004A
    2424 
    2425 > color /0/0?/0?? cyan
    2426 
    2427 > color /E/E/E?? cyan
    2428 
    2429 > color /4/4?/4?? #005887
    2430 
    2431 > color /A #FF004A
    2432 
    2433 > color /C #005887
    2434 
    2435 > color /F #b4e400
    2436 
    2437 > color /B #0075BE
    2438 
    2439 > color /D #FA8072
    2440 
    2441 > color /J #CAEF00
    2442 
    2443 > color /K #0098EB
    2444 
    2445 > color /Q #0098EB
    2446 
    2447 > color /M #436495
    2448 
    2449 > color /S #981E05
    2450 
    2451 > color /T #00C9CA
    2452 
    2453 > color /U #20639B
    2454 
    2455 > color /V #ed553B
    2456 
    2457 > color /W #00A567
    2458 
    2459 > color /Z #FFA04D
    2460 
    2461 > color /2 #23c6c8
    2462 
    2463 > color /3 #FFC200
    2464 
    2465 > color /4 #dc4c77
    2466 
    2467 > color /8 #9D003D
    2468 
    2469 > color /9 #5A3389
    2470 
    2471 > color /L #FF5851
    2472 
    2473 > color /N #4CC7ED
    2474 
    2475 > color /R #FFC459
    2476 
    2477 > color /P #FF8853
    2478 
    2479 > color /O #007F7E
    2480 
    2481 > color /H #00C9CA
    2482 
    2483 > color /I #006686
    2484 
    2485 > color /G #FF937A
    2486 
    2487 > color /A? #FF004A
    2488 
    2489 > color /C? #005887
    2490 
    2491 > color /F? #b4e400
    2492 
    2493 > color /B? #0075BE
    2494 
    2495 > color /D? #FA8072
    2496 
    2497 > color /J? #CAEF00
    2498 
    2499 > color /K? #0098EB
    2500 
    2501 > color /Q? #0098EB
    2502 
    2503 > color /M? #436495
    2504 
    2505 > color /S? #981E05
    2506 
    2507 > color /T? #00C9CA
    2508 
    2509 > color /U? #20639B
    2510 
    2511 > color /V? #ed553B
    2512 
    2513 > color /W? #00A567
    2514 
    2515 > color /Z? #FFA04D
    2516 
    2517 > color /2? #23c6c8
    2518 
    2519 > color /3? #FFC200
    2520 
    2521 > color /4? #dc4c77
    2522 
    2523 > color /8? #9D003D
    2524 
    2525 > color /9? #5A3389
    2526 
    2527 > color /L? #FF5851
    2528 
    2529 > color /N? #4CC7ED
    2530 
    2531 > color /R? #FFC459
    2532 
    2533 > color /P? #FF8853
    2534 
    2535 > color /O? #007F7E
    2536 
    2537 > color /H? #00C9CA
    2538 
    2539 > color /I? #006686
    2540 
    2541 > color /G? #FF937A
    2542 
    2543 > color /A?? #FF004A
    2544 
    2545 > color /C?? #005887
    2546 
    2547 > color /F?? #b4e400
    2548 
    2549 > color /B?? #0075BE
    2550 
    2551 > color /D?? #FA8072
    2552 
    2553 > color /J?? #CAEF00
    2554 
    2555 > color /K?? #0098EB
    2556 
    2557 > color /Q?? #0098EB
    2558 
    2559 > color /M?? #436495
    2560 
    2561 > color /S?? #981E05
    2562 
    2563 > color /T?? #00C9CA
    2564 
    2565 > color /U?? #20639B
    2566 
    2567 > color /V?? #ed553B
    2568 
    2569 > color /W?? #00A567
    2570 
    2571 > color /Z?? #FFA04D
    2572 
    2573 > color /2?? #23c6c8
    2574 
    2575 > color /3?? #FFC200
    2576 
    2577 > color /4?? #dc4c77
    2578 
    2579 > color /8?? #9D003D
    2580 
    2581 > color /9?? #5A3389
    2582 
    2583 > color /L?? #FF5851
    2584 
    2585 > color /N?? #4CC7ED
    2586 
    2587 > color /R?? #FFC459
    2588 
    2589 > color /P?? #FF8853
    2590 
    2591 > color /O?? #007F7E
    2592 
    2593 > color /H?? #00C9CA
    2594 
    2595 > color /I?? #006686
    2596 
    2597 > color /G?? #FF937A
    2598 
    2599 > select #17/0:620
    2600 
    2601 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2602 
    2603 > color /0* #b4e400
    2604 
    2605 > color /0* magenta
    2606 
    2607 > color /0* yellow
    2608 
    2609 > color /0* blue
    2610 
    2611 > color /0* purple
    2612 
    2613 > color /M* green
    2614 
    2615 > color /K* purple
    2616 
    2617 > color /0* blue
    2618 
    2619 > color /0* light blue
    2620 
    2621 > color /0* sky blue
    2622 
    2623 > color /L* orange
    2624 
    2625 > select #9/D:1094
    2626 
    2627 5 atoms, 4 bonds, 1 residue, 1 model selected 
    2628 
    2629 > color /P* #85ff7a
    2630 
    2631 > color /P* orange
    2632 
    2633 > color /M* #85ff7a
    2634 
    2635 > color /M* #45f248
    2636 
    2637 > color /A* #FF004A
    2638 
    2639 > color /C* #005887
    2640 
    2641 > color /F* #b4e400
    2642 
    2643 > color /B* #0075BE
    2644 
    2645 > color /D* #FA8072
    2646 
    2647 > color /J* #CAEF00
    2648 
    2649 > color /K* #0098EB
    2650 
    2651 > color /Q* #0098EB
    2652 
    2653 > color /M* #436495
    2654 
    2655 > color /S* #981E05
    2656 
    2657 > color /T* #00C9CA
    2658 
    2659 > color /U* #20639B
    2660 
    2661 > color /V* #ed553B
    2662 
    2663 > color /W* #00A567
    2664 
    2665 > color /Z* #FFA04D
    2666 
    2667 > color /2* #23c6c8
    2668 
    2669 > color /3* #FFC200
    2670 
    2671 > color /4* #dc4c77
    2672 
    2673 > color /8* #9D003D
    2674 
    2675 > color /9* #5A3389
    2676 
    2677 > color /L* #FF5851
    2678 
    2679 > color /N* #4CC7ED
    2680 
    2681 > color /R* #FFC459
    2682 
    2683 > color /P* #FF8853
    2684 
    2685 > color /O* #007F7E
    2686 
    2687 > color /H* #00C9CA
    2688 
    2689 > color /I* #006686
    2690 
    2691 > color /G* #FF937A
    2692 
    2693 > color /M* #d4ffb2
    2694 
    2695 > color /M* #45f248
    2696 
    2697 > color /O* #159493
    2698 
    2699 > color /N* magenta
    2700 
    2701 > select #13/O:236
    2702 
    2703 10 atoms, 10 bonds, 1 residue, 1 model selected 
    2704 
    2705 > hide #!9 models
    2706 
    2707 > show #!9 models
    2708 
    2709 > hide #!10 models
    2710 
    2711 > show #!10 models
    2712 
    2713 > close #9-22
    2714 
    2715 > color /N* magentaopen
    2716 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
    2717 
    2718 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    2719 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 
    2720 
    2721 > open
    2722 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
    2723 
    2724 Summary of feedback from opening
    2725 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb 
    2726 --- 
    2727 warnings | Duplicate atom serial number found: 616953 
    2728 Duplicate atom serial number found: 616954 
    2729 Duplicate atom serial number found: 616955 
    2730 Duplicate atom serial number found: 616956 
    2731 Duplicate atom serial number found: 616957 
    2732 130 messages similar to the above omitted 
    2733  
    2734 Chain information for IRcyt_inner.pdb #9 
    2735 --- 
    2736 Chain | Description 
    2737 A | No description available 
    2738 C | No description available 
    2739 D | No description available 
    2740 F | No description available 
    2741 H | No description available 
    2742 I | No description available 
    2743 J | No description available 
    2744 U | No description available 
    2745  
    2746 
    2747 > open
    2748 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
    2749 
    2750 Summary of feedback from opening
    2751 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb 
    2752 --- 
    2753 warnings | Duplicate atom serial number found: 652149 
    2754 Duplicate atom serial number found: 652150 
    2755 Duplicate atom serial number found: 652151 
    2756 Duplicate atom serial number found: 652152 
    2757 Duplicate atom serial number found: 652153 
    2758 130 messages similar to the above omitted 
    2759  
    2760 Chain information for IRnuc_inner.pdb #10 
    2761 --- 
    2762 Chain | Description 
    2763 A | No description available 
    2764 C | No description available 
    2765 D | No description available 
    2766 F | No description available 
    2767 H | No description available 
    2768 I | No description available 
    2769 J | No description available 
    2770 U | No description available 
    2771  
    2772 
    2773 > open
    2774 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
    2775 
    2776 Summary of feedback from opening
    2777 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb 
    2778 --- 
    2779 warnings | Duplicate atom serial number found: 687345 
    2780 Duplicate atom serial number found: 687346 
    2781 Duplicate atom serial number found: 687347 
    2782 Duplicate atom serial number found: 687348 
    2783 Duplicate atom serial number found: 687349 
    2784 130 messages similar to the above omitted 
    2785  
    2786 Chain information for IRnuc_outer.pdb #11 
    2787 --- 
    2788 Chain | Description 
    2789 4 | No description available 
    2790 A | No description available 
    2791 B | No description available 
    2792 D | No description available 
    2793 E | No description available 
    2794 F | No description available 
    2795 H | No description available 
    2796 I | No description available 
    2797 J | No description available 
    2798 U | No description available 
    2799  
    2800 
    2801 > open
    2802 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
    2803 
    2804 Summary of feedback from opening
    2805 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb 
    2806 --- 
    2807 warnings | Duplicate atom serial number found: 848673 
    2808 Duplicate atom serial number found: 848674 
    2809 Duplicate atom serial number found: 848675 
    2810 Duplicate atom serial number found: 848676 
    2811 Duplicate atom serial number found: 848677 
    2812 6155 messages similar to the above omitted 
    2813  
    2814 Chain information for Y.CRouter.pdb #12 
    2815 --- 
    2816 Chain | Description 
    2817 A | No description available 
    2818 C | No description available 
    2819 K | No description available 
    2820 L | No description available 
    2821 M | No description available 
    2822 N | No description available 
    2823 O | No description available 
    2824 P | No description available 
    2825 Q | No description available 
    2826 R | No description available 
    2827 S | No description available 
    2828 U | No description available 
    2829  
    2830 
    2831 > open
    2832 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
    2833 
    2834 Summary of feedback from opening
    2835 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb 
    2836 --- 
    2837 warnings | Duplicate atom serial number found: 811728 
    2838 Duplicate atom serial number found: 811729 
    2839 Duplicate atom serial number found: 811730 
    2840 Duplicate atom serial number found: 811731 
    2841 Duplicate atom serial number found: 811732 
    2842 6155 messages similar to the above omitted 
    2843  
    2844 Chain information for Y.CRinner.pdb #13 
    2845 --- 
    2846 Chain | Description 
    2847 A | No description available 
    2848 C | No description available 
    2849 K | No description available 
    2850 L | No description available 
    2851 M | No description available 
    2852 N | No description available 
    2853 O | No description available 
    2854 P | No description available 
    2855 Q | No description available 
    2856 R | No description available 
    2857 S | No description available 
    2858 U | No description available 
    2859  
    2860 
    2861 > open
    2862 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
    2863 
    2864 Summary of feedback from opening
    2865 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb 
    2866 --- 
    2867 warnings | Duplicate atom serial number found: 885606 
    2868 Duplicate atom serial number found: 885607 
    2869 Duplicate atom serial number found: 885608 
    2870 Duplicate atom serial number found: 885609 
    2871 Duplicate atom serial number found: 885610 
    2872 6155 messages similar to the above omitted 
    2873  
    2874 Chain information for Y.NRinner.pdb #14 
    2875 --- 
    2876 Chain | Description 
    2877 K | No description available 
    2878 L | No description available 
    2879 M | No description available 
    2880 N | No description available 
    2881 O | No description available 
    2882 P | No description available 
    2883 Q | No description available 
    2884 R | No description available 
    2885 S | No description available 
    2886 T | No description available 
    2887  
    2888 
    2889 > open
    2890 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
    2891 
    2892 Summary of feedback from opening
    2893 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb 
    2894 --- 
    2895 warnings | Duplicate atom serial number found: 922551 
    2896 Duplicate atom serial number found: 922552 
    2897 Duplicate atom serial number found: 922553 
    2898 Duplicate atom serial number found: 922554 
    2899 Duplicate atom serial number found: 922555 
    2900 6155 messages similar to the above omitted 
    2901  
    2902 Chain information for Y.NRouter.pdb #15 
    2903 --- 
    2904 Chain | Description 
    2905 A | No description available 
    2906 C | No description available 
    2907 F | No description available 
    2908 K | No description available 
    2909 L | No description available 
    2910 M | No description available 
    2911 N | No description available 
    2912 O | No description available 
    2913 P | No description available 
    2914 Q | No description available 
    2915 R | No description available 
    2916 S | No description available 
    2917 T | No description available 
    2918 U | No description available 
    2919  
    2920 
    2921 > open
    2922 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
    2923 
    2924 Summary of feedback from opening
    2925 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb 
    2926 --- 
    2927 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    2928 THR A 20 1 14 
    2929 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    2930 17 
    2931 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    2932 15 
    2933 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    2934 13 
    2935 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    2936 53 
    2937 10570 messages similar to the above omitted 
    2938  
    2939 Chain information for hNup358_1_CRouter.pdb #16 
    2940 --- 
    2941 Chain | Description 
    2942 0 | No description available 
    2943  
    2944 
    2945 > open
    2946 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
    2947 
    2948 Summary of feedback from opening
    2949 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb 
    2950 --- 
    2951 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    2952 THR A 20 1 14 
    2953 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    2954 17 
    2955 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    2956 15 
    2957 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    2958 13 
    2959 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    2960 53 
    2961 10570 messages similar to the above omitted 
    2962  
    2963 Chain information for hNup358_2_CRouter.pdb #17 
    2964 --- 
    2965 Chain | Description 
    2966 0 | No description available 
    2967  
    2968 
    2969 > open
    2970 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
    2971 
    2972 Summary of feedback from opening
    2973 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb 
    2974 --- 
    2975 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    2976 THR A 20 1 14 
    2977 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    2978 17 
    2979 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    2980 15 
    2981 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    2982 13 
    2983 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    2984 53 
    2985 10570 messages similar to the above omitted 
    2986  
    2987 Chain information for hNup358_1_CRinner.pdb #18 
    2988 --- 
    2989 Chain | Description 
    2990 0 | No description available 
    2991  
    2992 
    2993 > open
    2994 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
    2995 
    2996 Summary of feedback from opening
    2997 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb 
    2998 --- 
    2999 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3000 THR A 20 1 14 
    3001 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3002 17 
    3003 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3004 15 
    3005 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3006 13 
    3007 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3008 53 
    3009 10570 messages similar to the above omitted 
    3010  
    3011 Chain information for hNup358_2_CRinner.pdb #19 
    3012 --- 
    3013 Chain | Description 
    3014 0 | No description available 
    3015  
    3016 
    3017 > open
    3018 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
    3019 
    3020 Summary of feedback from opening
    3021 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb 
    3022 --- 
    3023 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3024 THR A 20 1 14 
    3025 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3026 17 
    3027 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3028 15 
    3029 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3030 13 
    3031 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3032 53 
    3033 10570 messages similar to the above omitted 
    3034  
    3035 Chain information for hNup358_CRmiddle.pdb #20 
    3036 --- 
    3037 Chain | Description 
    3038 0 | No description available 
    3039  
    3040 
    3041 > open
    3042 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
    3043 
    3044 Summary of feedback from opening
    3045 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb 
    3046 --- 
    3047 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3048 THR A 20 1 14 
    3049 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3050 17 
    3051 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3052 15 
    3053 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3054 13 
    3055 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3056 53 
    3057 9610 messages similar to the above omitted 
    3058  
    3059 Chain information for hNup155_CRconnector.pdb #21 
    3060 --- 
    3061 Chain | Description 
    3062 D | No description available 
    3063 F | No description available 
    3064 U | No description available 
    3065  
    3066 
    3067 > open
    3068 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
    3069 
    3070 Summary of feedback from opening
    3071 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb 
    3072 --- 
    3073 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3074 THR A 20 1 14 
    3075 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3076 17 
    3077 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3078 15 
    3079 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3080 13 
    3081 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3082 53 
    3083 9610 messages similar to the above omitted 
    3084  
    3085 Chain information for hNup155_NRconnector.pdb #22 
    3086 --- 
    3087 Chain | Description 
    3088 D | No description available 
    3089 F | No description available 
    3090 U | No description available 
    3091  
    3092 
    3093 > hide #9-22
    3094 
    3095 > ribbon #9-22
    3096 
    3097 > color /A* #FF004A
    3098 
    3099 > color /C* #005887
    3100 
    3101 > color /F* #b4e400
    3102 
    3103 > color /B* #0075BE
    3104 
    3105 > color /D* #FA8072
    3106 
    3107 > color /J* #CAEF00
    3108 
    3109 > color /K* #0098EB
    3110 
    3111 > color /Q* #0098EB
    3112 
    3113 > color /M* #436495
    3114 
    3115 > color /S* #981E05
    3116 
    3117 > color /T* #00C9CA
    3118 
    3119 > color /U* #20639B
    3120 
    3121 > color /V* #ed553B
    3122 
    3123 > color /W* #00A567
    3124 
    3125 > color /Z* #FFA04D
    3126 
    3127 > color /2* #23c6c8
    3128 
    3129 > color /3* #FFC200
    3130 
    3131 > color /4* #dc4c77
    3132 
    3133 > color /8* #9D003D
    3134 
    3135 > color /9* #5A3389
    3136 
    3137 > color /L* #FF5851
    3138 
    3139 > color /N* #4CC7ED
    3140 
    3141 > color /R* #FFC459
    3142 
    3143 > color /P* #FF8853
    3144 
    3145 > color /O* #159493
    3146 
    3147 > color /H* #00C9CA
    3148 
    3149 > color /I* #006686
    3150 
    3151 > color /G* #FF937A
    3152 
    3153 > open
    3154 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
    3155 
    3156 Summary of feedback from opening
    3157 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb 
    3158 --- 
    3159 warnings | Duplicate atom serial number found: 272408 
    3160 Duplicate atom serial number found: 272409 
    3161 Duplicate atom serial number found: 272410 
    3162 Duplicate atom serial number found: 272411 
    3163 Duplicate atom serial number found: 272412 
    3164 44904 messages similar to the above omitted 
    3165  
    3166 Chain information for IRcyt_outer.pdb #23 
    3167 --- 
    3168 Chain | Description 
    3169 4 | No description available 
    3170 A | No description available 
    3171 B | No description available 
    3172 D | No description available 
    3173 E | No description available 
    3174 F | No description available 
    3175 H | No description available 
    3176 I | No description available 
    3177 J | No description available 
    3178 U | No description available 
    3179  
    3180 
    3181 > close #9-23
    3182 
    3183 > open
    3184 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
    3185 
    3186 Summary of feedback from opening
    3187 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb 
    3188 --- 
    3189 warnings | Duplicate atom serial number found: 272408 
    3190 Duplicate atom serial number found: 272409 
    3191 Duplicate atom serial number found: 272410 
    3192 Duplicate atom serial number found: 272411 
    3193 Duplicate atom serial number found: 272412 
    3194 44904 messages similar to the above omitted 
    3195  
    3196 Chain information for IRcyt_outer.pdb #9 
    3197 --- 
    3198 Chain | Description 
    3199 4 | No description available 
    3200 A | No description available 
    3201 B | No description available 
    3202 D | No description available 
    3203 E | No description available 
    3204 F | No description available 
    3205 H | No description available 
    3206 I | No description available 
    3207 J | No description available 
    3208 U | No description available 
    3209  
    3210 
    3211 > open
    3212 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
    3213 
    3214 Summary of feedback from opening
    3215 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb 
    3216 --- 
    3217 warnings | Duplicate atom serial number found: 616953 
    3218 Duplicate atom serial number found: 616954 
    3219 Duplicate atom serial number found: 616955 
    3220 Duplicate atom serial number found: 616956 
    3221 Duplicate atom serial number found: 616957 
    3222 130 messages similar to the above omitted 
    3223  
    3224 Chain information for IRcyt_inner.pdb #10 
    3225 --- 
    3226 Chain | Description 
    3227 A | No description available 
    3228 C | No description available 
    3229 D | No description available 
    3230 F | No description available 
    3231 H | No description available 
    3232 I | No description available 
    3233 J | No description available 
    3234 U | No description available 
    3235  
    3236 
    3237 > open
    3238 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
    3239 
    3240 Summary of feedback from opening
    3241 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb 
    3242 --- 
    3243 warnings | Duplicate atom serial number found: 652149 
    3244 Duplicate atom serial number found: 652150 
    3245 Duplicate atom serial number found: 652151 
    3246 Duplicate atom serial number found: 652152 
    3247 Duplicate atom serial number found: 652153 
    3248 130 messages similar to the above omitted 
    3249  
    3250 Chain information for IRnuc_inner.pdb #11 
    3251 --- 
    3252 Chain | Description 
    3253 A | No description available 
    3254 C | No description available 
    3255 D | No description available 
    3256 F | No description available 
    3257 H | No description available 
    3258 I | No description available 
    3259 J | No description available 
    3260 U | No description available 
    3261  
    3262 
    3263 > open
    3264 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
    3265 
    3266 Summary of feedback from opening
    3267 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb 
    3268 --- 
    3269 warnings | Duplicate atom serial number found: 687345 
    3270 Duplicate atom serial number found: 687346 
    3271 Duplicate atom serial number found: 687347 
    3272 Duplicate atom serial number found: 687348 
    3273 Duplicate atom serial number found: 687349 
    3274 130 messages similar to the above omitted 
    3275  
    3276 Chain information for IRnuc_outer.pdb #12 
    3277 --- 
    3278 Chain | Description 
    3279 4 | No description available 
    3280 A | No description available 
    3281 B | No description available 
    3282 D | No description available 
    3283 E | No description available 
    3284 F | No description available 
    3285 H | No description available 
    3286 I | No description available 
    3287 J | No description available 
    3288 U | No description available 
    3289  
    3290 
    3291 > open
    3292 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
    3293 
    3294 Summary of feedback from opening
    3295 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb 
    3296 --- 
    3297 warnings | Duplicate atom serial number found: 848673 
    3298 Duplicate atom serial number found: 848674 
    3299 Duplicate atom serial number found: 848675 
    3300 Duplicate atom serial number found: 848676 
    3301 Duplicate atom serial number found: 848677 
    3302 6155 messages similar to the above omitted 
    3303  
    3304 Chain information for Y.CRouter.pdb #13 
    3305 --- 
    3306 Chain | Description 
    3307 A | No description available 
    3308 C | No description available 
    3309 J | No description available 
    3310 K | No description available 
    3311 L | No description available 
    3312 M | No description available 
    3313 N | No description available 
    3314 O | No description available 
    3315 P | No description available 
    3316 Q | No description available 
    3317 R | No description available 
    3318 S | No description available 
    3319 U | No description available 
    3320 V | No description available 
    3321 W | No description available 
    3322  
    3323 
    3324 > open
    3325 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
    3326 
    3327 Summary of feedback from opening
    3328 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb 
    3329 --- 
    3330 warnings | Duplicate atom serial number found: 811728 
    3331 Duplicate atom serial number found: 811729 
    3332 Duplicate atom serial number found: 811730 
    3333 Duplicate atom serial number found: 811731 
    3334 Duplicate atom serial number found: 811732 
    3335 6155 messages similar to the above omitted 
    3336  
    3337 Chain information for Y.CRinner.pdb #14 
    3338 --- 
    3339 Chain | Description 
    3340 A | No description available 
    3341 C | No description available 
    3342 K | No description available 
    3343 L | No description available 
    3344 M | No description available 
    3345 N | No description available 
    3346 O | No description available 
    3347 P | No description available 
    3348 Q | No description available 
    3349 R | No description available 
    3350 S | No description available 
    3351 U | No description available 
    3352  
    3353 
    3354 > open
    3355 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
    3356 
    3357 Summary of feedback from opening
    3358 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb 
    3359 --- 
    3360 warnings | Duplicate atom serial number found: 885606 
    3361 Duplicate atom serial number found: 885607 
    3362 Duplicate atom serial number found: 885608 
    3363 Duplicate atom serial number found: 885609 
    3364 Duplicate atom serial number found: 885610 
    3365 6155 messages similar to the above omitted 
    3366  
    3367 Chain information for Y.NRinner.pdb #15 
    3368 --- 
    3369 Chain | Description 
    3370 K | No description available 
    3371 L | No description available 
    3372 M | No description available 
    3373 N | No description available 
    3374 O | No description available 
    3375 P | No description available 
    3376 Q | No description available 
    3377 R | No description available 
    3378 S | No description available 
    3379 T | No description available 
    3380  
    3381 
    3382 > open
    3383 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
    3384 
    3385 Summary of feedback from opening
    3386 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb 
    3387 --- 
    3388 warnings | Duplicate atom serial number found: 922551 
    3389 Duplicate atom serial number found: 922552 
    3390 Duplicate atom serial number found: 922553 
    3391 Duplicate atom serial number found: 922554 
    3392 Duplicate atom serial number found: 922555 
    3393 6155 messages similar to the above omitted 
    3394  
    3395 Chain information for Y.NRouter.pdb #16 
    3396 --- 
    3397 Chain | Description 
    3398 A | No description available 
    3399 C | No description available 
    3400 F | No description available 
    3401 K | No description available 
    3402 L | No description available 
    3403 M | No description available 
    3404 N | No description available 
    3405 O | No description available 
    3406 P | No description available 
    3407 Q | No description available 
    3408 R | No description available 
    3409 S | No description available 
    3410 T | No description available 
    3411 U | No description available 
    3412  
    3413 
    3414 > open
    3415 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
    3416 
    3417 Summary of feedback from opening
    3418 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb 
    3419 --- 
    3420 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3421 THR A 20 1 14 
    3422 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3423 17 
    3424 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3425 15 
    3426 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3427 13 
    3428 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3429 53 
    3430 10570 messages similar to the above omitted 
    3431  
    3432 Chain information for hNup358_1_CRouter.pdb #17 
    3433 --- 
    3434 Chain | Description 
    3435 0 | No description available 
    3436  
    3437 
    3438 > open
    3439 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
    3440 
    3441 Summary of feedback from opening
    3442 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb 
    3443 --- 
    3444 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3445 THR A 20 1 14 
    3446 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3447 17 
    3448 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3449 15 
    3450 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3451 13 
    3452 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3453 53 
    3454 10570 messages similar to the above omitted 
    3455  
    3456 Chain information for hNup358_2_CRouter.pdb #18 
    3457 --- 
    3458 Chain | Description 
    3459 0 | No description available 
    3460  
    3461 
    3462 > open
    3463 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
    3464 
    3465 Summary of feedback from opening
    3466 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb 
    3467 --- 
    3468 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3469 THR A 20 1 14 
    3470 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3471 17 
    3472 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3473 15 
    3474 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3475 13 
    3476 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3477 53 
    3478 10570 messages similar to the above omitted 
    3479  
    3480 Chain information for hNup358_1_CRinner.pdb #19 
    3481 --- 
    3482 Chain | Description 
    3483 0 | No description available 
    3484  
    3485 
    3486 > open
    3487 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
    3488 
    3489 Summary of feedback from opening
    3490 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb 
    3491 --- 
    3492 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3493 THR A 20 1 14 
    3494 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3495 17 
    3496 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3497 15 
    3498 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3499 13 
    3500 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3501 53 
    3502 10570 messages similar to the above omitted 
    3503  
    3504 Chain information for hNup358_2_CRinner.pdb #20 
    3505 --- 
    3506 Chain | Description 
    3507 0 | No description available 
    3508  
    3509 
    3510 > open
    3511 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
    3512 
    3513 Summary of feedback from opening
    3514 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb 
    3515 --- 
    3516 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3517 THR A 20 1 14 
    3518 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3519 17 
    3520 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3521 15 
    3522 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3523 13 
    3524 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3525 53 
    3526 10570 messages similar to the above omitted 
    3527  
    3528 Chain information for hNup358_CRmiddle.pdb #21 
    3529 --- 
    3530 Chain | Description 
    3531 0 | No description available 
    3532  
    3533 
    3534 > open
    3535 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
    3536 
    3537 Summary of feedback from opening
    3538 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb 
    3539 --- 
    3540 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3541 THR A 20 1 14 
    3542 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3543 17 
    3544 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3545 15 
    3546 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3547 13 
    3548 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3549 53 
    3550 9610 messages similar to the above omitted 
    3551  
    3552 Chain information for hNup155_CRconnector.pdb #22 
    3553 --- 
    3554 Chain | Description 
    3555 D | No description available 
    3556 F | No description available 
    3557 U | No description available 
    3558  
    3559 
    3560 > open
    3561 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
    3562 
    3563 Summary of feedback from opening
    3564 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb 
    3565 --- 
    3566 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    3567 THR A 20 1 14 
    3568 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    3569 17 
    3570 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    3571 15 
    3572 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    3573 13 
    3574 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    3575 53 
    3576 9610 messages similar to the above omitted 
    3577  
    3578 Chain information for hNup155_NRconnector.pdb #23 
    3579 --- 
    3580 Chain | Description 
    3581 D | No description available 
    3582 F | No description available 
    3583 U | No description available 
    3584  
    3585 
    3586 > hide #9-22
    3587 
    3588 > ribbon #9-22
    3589 
    3590 > color /A* #FF004A
    3591 
    3592 > color /C* #005887
    3593 
    3594 > color /F* #b4e400
    3595 
    3596 > color /B* #0075BE
    3597 
    3598 > color /D* #FA8072
    3599 
    3600 > color /J* #CAEF00
    3601 
    3602 > color /K* #0098EB
    3603 
    3604 > color /Q* #0098EB
    3605 
    3606 > color /M* #436495
    3607 
    3608 > color /S* #981E05
    3609 
    3610 > color /T* #00C9CA
    3611 
    3612 > color /U* #20639B
    3613 
    3614 > color /V* #ed553B
    3615 
    3616 > color /W* #00A567
    3617 
    3618 > color /Z* #FFA04D
    3619 
    3620 > color /2* #23c6c8
    3621 
    3622 > color /3* #FFC200
    3623 
    3624 > color /4* #dc4c77
    3625 
    3626 > color /8* #9D003D
    3627 
    3628 > color /9* #5A3389
    3629 
    3630 > color /L* #FF5851
    3631 
    3632 > color /N* #4CC7ED
    3633 
    3634 > color /R* #FFC459
    3635 
    3636 > color /P* #FF8853
    3637 
    3638 > color /O* #159493
    3639 
    3640 > color /H* #00C9CA
    3641 
    3642 > color /I* #006686
    3643 
    3644 > color /G* #FF937A
    3645 
    3646 > color /0* #0098EB
    3647 
    3648 > select clear
    3649 
    3650 > color /K* #45f248
    3651 
    3652 > select #22/D:881
    3653 
    3654 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3655 
    3656 > color /L* #FF8853
    3657 
    3658 > select #14/A:220
    3659 
    3660 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3661 
    3662 > color /P* #FF5851
    3663 
    3664 > color /0* #0098EB
    3665 
    3666 > color /L* #FF8853
    3667 
    3668 > color /P* #FF5851
    3669 
    3670 > color /R* #45f248
    3671 
    3672 > color /M* #8f00f1
    3673 
    3674 > color /M* #D99DE48f00f1
    3675 
    3676 > color /M* #D99DE4
    3677 
    3678 > color /M* #D99DE48f00f1
    3679 
    3680 > color /N* #D99DE48f00f1
    3681 
    3682 > color /M* #D99DE4
    3683 
    3684 > color /M* #917db6
    3685 
    3686 > color /C* #167a9e
    3687 
    3688 > color /C* #168c9e
    3689 
    3690 > color /C* #16939e
    3691 
    3692 > color /C* #067fbf
    3693 
    3694 > color /C* #11a6f5
    3695 
    3696 > color /B* #11a6f5
    3697 
    3698 > color /C* #005887
    3699 
    3700 > color /C* #055d9c
    3701 
    3702 > color /C* #0259b0
    3703 
    3704 > color /M* #917db6
    3705 
    3706 > color /B* #11a6f5
    3707 
    3708 > color /B* #11a6f5
    3709 
    3710 > color /M* #8c05fa
    3711 
    3712 > color /M* #917db68c05fa
    3713 
    3714 > select #14/C:1263
    3715 
    3716 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3717 
    3718 > color /M* #917db6
    3719 
    3720 > color /0* #0098EB
    3721 
    3722 > color /P* #FF8853
    3723 
    3724 > color /L* #FF5851
    3725 
    3726 > color /R* #45f248
    3727 
    3728 > color /M* #917db6
    3729 
    3730 > color /B* #11a6f5
    3731 
    3732 > color /C* #0259b0917db6
    3733 
    3734 > color /R* #99ffb2
    3735 
    3736 > view
    3737 
    3738 > color /R* #159493
    3739 
    3740 > color /C* #0259b0159493
    3741 
    3742 > color /C* #0259b0
    3743 
    3744 > color /T* magenta
    3745 
    3746 > color /T* #ac79c9
    3747 
    3748 > color /T* #bd79c9
    3749 
    3750 > color /R* #159493
    3751 
    3752 > color /T* #45f248
    3753 
    3754 > select #15/T:47
    3755 
    3756 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3757 
    3758 > color /T* #79f245
    3759 
    3760 > color /T* #8df245
    3761 
    3762 > color /T* #8df245
    3763 
    3764 > color /K* #0098EB
    3765 
    3766 > color /0* #0098EB
    3767 
    3768 > color /L* #FF8853
    3769 
    3770 > color /P* #FF5851
    3771 
    3772 > color /R* #45f248
    3773 
    3774 > color /M* #917db6
    3775 
    3776 > color /B* #11a6f5
    3777 
    3778 > color /C* #0259b0
    3779 
    3780 > color /R* #159493
    3781 
    3782 > color /T* #8df245
    3783 
    3784 > color /K* #0098EB
    3785 
    3786 > color /Q* #8df245
    3787 
    3788 > color /O* cyan
    3789 
    3790 > color /M* #8df245
    3791 
    3792 > color /Q* #917db6
    3793 
    3794 > color /0* #0098EB
    3795 
    3796 > color /L* #FF8853
    3797 
    3798 > color /P* #FF5851
    3799 
    3800 > color /R* #45f248
    3801 
    3802 > color /M* #917db6
    3803 
    3804 > color /B* #11a6f5
    3805 
    3806 > color /C* #0259b0
    3807 
    3808 > color /R* #159493
    3809 
    3810 > color /T* #8df245
    3811 
    3812 > color /K* #0098EB
    3813 
    3814 > color /N* #8df245
    3815 
    3816 > color /O* cyan8df245
    3817 
    3818 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    3819 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 
    3820 
    3821 > color /Q* yellow
    3822 
    3823 > color /O* yellow
    3824 
    3825 > color /Q* cyan
    3826 
    3827 > color /D* pink
    3828 
    3829 > color /D* #FFC459
    3830 
    3831 > color /F* green
    3832 
    3833 > color /F* lime green
    3834 
    3835 > color /4* magenta
    3836 
    3837 > color /F* #b4e400
    3838 
    3839 > color /I* #b4e400
    3840 
    3841 > color /J* orange
    3842 
    3843 > color /J* magenta
    3844 
    3845 > color /J* violet
    3846 
    3847 > color /H* purple
    3848 
    3849 > select up
    3850 
    3851 38 atoms, 37 bonds, 6 residues, 1 model selected 
    3852 
    3853 > select up
    3854 
    3855 7941 atoms, 8121 bonds, 1001 residues, 1 model selected 
    3856 
    3857 > color /I* #b4e400
    3858 
    3859 > color /H* violet
    3860 
    3861 > color /J* purple
    3862 
    3863 > color /I* #b4e400
    3864 
    3865 > color /H* violet
    3866 
    3867 > color /J* purple
    3868 
    3869 > select clear
    3870 
    3871 > color /D* #FFC459
    3872 
    3873 > color /D* #d3ffd8
    3874 
    3875 > color /D* #daffd3
    3876 
    3877 > color /D* #c4e3a6
    3878 
    3879 > color /D* #feffba
    3880 
    3881 > color /D* #fce88b
    3882 
    3883 > color /F* #8df245
    3884 
    3885 > color /4* #45f248
    3886 
    3887 > color /R* #159493
    3888 
    3889 > color /E* #159493
    3890 
    3891 > color /K* purple
    3892 
    3893 > color /F cyan
    3894 
    3895 > color /A* #FF004A
    3896 
    3897 > color /C* #005887
    3898 
    3899 > color /F* #b4e400
    3900 
    3901 > color /B* #0075BE
    3902 
    3903 > color /D* #FA8072
    3904 
    3905 > color /J* #CAEF00
    3906 
    3907 > color /Q* #0098EB
    3908 
    3909 > color /M* #436495
    3910 
    3911 > color /S* #981E05
    3912 
    3913 > color /T* #00C9CA
    3914 
    3915 > color /U* #20639B
    3916 
    3917 > color /V* #ed553B
    3918 
    3919 > color /W* #00A567
    3920 
    3921 > color /Z* #FFA04D
    3922 
    3923 > color /2* #23c6c8
    3924 
    3925 > color /3* #FFC200
    3926 
    3927 > color /4* #dc4c77
    3928 
    3929 > color /8* #9D003D
    3930 
    3931 > color /9* #5A3389
    3932 
    3933 > color /L* #FF5851
    3934 
    3935 > color /N* #4CC7ED
    3936 
    3937 > color /R* #FFC459
    3938 
    3939 > color /P* #FF8853
    3940 
    3941 > color /O* #159493
    3942 
    3943 > color /H* #00C9CA
    3944 
    3945 > color /I* #006686
    3946 
    3947 > color /G* #FF937A
    3948 
    3949 > color /0* #0098EB
    3950 
    3951 > color /L* #FF8853
    3952 
    3953 > color /P* #FF5851
    3954 
    3955 > color /R* #45f248
    3956 
    3957 > color /M* #917db6
    3958 
    3959 > color /B* #11a6f5
    3960 
    3961 > color /C* #0259b0
    3962 
    3963 > color /R* #159493
    3964 
    3965 > color /T* #8df245
    3966 
    3967 > color /K* #0098EB
    3968 
    3969 > color /N* #8df245
    3970 
    3971 > color /O* yellow
    3972 
    3973 > color /Q* cyan
    3974 
    3975 > color /D* #FFC459
    3976 
    3977 > color /F* #b4e400
    3978 
    3979 > color /I* #b4e400
    3980 
    3981 > color /H* violet
    3982 
    3983 > color /D* #fce88b
    3984 
    3985 > color /F* #8df245
    3986 
    3987 > color /4* #45f248
    3988 
    3989 > color /K* purple
    3990 
    3991 > color /E* #159493
    3992 
    3993 > color /J* purple
    3994 
    3995 > color /V* #8df245
    3996 
    3997 > color /V* #adf245
    3998 
    3999 > color /U* magenta
    4000 
    4001 > color /W* #00b5a3
    4002 
    4003 > show #!1 models
    4004 
    4005 > volume transparency ).7
    4006 
    4007 Invalid "transparency" argument: Expected a number 
    4008 
    4009 > volume transparency 0.7
    4010 
    4011 > volume transparency 0.9
    4012 
    4013 > volume transparency 0.8
    4014 
    4015 > hide #!1 models
    4016 
    4017 > show #!1 models
    4018 
    4019 > show #!2 models
    4020 
    4021 > hide #!2 models
    4022 
    4023 > show #!5 models
    4024 
    4025 > show #!6 models
    4026 
    4027 > hide #!5 models
    4028 
    4029 > lighting soft
    4030 
    4031 > graphics silhouettes true width 2
    4032 
    4033 > volume transparency 0.6
    4034 
    4035 > volume transparency 0.8
    4036 
    4037 > lighting simple
    4038 
    4039 > lighting soft
    4040 
    4041 > lighting simple
    4042 
    4043 > measure symmetry #1
    4044 
    4045 Symmetry pore_whole_resample.mrc: C8, center 288 288 298 
    4046 
    4047 > sym #9-23 symmetry #1
    4048 
    4049 > hide #!20 models
    4050 
    4051 > show #!20 models
    4052 
    4053 > view
    4054 
    4055 > view
    4056 
    4057 > view name ouside
    4058 
    4059 > view name side_ouside
    4060 
    4061 > view name top
    4062 
    4063 > view side_ouside
    4064 
    4065 > ui tool show "Side View"
    4066 
    4067 > view side_ouside_cut
    4068 
    4069 Expected an objects specifier or a view name or a keyword 
    4070 
    4071 > view name side_cut
    4072 
    4073 > view name side_outside
    4074 
    4075 > view name side_cut
    4076 
    4077 > show #!8 models
    4078 
    4079 > view name top
    4080 
    4081 > hide #!8 models
    4082 
    4083 > show #!8 models
    4084 
    4085 > view name top
    4086 
    4087 > show #!7 models
    4088 
    4089 > hide #!6 models
    4090 
    4091 > hide #!7 models
    4092 
    4093 > view side
    4094 
    4095 Expected an objects specifier or a view name or a keyword 
    4096 
    4097 > view side_outside
    4098 
    4099 > show #!7 models
    4100 
    4101 > hide #!7 models
    4102 
    4103 > hide #!1 models
    4104 
    4105 > hide #!8 models
    4106 
    4107 > show #!1 models
    4108 
    4109 > show #!6 models
    4110 
    4111 > volume transparency 0.8
    4112 
    4113 > volume transparency 0.7
    4114 
    4115 > volume transparency 0.75
    4116 
    4117 > close #19#9-18,20-23
    4118 
    4119 > save
    4120 > /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview.cxc.cxs
    4121 
    4122 opened ChimeraX session 
    4123 
    4124 > view side_outside
    4125 
    4126 > turn x, 45
    4127 
    4128 Expected an axis vector or a keyword 
    4129 
    4130 > turn x -45
    4131 
    4132 > turn x 45
    4133 
    4134 > turn x 45
    4135 
    4136 > show #!7 models
    4137 
    4138 > hide #!7 models
    4139 
    4140 > show #!8 models
    4141 
    4142 > view name tilt
    4143 
    4144 > save /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview1.cxs
    4145 
    4146 > hide #!8 models
    4147 
    4148 > ui tool show "Side View"
    4149 
    4150 > view name tilt
    4151 
    4152 > save /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview1.cxs
    4153 
    4154 opened ChimeraX session 
    4155 
    4156 > open
    4157 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
    4158 
    4159 Summary of feedback from opening
    4160 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb 
    4161 --- 
    4162 warnings | Duplicate atom serial number found: 272408 
    4163 Duplicate atom serial number found: 272409 
    4164 Duplicate atom serial number found: 272410 
    4165 Duplicate atom serial number found: 272411 
    4166 Duplicate atom serial number found: 272412 
    4167 44904 messages similar to the above omitted 
    4168  
    4169 Chain information for IRcyt_outer.pdb #9 
    4170 --- 
    4171 Chain | Description 
    4172 4 | No description available 
    4173 A | No description available 
    4174 B | No description available 
    4175 D | No description available 
    4176 E | No description available 
    4177 F | No description available 
    4178 H | No description available 
    4179 I | No description available 
    4180 J | No description available 
    4181 U | No description available 
    4182  
    4183 
    4184 > open
    4185 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
    4186 
    4187 Summary of feedback from opening
    4188 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb 
    4189 --- 
    4190 warnings | Duplicate atom serial number found: 616953 
    4191 Duplicate atom serial number found: 616954 
    4192 Duplicate atom serial number found: 616955 
    4193 Duplicate atom serial number found: 616956 
    4194 Duplicate atom serial number found: 616957 
    4195 130 messages similar to the above omitted 
    4196  
    4197 Chain information for IRcyt_inner.pdb #10 
    4198 --- 
    4199 Chain | Description 
    4200 A | No description available 
    4201 C | No description available 
    4202 D | No description available 
    4203 F | No description available 
    4204 H | No description available 
    4205 I | No description available 
    4206 J | No description available 
    4207 U | No description available 
    4208  
    4209 
    4210 > open
    4211 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
    4212 
    4213 Summary of feedback from opening
    4214 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb 
    4215 --- 
    4216 warnings | Duplicate atom serial number found: 652149 
    4217 Duplicate atom serial number found: 652150 
    4218 Duplicate atom serial number found: 652151 
    4219 Duplicate atom serial number found: 652152 
    4220 Duplicate atom serial number found: 652153 
    4221 130 messages similar to the above omitted 
    4222  
    4223 Chain information for IRnuc_inner.pdb #11 
    4224 --- 
    4225 Chain | Description 
    4226 A | No description available 
    4227 C | No description available 
    4228 D | No description available 
    4229 F | No description available 
    4230 H | No description available 
    4231 I | No description available 
    4232 J | No description available 
    4233 U | No description available 
    4234  
    4235 
    4236 > open
    4237 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
    4238 
    4239 Summary of feedback from opening
    4240 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb 
    4241 --- 
    4242 warnings | Duplicate atom serial number found: 687345 
    4243 Duplicate atom serial number found: 687346 
    4244 Duplicate atom serial number found: 687347 
    4245 Duplicate atom serial number found: 687348 
    4246 Duplicate atom serial number found: 687349 
    4247 130 messages similar to the above omitted 
    4248  
    4249 Chain information for IRnuc_outer.pdb #12 
    4250 --- 
    4251 Chain | Description 
    4252 4 | No description available 
    4253 A | No description available 
    4254 B | No description available 
    4255 D | No description available 
    4256 E | No description available 
    4257 F | No description available 
    4258 H | No description available 
    4259 I | No description available 
    4260 J | No description available 
    4261 U | No description available 
    4262  
    4263 
    4264 > open
    4265 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
    4266 
    4267 Summary of feedback from opening
    4268 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb 
    4269 --- 
    4270 warnings | Duplicate atom serial number found: 848673 
    4271 Duplicate atom serial number found: 848674 
    4272 Duplicate atom serial number found: 848675 
    4273 Duplicate atom serial number found: 848676 
    4274 Duplicate atom serial number found: 848677 
    4275 6155 messages similar to the above omitted 
    4276  
    4277 Chain information for Y.CRouter.pdb #13 
    4278 --- 
    4279 Chain | Description 
    4280 A | No description available 
    4281 C | No description available 
    4282 J | No description available 
    4283 K | No description available 
    4284 L | No description available 
    4285 M | No description available 
    4286 N | No description available 
    4287 O | No description available 
    4288 P | No description available 
    4289 Q | No description available 
    4290 R | No description available 
    4291 S | No description available 
    4292 U | No description available 
    4293 V | No description available 
    4294 W | No description available 
    4295  
    4296 
    4297 > open
    4298 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
    4299 
    4300 Summary of feedback from opening
    4301 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb 
    4302 --- 
    4303 warnings | Duplicate atom serial number found: 811728 
    4304 Duplicate atom serial number found: 811729 
    4305 Duplicate atom serial number found: 811730 
    4306 Duplicate atom serial number found: 811731 
    4307 Duplicate atom serial number found: 811732 
    4308 6155 messages similar to the above omitted 
    4309  
    4310 Chain information for Y.CRinner.pdb #14 
    4311 --- 
    4312 Chain | Description 
    4313 A | No description available 
    4314 C | No description available 
    4315 K | No description available 
    4316 L | No description available 
    4317 M | No description available 
    4318 N | No description available 
    4319 O | No description available 
    4320 P | No description available 
    4321 Q | No description available 
    4322 R | No description available 
    4323 S | No description available 
    4324 U | No description available 
    4325  
    4326 
    4327 > open
    4328 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
    4329 
    4330 Summary of feedback from opening
    4331 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb 
    4332 --- 
    4333 warnings | Duplicate atom serial number found: 885606 
    4334 Duplicate atom serial number found: 885607 
    4335 Duplicate atom serial number found: 885608 
    4336 Duplicate atom serial number found: 885609 
    4337 Duplicate atom serial number found: 885610 
    4338 6155 messages similar to the above omitted 
    4339  
    4340 Chain information for Y.NRinner.pdb #15 
    4341 --- 
    4342 Chain | Description 
    4343 K | No description available 
    4344 L | No description available 
    4345 M | No description available 
    4346 N | No description available 
    4347 O | No description available 
    4348 P | No description available 
    4349 Q | No description available 
    4350 R | No description available 
    4351 S | No description available 
    4352 T | No description available 
    4353  
    4354 
    4355 > open
    4356 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
    4357 
    4358 Summary of feedback from opening
    4359 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb 
    4360 --- 
    4361 warnings | Duplicate atom serial number found: 922551 
    4362 Duplicate atom serial number found: 922552 
    4363 Duplicate atom serial number found: 922553 
    4364 Duplicate atom serial number found: 922554 
    4365 Duplicate atom serial number found: 922555 
    4366 6155 messages similar to the above omitted 
    4367  
    4368 Chain information for Y.NRouter.pdb #16 
    4369 --- 
    4370 Chain | Description 
    4371 A | No description available 
    4372 C | No description available 
    4373 F | No description available 
    4374 K | No description available 
    4375 L | No description available 
    4376 M | No description available 
    4377 N | No description available 
    4378 O | No description available 
    4379 P | No description available 
    4380 Q | No description available 
    4381 R | No description available 
    4382 S | No description available 
    4383 T | No description available 
    4384 U | No description available 
    4385  
    4386 
    4387 > open
    4388 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
    4389 
    4390 Summary of feedback from opening
    4391 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb 
    4392 --- 
    4393 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    4394 THR A 20 1 14 
    4395 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    4396 17 
    4397 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    4398 15 
    4399 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    4400 13 
    4401 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    4402 53 
    4403 10570 messages similar to the above omitted 
    4404  
    4405 Chain information for hNup358_1_CRouter.pdb #17 
    4406 --- 
    4407 Chain | Description 
    4408 0 | No description available 
    4409  
    4410 
    4411 > open
    4412 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
    4413 
    4414 Summary of feedback from opening
    4415 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb 
    4416 --- 
    4417 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    4418 THR A 20 1 14 
    4419 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    4420 17 
    4421 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    4422 15 
    4423 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    4424 13 
    4425 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    4426 53 
    4427 10570 messages similar to the above omitted 
    4428  
    4429 Chain information for hNup358_2_CRouter.pdb #18 
    4430 --- 
    4431 Chain | Description 
    4432 0 | No description available 
    4433  
    4434 
    4435 > open
    4436 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
    4437 
    4438 Summary of feedback from opening
    4439 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb 
    4440 --- 
    4441 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    4442 THR A 20 1 14 
    4443 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    4444 17 
    4445 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    4446 15 
    4447 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    4448 13 
    4449 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    4450 53 
    4451 10570 messages similar to the above omitted 
    4452  
    4453 Chain information for hNup358_1_CRinner.pdb #19 
    4454 --- 
    4455 Chain | Description 
    4456 0 | No description available 
    4457  
    4458 
    4459 > open
    4460 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
    4461 
    4462 Summary of feedback from opening
    4463 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb 
    4464 --- 
    4465 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    4466 THR A 20 1 14 
    4467 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    4468 17 
    4469 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    4470 15 
    4471 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    4472 13 
    4473 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    4474 53 
    4475 10570 messages similar to the above omitted 
    4476  
    4477 Chain information for hNup358_2_CRinner.pdb #20 
    4478 --- 
    4479 Chain | Description 
    4480 0 | No description available 
    4481  
    4482 
    4483 > open
    4484 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
    4485 
    4486 Summary of feedback from opening
    4487 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb 
    4488 --- 
    4489 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    4490 THR A 20 1 14 
    4491 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    4492 17 
    4493 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    4494 15 
    4495 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    4496 13 
    4497 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    4498 53 
    4499 10570 messages similar to the above omitted 
    4500  
    4501 Chain information for hNup358_CRmiddle.pdb #21 
    4502 --- 
    4503 Chain | Description 
    4504 0 | No description available 
    4505  
    4506 
    4507 > open
    4508 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
    4509 
    4510 Summary of feedback from opening
    4511 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb 
    4512 --- 
    4513 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    4514 THR A 20 1 14 
    4515 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    4516 17 
    4517 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    4518 15 
    4519 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    4520 13 
    4521 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    4522 53 
    4523 9610 messages similar to the above omitted 
    4524  
    4525 Chain information for hNup155_CRconnector.pdb #22 
    4526 --- 
    4527 Chain | Description 
    4528 D | No description available 
    4529 F | No description available 
    4530 U | No description available 
    4531  
    4532 
    4533 > open
    4534 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
    4535 
    4536 Summary of feedback from opening
    4537 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb 
    4538 --- 
    4539 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    4540 THR A 20 1 14 
    4541 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    4542 17 
    4543 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    4544 15 
    4545 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    4546 13 
    4547 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    4548 53 
    4549 9610 messages similar to the above omitted 
    4550  
    4551 Chain information for hNup155_NRconnector.pdb #23 
    4552 --- 
    4553 Chain | Description 
    4554 D | No description available 
    4555 F | No description available 
    4556 U | No description available 
    4557  
    4558 
    4559 > set bgColor black
    4560 
    4561 > hide #9-22
    4562 
    4563 > ribbon #9-22
    4564 
    4565 > view #17-21
    4566 
    4567 > color #13 #a5e6fa
    4568 
    4569 > color #14 #a7c0d6
    4570 
    4571 > color #15-16 gray
    4572 
    4573 > color #19 #004c61
    4574 
    4575 > color #20 #18b8db
    4576 
    4577 > color #18 #004f7d
    4578 
    4579 > color #17 #2d6291
    4580 
    4581 > color #20 #188dd6
    4582 
    4583 > color #13/A:170-2000 #FF004A
    4584 
    4585 > ~ribbon
    4586 
    4587 > ribbon #17-21
    4588 
    4589 > ribbon #13/A:170-2000#17-21
    4590 
    4591 > ribbon style #17-21#13/A width 2.5 thickness 0.6
    4592 
    4593 > volume #1 color #808080
    4594 
    4595 > volume #1 transparency 0.75
    4596 
    4597 > material ambientReflectivity 1
    4598 
    4599 > material specularReflectivity 0
    4600 
    4601 > lighting intensity 1.6
    4602 
    4603 > lighting fillDirection 1,-1,-1
    4604 
    4605 > lighting direction 1,-1,-2
    4606 
    4607 > graphics silhouettes true width 3
    4608 
    4609 > view 358_side1
    4610 
    4611 Expected an objects specifier or a view name or a keyword 
    4612 
    4613 > save 358_side1.png supersample 3 transparentBackground true
    4614 
    4615 > save 358_side1.png supersample 3 transparentBackground true
    4616 
    4617 > save 358_side12png supersample 3 transparentBackground true
    4618 
    4619 Cannot determine format for '358_side12png' 
    4620 
    4621 > save 358_side12.png supersample 3 transparentBackground true
    4622 
    4623 > lighting simple
    4624 
    4625 > save 358_side12.png supersample 3 transparentBackground true
    4626 
    4627 > save 358_side12.png supersample 3 transparentBackground true
    4628 
    4629 > volume #1 color #808080
    4630 
    4631 > volume #1 transparency 0.75
    4632 
    4633 > material ambientReflectivity 1
    4634 
    4635 > material specularReflectivity 0
    4636 
    4637 > lighting intensity 1.6
    4638 
    4639 > lighting fillDirection 1,-1,-1
    4640 
    4641 > lighting direction 1,-1,-2
    4642 
    4643 > graphics silhouettes true width 3
    4644 
    4645 > view 358_side1
    4646 
    4647 Expected an objects specifier or a view name or a keyword 
    4648 
    4649 > save 358_side1.png supersample 3 transparentBackground true
    4650 
    4651 > lighting simple
    4652 
    4653 > save 358_side1.png supersample 3 transparentBackground true
    4654 
    4655 > volume #1 transparency 0.75
    4656 
    4657 > volume #1 color #808080
    4658 
    4659 > volume #1 transparency 0.75
    4660 
    4661 > save 358_side1.png supersample 3 transparentBackground true
    4662 
    4663 > lighting intensity 5
    4664 
    4665 > save 358_side1.png supersample 3 transparentBackground true
    4666 
    4667 > material ambientReflectivity 2
    4668 
    4669 > save 358_side1.png supersample 3 transparentBackground true
    4670 
    4671 > save 358_side1.png supersample 3 transparentBackground true
    4672 
    4673 > lighting intensity 3
    4674 
    4675 > save 358_side1.png supersample 3 transparentBackground true
    4676 
    4677 > material specularReflectivity 0
    4678 
    4679 > lighting intensity 1
    4680 
    4681 > lighting intensity 2
    4682 
    4683 > material ambientReflectivity 0.5
    4684 
    4685 > save 358_side1.png supersample 3 transparentBackground true
    4686 
    4687 > material ambientReflectivity 0.1
    4688 
    4689 > save 358_side1.png supersample 3 transparentBackground true
    4690 
    4691 > material ambientReflectivity 0
    4692 
    4693 > save 358_side1.png supersample 3 transparentBackground true
    4694 
    4695 > lighting intensity 4
    4696 
    4697 > save 358_side1.png supersample 3 transparentBackground true
    4698 
    4699 > lighting intensity 3
    4700 
    4701 > save 358_side1.png supersample 3 transparentBackground true
    4702 
    4703 > lighting intensity 1
    4704 
    4705 > save 358_side1.png supersample 3 transparentBackground true
    4706 
    4707 > lighting intensity 2.5
    4708 
    4709 > save 358_side1.png supersample 3 transparentBackground true
    4710 
    4711 > material specularReflectivity 0.1
    4712 
    4713 > save 358_side1.png supersample 3 transparentBackground true
    4714 
    4715 > material specularReflectivity 0.1
    4716 
    4717 > material specularReflectivity 0
    4718 
    4719 > save 358_side1.png supersample 3 transparentBackground true
    4720 
    4721 > material ambientReflectivity 0
    4722 
    4723 > lighting direction 1,-1,-2
    4724 
    4725 > lighting direction -1,-1,-1
    4726 
    4727 > save 358_side1.png supersample 3 transparentBackground true
    4728 
    4729 > lighting direction -1,-1,1
    4730 
    4731 > lighting direction -1,-1,1
    4732 
    4733 > lighting direction 1,-1,-1
    4734 
    4735 > lighting direction 1,-1,-2
    4736 
    4737 > lighting direction 1,-1,-1
    4738 
    4739 > lighting direction 1,-1,-2
    4740 
    4741 > lighting direction 1,-2,-2
    4742 
    4743 > lighting direction 1,-1,-2
    4744 
    4745 > save 358_side1.png supersample 3 transparentBackground true
    4746 
    4747 > lighting fillDirection 0,0,0
    4748 
    4749 > save 358_side1.png supersample 3 transparentBackground true
    4750 
    4751 > lighting direction -1,-1,-2
    4752 
    4753 > save 358_side1.png supersample 3 transparentBackground true
    4754 
    4755 > lighting fillDirection 0,0,0
    4756 
    4757 > lighting fillDirection 0,0,-1
    4758 
    4759 > lighting fillDirection 0,-1,-1
    4760 
    4761 > lighting fillDirection -1,-1,-1
    4762 
    4763 > lighting simple
    4764 
    4765 > save 358_side1.png supersample 3 transparentBackground true
    4766 
    4767 > lighting fillDirection -1,-1,-1
    4768 
    4769 > lighting direction 1,-1,-2
    4770 
    4771 > lighting direction 1,-1,-1
    4772 
    4773 > lighting fillDirection 1,-1,-1
    4774 
    4775 > lighting fillDirection -1,-1,-1
    4776 
    4777 > lighting fillDirection -1,-1,1
    4778 
    4779 > lighting fillDirection -1,1,1
    4780 
    4781 > lighting fillDirection -1,-1,-1
    4782 
    4783 > lighting fillDirection -1,-11,-1
    4784 
    4785 > lighting fillDirection -1,-1,-1
    4786 
    4787 > lighting direction 1,-1,-1
    4788 
    4789 > lighting direction 1,-1,1
    4790 
    4791 > lighting direction 0.5,-1,-1
    4792 
    4793 > lighting direction 0,-1,-1
    4794 
    4795 > lighting direction 1,-1,-1
    4796 
    4797 > lighting direction 1,-1,-1
    4798 
    4799 > material specularReflectivity 0
    4800 
    4801 > material ambientReflectivity 0
    4802 
    4803 > lighting intensity 2.5
    4804 
    4805 > save 358_side1.png supersample 3 transparentBackground true
    4806 
    4807 > lighting intensity 2
    4808 
    4809 > save 358_side1.png supersample 3 transparentBackground true
    4810 
    4811 > lighting intensity 2.2
    4812 
    4813 > save 358_side1.png supersample 3 transparentBackground true
    4814 
    4815 > material ambientReflectivity 0.5
    4816 
    4817 > save 358_side1.png supersample 3 transparentBackground true
    4818 
    4819 > material ambientReflectivity 0.2
    4820 
    4821 > save 358_side1.png supersample 3 transparentBackground true
    4822 
    4823 > lighting intensity 2.4
    4824 
    4825 > save 358_side1.png supersample 3 transparentBackground true
    4826 
    4827 > material ambientReflectivity 0
    4828 
    4829 > save 358_side1.png supersample 3 transparentBackground true
    4830 
    4831 > lighting intensity 2.5
    4832 
    4833 > lighting direction 1,-1,-2
    4834 
    4835 > 123angle
    4836 
    4837 123angle is provided by the uninstalled bundle SEQCROW 
    4838 
    4839 > save 358_side1.png supersample 3 transparentBackground true
    4840 
    4841 > lighting fillDirection -1,-1,-1
    4842 
    4843 > save 358_side1.png supersample 3 transparentBackground true
    4844 
    4845 > lighting fillDirection 1,-1,-1
    4846 
    4847 > save 358_side1.png supersample 3 transparentBackground true
    4848 
    4849 > lighting intensity 2.3
    4850 
    4851 > save 358_side1.png supersample 3 transparentBackground true
    4852 
    4853 > lighting intensity 2
    4854 
    4855 > save 358_side1.png supersample 3 transparentBackground true
    4856 
    4857 > lighting intensity 1
    4858 
    4859 > save 358_side1.png supersample 3 transparentBackground true
    4860 
    4861 > lighting intensity 2
    4862 
    4863 > save 358_side1.png supersample 3 transparentBackground true
    4864 
    4865 > lighting intensity 2.2
    4866 
    4867 > save 358_side1.png supersample 3 transparentBackground true
    4868 
    4869 > volume #1 color #808080
    4870 
    4871 > volume #1 transparency 0.75
    4872 
    4873 > material ambientReflectivity 0
    4874 
    4875 > material specularReflectivity 0
    4876 
    4877 > lighting intensity 2.2
    4878 
    4879 > lighting fillDirection 1,-1,-1
    4880 
    4881 > lighting direction 1,-1,-22
    4882 
    4883 > save 358_side1.png supersample 3 transparentBackground true
    4884 
    4885 > volume #1 color #808080
    4886 
    4887 > volume #1 transparency 0.75
    4888 
    4889 > material ambientReflectivity 0
    4890 
    4891 > material specularReflectivity 0
    4892 
    4893 > lighting intensity 2.2
    4894 
    4895 > lighting fillDirection 1,-1,-1
    4896 
    4897 > lighting direction 1,-1,-2
    4898 
    4899 > save 358_side1.png supersample 3 transparentBackground true
    4900 
    4901 > view name side3
    4902 
    4903 > view side1
    4904 
    4905 Expected an objects specifier or a view name or a keyword 
    4906 
    4907 > view side2
    4908 
    4909 Expected an objects specifier or a view name or a keyword 
    4910 
    4911 > view name side1
    4912 
    4913 > view side1
    4914 
    4915 > hide #!1 models
    4916 
    4917 > hide #!6 models
    4918 
    4919 > view side1
    4920 
    4921 > show #!1 models
    4922 
    4923 > hide #!1 models
    4924 
    4925 > show #!1 models
    4926 
    4927 > view name side1
    4928 
    4929 > view 358_side1
    4930 
    4931 Expected an objects specifier or a view name or a keyword 
    4932 
    4933 > view 358_side2
    4934 
    4935 Expected an objects specifier or a view name or a keyword 
    4936 
    4937 > view 358_side3
    4938 
    4939 Expected an objects specifier or a view name or a keyword 
    4940 
    4941 > view name 358_side1
    4942 
    4943 > select #1
    4944 
    4945 4 models selected 
    4946 
    4947 > select clear
    4948 
    4949 > volume #1 level 2.38
    4950 
    4951 > volume #1 level 2.6
    4952 
    4953 > volume #1 level 2.7
    4954 
    4955 > volume #1 level 3
    4956 
    4957 > volume #1 level 3.3
    4958 
    4959 > volume #1 level 3
    4960 
    4961 > volume #1 level 2.8
    4962 
    4963 > view name 358_side2
    4964 
    4965 > view name 358_top
    4966 
    4967 > graphics silhouettes true width 3
    4968 
    4969 > view 358_side1
    4970 
    4971 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    4972 
    4973 > view 358_side1
    4974 
    4975 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    4976 
    4977 > view 358_top
    4978 
    4979 > save NPC_overview/358_top.png supersample 3 transparentBackground true
    4980 
    4981 > volume #1 color #808080
    4982 
    4983 > graphics silhouettes true width 3
    4984 
    4985 > view 358_side1
    4986 
    4987 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    4988 
    4989 > view 358_side1
    4990 
    4991 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    4992 
    4993 > view 358_top
    4994 
    4995 > save NPC_overview/358_top.png supersample 3 transparentBackground true
    4996 
    4997 > volume #1 color #808080
    4998 
    4999 > volume #1 transparency 0.75
    5000 
    5001 > material ambientReflectivity 0
    5002 
    5003 > material specularReflectivity 0
    5004 
    5005 > lighting intensity 2.2
    5006 
    5007 > lighting fillDirection 1,-1,-1
    5008 
    5009 > lighting direction 1,-1,-2
    5010 
    5011 > graphics silhouettes true width 3
    5012 
    5013 > view 358_side1
    5014 
    5015 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    5016 
    5017 > view 358_side1
    5018 
    5019 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    5020 
    5021 > view 358_top
    5022 
    5023 > save NPC_overview/358_top.png supersample 3 transparentBackground true
    5024 
    5025 > lighting intensity 2
    5026 
    5027 > lighting fillDirection 1,-1,-1
    5028 
    5029 > lighting direction 1,-1,-2
    5030 
    5031 > graphics silhouettes true width 3
    5032 
    5033 > view 358_side1
    5034 
    5035 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    5036 
    5037 > view 358_side1
    5038 
    5039 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    5040 
    5041 > view 358_top
    5042 
    5043 > save NPC_overview/358_top.png supersample 3 transparentBackground true
    5044 
    5045 > graphics silhouettes true width 3
    5046 
    5047 > view 358_side1
    5048 
    5049 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    5050 
    5051 > view 358_side2
    5052 
    5053 > save NPC_overview/358_side2.png supersample 3 transparentBackground true
    5054 
    5055 > view 358_top
    5056 
    5057 > save NPC_overview/358_top.png supersample 3 transparentBackground true
    5058 
    5059 > color #19 #004c61
    5060 
    5061 > color #20 #18b8db
    5062 
    5063 > color #18 #004f7d
    5064 
    5065 > color #17 #2d6291
    5066 
    5067 > color #20 #188dd6
    5068 
    5069 > color #13/A:170-2000 #FF004A
    5070 
    5071 > color #19 #004c61
    5072 
    5073 > color #20 #18b8db
    5074 
    5075 > color #18 #004f7d
    5076 
    5077 > color #17 #2d6291
    5078 
    5079 > color #21 #188dd6
    5080 
    5081 > color #21 #054266
    5082 
    5083 > graphics silhouettes true width 3
    5084 
    5085 > view 358_side1
    5086 
    5087 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    5088 
    5089 > view 358_side2
    5090 
    5091 > save NPC_overview/358_side2.png supersample 3 transparentBackground true
    5092 
    5093 > view 358_top
    5094 
    5095 > save NPC_overview/358_top.png supersample 3 transparentBackground true
    5096 
    5097 > color #19 #004c61
    5098 
    5099 > color #20 #18aadb
    5100 
    5101 > color #18 #004f7d
    5102 
    5103 > color #17 #2d6291
    5104 
    5105 > color #21 #054266
    5106 
    5107 > graphics silhouettes true width 3
    5108 
    5109 > view 358_side1
    5110 
    5111 > save NPC_overview/358_side1.png supersample 3 transparentBackground true
    5112 
    5113 > view 358_side2
    5114 
    5115 > save NPC_overview/358_side2.png supersample 3 transparentBackground true
    5116 
    5117 > view 358_top
    5118 
    5119 > save NPC_overview/358_top.png supersample 3 transparentBackground true
    5120 
    5121 > close #9-23
    5122 
    5123 > save /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview2.cxs
    5124 
    5125 > open
    5126 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
    5127 
    5128 No such file/path:
    5129 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb 
    5130 
    5131 > open
    5132 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
    5133 
    5134 No such file/path:
    5135 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb 
    5136 
    5137 > open
    5138 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
    5139 
    5140 No such file/path:
    5141 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb 
    5142 
    5143 > open
    5144 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
    5145 
    5146 No such file/path:
    5147 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb 
    5148 
    5149 > open
    5150 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
    5151 
    5152 No such file/path:
    5153 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb 
    5154 
    5155 > open
    5156 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
    5157 
    5158 No such file/path:
    5159 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb 
    5160 
    5161 > open
    5162 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
    5163 
    5164 No such file/path:
    5165 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb 
    5166 
    5167 > open
    5168 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
    5169 
    5170 No such file/path:
    5171 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb 
    5172 
    5173 > open
    5174 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
    5175 
    5176 No such file/path:
    5177 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb 
    5178 
    5179 > open
    5180 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
    5181 
    5182 No such file/path:
    5183 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb 
    5184 
    5185 > open
    5186 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
    5187 
    5188 No such file/path:
    5189 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb 
    5190 
    5191 > open
    5192 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
    5193 
    5194 No such file/path:
    5195 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb 
    5196 
    5197 > open
    5198 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
    5199 
    5200 No such file/path:
    5201 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb 
    5202 
    5203 > open
    5204 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
    5205 
    5206 No such file/path:
    5207 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb 
    5208 
    5209 > open
    5210 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
    5211 
    5212 No such file/path:
    5213 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb 
    5214 
    5215 > open
    5216 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
    5217 
    5218 No such file/path:
    5219 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb 
    5220 
    5221 > open
    5222 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
    5223 
    5224 No such file/path:
    5225 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb 
    5226 
    5227 > open
    5228 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
    5229 
    5230 No such file/path:
    5231 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb 
    5232 
    5233 > open
    5234 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
    5235 
    5236 No such file/path:
    5237 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb 
    5238 
    5239 > open
    5240 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
    5241 
    5242 No such file/path:
    5243 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb 
    5244 
    5245 > open
    5246 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
    5247 
    5248 No such file/path:
    5249 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb 
    5250 
    5251 > open
    5252 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
    5253 
    5254 No such file/path:
    5255 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb 
    5256 
    5257 > open
    5258 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
    5259 
    5260 No such file/path:
    5261 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb 
    5262 
    5263 > open
    5264 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
    5265 
    5266 No such file/path:
    5267 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb 
    5268 
    5269 > open
    5270 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
    5271 
    5272 No such file/path:
    5273 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb 
    5274 
    5275 > open
    5276 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
    5277 
    5278 No such file/path:
    5279 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb 
    5280 
    5281 > open
    5282 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
    5283 
    5284 No such file/path:
    5285 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb 
    5286 
    5287 > open
    5288 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
    5289 
    5290 No such file/path:
    5291 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb 
    5292 
    5293 > open
    5294 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
    5295 
    5296 No such file/path:
    5297 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb 
    5298 
    5299 > open
    5300 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
    5301 
    5302 No such file/path:
    5303 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb 
    5304 
    5305 > open
    5306 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
    5307 
    5308 Summary of feedback from opening
    5309 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb 
    5310 --- 
    5311 warnings | Duplicate atom serial number found: 272408 
    5312 Duplicate atom serial number found: 272409 
    5313 Duplicate atom serial number found: 272410 
    5314 Duplicate atom serial number found: 272411 
    5315 Duplicate atom serial number found: 272412 
    5316 44904 messages similar to the above omitted 
    5317  
    5318 Chain information for IRcyt_outer.pdb #9 
    5319 --- 
    5320 Chain | Description 
    5321 4 | No description available 
    5322 A | No description available 
    5323 B | No description available 
    5324 D | No description available 
    5325 E | No description available 
    5326 F | No description available 
    5327 H | No description available 
    5328 I | No description available 
    5329 J | No description available 
    5330 U | No description available 
    5331  
    5332 
    5333 > open
    5334 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
    5335 
    5336 Summary of feedback from opening
    5337 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb 
    5338 --- 
    5339 warnings | Duplicate atom serial number found: 616953 
    5340 Duplicate atom serial number found: 616954 
    5341 Duplicate atom serial number found: 616955 
    5342 Duplicate atom serial number found: 616956 
    5343 Duplicate atom serial number found: 616957 
    5344 130 messages similar to the above omitted 
    5345  
    5346 Chain information for IRcyt_inner.pdb #10 
    5347 --- 
    5348 Chain | Description 
    5349 A | No description available 
    5350 C | No description available 
    5351 D | No description available 
    5352 F | No description available 
    5353 H | No description available 
    5354 I | No description available 
    5355 J | No description available 
    5356 U | No description available 
    5357  
    5358 
    5359 > open
    5360 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
    5361 
    5362 Summary of feedback from opening
    5363 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb 
    5364 --- 
    5365 warnings | Duplicate atom serial number found: 652149 
    5366 Duplicate atom serial number found: 652150 
    5367 Duplicate atom serial number found: 652151 
    5368 Duplicate atom serial number found: 652152 
    5369 Duplicate atom serial number found: 652153 
    5370 130 messages similar to the above omitted 
    5371  
    5372 Chain information for IRnuc_inner.pdb #11 
    5373 --- 
    5374 Chain | Description 
    5375 A | No description available 
    5376 C | No description available 
    5377 D | No description available 
    5378 F | No description available 
    5379 H | No description available 
    5380 I | No description available 
    5381 J | No description available 
    5382 U | No description available 
    5383  
    5384 
    5385 > open
    5386 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
    5387 
    5388 Summary of feedback from opening
    5389 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb 
    5390 --- 
    5391 warnings | Duplicate atom serial number found: 687345 
    5392 Duplicate atom serial number found: 687346 
    5393 Duplicate atom serial number found: 687347 
    5394 Duplicate atom serial number found: 687348 
    5395 Duplicate atom serial number found: 687349 
    5396 130 messages similar to the above omitted 
    5397  
    5398 Chain information for IRnuc_outer.pdb #12 
    5399 --- 
    5400 Chain | Description 
    5401 4 | No description available 
    5402 A | No description available 
    5403 B | No description available 
    5404 D | No description available 
    5405 E | No description available 
    5406 F | No description available 
    5407 H | No description available 
    5408 I | No description available 
    5409 J | No description available 
    5410 U | No description available 
    5411  
    5412 
    5413 > open
    5414 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
    5415 
    5416 Summary of feedback from opening
    5417 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb 
    5418 --- 
    5419 warnings | Duplicate atom serial number found: 848673 
    5420 Duplicate atom serial number found: 848674 
    5421 Duplicate atom serial number found: 848675 
    5422 Duplicate atom serial number found: 848676 
    5423 Duplicate atom serial number found: 848677 
    5424 6155 messages similar to the above omitted 
    5425  
    5426 Chain information for Y.CRouter.pdb #13 
    5427 --- 
    5428 Chain | Description 
    5429 A | No description available 
    5430 C | No description available 
    5431 J | No description available 
    5432 K | No description available 
    5433 L | No description available 
    5434 M | No description available 
    5435 N | No description available 
    5436 O | No description available 
    5437 P | No description available 
    5438 Q | No description available 
    5439 R | No description available 
    5440 S | No description available 
    5441 U | No description available 
    5442 V | No description available 
    5443 W | No description available 
    5444  
    5445 
    5446 > open
    5447 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
    5448 
    5449 Summary of feedback from opening
    5450 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb 
    5451 --- 
    5452 warnings | Duplicate atom serial number found: 811728 
    5453 Duplicate atom serial number found: 811729 
    5454 Duplicate atom serial number found: 811730 
    5455 Duplicate atom serial number found: 811731 
    5456 Duplicate atom serial number found: 811732 
    5457 6155 messages similar to the above omitted 
    5458  
    5459 Chain information for Y.CRinner.pdb #14 
    5460 --- 
    5461 Chain | Description 
    5462 A | No description available 
    5463 C | No description available 
    5464 K | No description available 
    5465 L | No description available 
    5466 M | No description available 
    5467 N | No description available 
    5468 O | No description available 
    5469 P | No description available 
    5470 Q | No description available 
    5471 R | No description available 
    5472 S | No description available 
    5473 U | No description available 
    5474  
    5475 
    5476 > open
    5477 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
    5478 
    5479 Summary of feedback from opening
    5480 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb 
    5481 --- 
    5482 warnings | Duplicate atom serial number found: 885606 
    5483 Duplicate atom serial number found: 885607 
    5484 Duplicate atom serial number found: 885608 
    5485 Duplicate atom serial number found: 885609 
    5486 Duplicate atom serial number found: 885610 
    5487 6155 messages similar to the above omitted 
    5488  
    5489 Chain information for Y.NRinner.pdb #15 
    5490 --- 
    5491 Chain | Description 
    5492 K | No description available 
    5493 L | No description available 
    5494 M | No description available 
    5495 N | No description available 
    5496 O | No description available 
    5497 P | No description available 
    5498 Q | No description available 
    5499 R | No description available 
    5500 S | No description available 
    5501 T | No description available 
    5502  
    5503 
    5504 > open
    5505 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
    5506 
    5507 Summary of feedback from opening
    5508 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb 
    5509 --- 
    5510 warnings | Duplicate atom serial number found: 922551 
    5511 Duplicate atom serial number found: 922552 
    5512 Duplicate atom serial number found: 922553 
    5513 Duplicate atom serial number found: 922554 
    5514 Duplicate atom serial number found: 922555 
    5515 6155 messages similar to the above omitted 
    5516  
    5517 Chain information for Y.NRouter.pdb #16 
    5518 --- 
    5519 Chain | Description 
    5520 A | No description available 
    5521 C | No description available 
    5522 F | No description available 
    5523 K | No description available 
    5524 L | No description available 
    5525 M | No description available 
    5526 N | No description available 
    5527 O | No description available 
    5528 P | No description available 
    5529 Q | No description available 
    5530 R | No description available 
    5531 S | No description available 
    5532 T | No description available 
    5533 U | No description available 
    5534  
    5535 
    5536 > open
    5537 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
    5538 
    5539 Summary of feedback from opening
    5540 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb 
    5541 --- 
    5542 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    5543 THR A 20 1 14 
    5544 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    5545 17 
    5546 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    5547 15 
    5548 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    5549 13 
    5550 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    5551 53 
    5552 10570 messages similar to the above omitted 
    5553  
    5554 Chain information for hNup358_1_CRouter.pdb #17 
    5555 --- 
    5556 Chain | Description 
    5557 0 | No description available 
    5558  
    5559 
    5560 > open
    5561 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
    5562 
    5563 Summary of feedback from opening
    5564 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb 
    5565 --- 
    5566 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    5567 THR A 20 1 14 
    5568 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    5569 17 
    5570 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    5571 15 
    5572 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    5573 13 
    5574 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    5575 53 
    5576 10570 messages similar to the above omitted 
    5577  
    5578 Chain information for hNup358_2_CRouter.pdb #18 
    5579 --- 
    5580 Chain | Description 
    5581 0 | No description available 
    5582  
    5583 
    5584 > open
    5585 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
    5586 
    5587 Summary of feedback from opening
    5588 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb 
    5589 --- 
    5590 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    5591 THR A 20 1 14 
    5592 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    5593 17 
    5594 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    5595 15 
    5596 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    5597 13 
    5598 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    5599 53 
    5600 10570 messages similar to the above omitted 
    5601  
    5602 Chain information for hNup358_1_CRinner.pdb #19 
    5603 --- 
    5604 Chain | Description 
    5605 0 | No description available 
    5606  
    5607 
    5608 > open
    5609 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
    5610 
    5611 Summary of feedback from opening
    5612 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb 
    5613 --- 
    5614 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    5615 THR A 20 1 14 
    5616 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    5617 17 
    5618 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    5619 15 
    5620 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    5621 13 
    5622 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    5623 53 
    5624 10570 messages similar to the above omitted 
    5625  
    5626 Chain information for hNup358_2_CRinner.pdb #20 
    5627 --- 
    5628 Chain | Description 
    5629 0 | No description available 
    5630  
    5631 
    5632 > open
    5633 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
    5634 
    5635 Summary of feedback from opening
    5636 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb 
    5637 --- 
    5638 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    5639 THR A 20 1 14 
    5640 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    5641 17 
    5642 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    5643 15 
    5644 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    5645 13 
    5646 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    5647 53 
    5648 10570 messages similar to the above omitted 
    5649  
    5650 Chain information for hNup358_CRmiddle.pdb #21 
    5651 --- 
    5652 Chain | Description 
    5653 0 | No description available 
    5654  
    5655 
    5656 > open
    5657 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
    5658 
    5659 Summary of feedback from opening
    5660 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb 
    5661 --- 
    5662 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    5663 THR A 20 1 14 
    5664 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    5665 17 
    5666 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    5667 15 
    5668 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    5669 13 
    5670 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    5671 53 
    5672 9610 messages similar to the above omitted 
    5673  
    5674 Chain information for hNup155_CRconnector.pdb #22 
    5675 --- 
    5676 Chain | Description 
    5677 D | No description available 
    5678 F | No description available 
    5679 U | No description available 
    5680  
    5681 
    5682 > open
    5683 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
    5684 
    5685 Summary of feedback from opening
    5686 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb 
    5687 --- 
    5688 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    5689 THR A 20 1 14 
    5690 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    5691 17 
    5692 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    5693 15 
    5694 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    5695 13 
    5696 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    5697 53 
    5698 9610 messages similar to the above omitted 
    5699  
    5700 Chain information for hNup155_NRconnector.pdb #23 
    5701 --- 
    5702 Chain | Description 
    5703 D | No description available 
    5704 F | No description available 
    5705 U | No description available 
    5706  
    5707 
    5708 > hide #9-22
    5709 
    5710 > ribbon #9-22
    5711 
    5712 > color /A* #FF004A
    5713 
    5714 > color /0* #0098EB
    5715 
    5716 > color /L* #FF8853
    5717 
    5718 > color /P* #FF5851
    5719 
    5720 > color /R* #45f248
    5721 
    5722 > color /M* #917db6
    5723 
    5724 > color /B* #11a6f5
    5725 
    5726 > color /C* #0259b0
    5727 
    5728 > color /R* #159493
    5729 
    5730 > color /T* #8df245
    5731 
    5732 > color /K* #0098EB
    5733 
    5734 > color /N* #8df245
    5735 
    5736 > color /O* yellow
    5737 
    5738 > color /Q* cyan
    5739 
    5740 > color /D* #FFC459
    5741 
    5742 > color /F* #b4e400
    5743 
    5744 > color /I* #b4e400
    5745 
    5746 > color /H* violet
    5747 
    5748 > color /D* #fce88b
    5749 
    5750 > color /F* #8df245
    5751 
    5752 > color /4* #45f248
    5753 
    5754 > color /K* purple
    5755 
    5756 > color /E* #159493
    5757 
    5758 > color /J* purple
    5759 
    5760 > color /V* #adf245
    5761 
    5762 > color /U* magenta
    5763 
    5764 > color /W* #00b5a3
    5765 
    5766 > view 358_side1
    5767 
    5768 > view #13/C
    5769 
    5770 > set bgColor white
    5771 
    5772 > ~ribbon
    5773 
    5774 > ribbon #13/C
    5775 
    5776 > ~ribbon #13/C
    5777 
    5778 > ~ribbon #14/C
    5779 
    5780 > ribbon #14/C
    5781 
    5782 > ribbon #14/A:94-155
    5783 
    5784 > view #14/A:94-155/C
    5785 
    5786 > ui tool show "Side View"
    5787 
    5788 > view name 205_CRinner_side1
    5789 
    5790 > save 205_side1.png supersample 3 transparentBackground true
    5791 
    5792 > view name 205_CRinner_side2
    5793 
    5794 > save 205_side2.png supersample 3 transparentBackground true
    5795 
    5796 > view #13/V/W/J
    5797 
    5798 > ~ribbon
    5799 
    5800 > ribbon #13/V/W/J/U
    5801 
    5802 > color /V* #adf245
    5803 
    5804 > color /V* purple
    5805 
    5806 > color /V* #b4e400
    5807 
    5808 > color /J* violet
    5809 
    5810 > color /J* purple
    5811 
    5812 > color /U*magenta
    5813 
    5814 > set bgColor white
    5815 
    5816 > set bgColor black
    5817 
    5818 > set bgColor white
    5819 
    5820 > set bgColor black
    5821 
    5822 > view 214_side1
    5823 
    5824 Expected an objects specifier or a view name or a keyword 
    5825 
    5826 > view name 214_side1
    5827 
    5828 > save 214_side1.png supersample 3 transparentBackground true
    5829 
    5830 > set bgColor black
    5831 
    5832 > ~ribbon
    5833 
    5834 > ribbon #14/A:94-155/C
    5835 
    5836 > view 205_side1
    5837 
    5838 Expected an objects specifier or a view name or a keyword 
    5839 
    5840 > save 205_side1.png supersample 3 transparentBackground true
    5841 
    5842 > view 205_side2
    5843 
    5844 Expected an objects specifier or a view name or a keyword 
    5845 
    5846 > save 205_side2.png supersample 3 transparentBackground true
    5847 
    5848 > view 205_side1
    5849 
    5850 Expected an objects specifier or a view name or a keyword 
    5851 
    5852 > set bgColor black
    5853 
    5854 > ~ribbon
    5855 
    5856 > ribbon #14/A:94-155/C
    5857 
    5858 > view 205_CRinner_side1
    5859 
    5860 > save 205_side1.png supersample 3 transparentBackground true
    5861 
    5862 > view 205_CRinner_side2
    5863 
    5864 > save 205_side2.png supersample 3 transparentBackground true
    5865 
    5866 > view 214_side1
    5867 
    5868 > ~ribbon
    5869 
    5870 > ribbon #13/V/W/J/U
    5871 
    5872 > set bgColor black
    5873 
    5874 > view 214_side1
    5875 
    5876 > volume #1 level 3.314
    5877 
    5878 > set bgColor white
    5879 
    5880 > volume #1 level 2.8
    5881 
    5882 > volume #1 level 3.2
    5883 
    5884 > volume #1 level 1.5
    5885 
    5886 > volume #1 level 1
    5887 
    5888 > volume #1 level 0.5
    5889 
    5890 > volume #1 level 0.1
    5891 
    5892 > volume #1 level 0.01
    5893 
    5894 > volume #1 level 2.8
    5895 
    5896 > select /V:1-700
    5897 
    5898 3183 atoms, 3257 bonds, 2 pseudobonds, 409 residues, 2 models selected 
    5899 
    5900 > select /V:1-650
    5901 
    5902 3175 atoms, 3250 bonds, 408 residues, 1 model selected 
    5903 
    5904 > select /V:1-680
    5905 
    5906 3175 atoms, 3250 bonds, 408 residues, 1 model selected 
    5907 
    5908 > select /V:1-690
    5909 
    5910 3175 atoms, 3250 bonds, 408 residues, 1 model selected 
    5911 
    5912 > select /V:1-700
    5913 
    5914 3183 atoms, 3257 bonds, 2 pseudobonds, 409 residues, 2 models selected 
    5915 
    5916 > select /V:1-699
    5917 
    5918 3175 atoms, 3250 bonds, 408 residues, 1 model selected 
    5919 
    5920 > ~ribbon /V:1-700
    5921 
    5922 > view 214_side1
    5923 
    5924 > view name 214_side2
    5925 
    5926 > ui mousemode right zoom
    5927 
    5928 > view name 214_top1
    5929 
    5930 > view name 214_side2
    5931 
    5932 > ~ribbon /V:1-700
    5933 
    5934 > set bgColor black
    5935 
    5936 > view 214_side2
    5937 
    5938 > save 214_side1.png supersample 3 transparentBackground true
    5939 
    5940 > view 214_top1
    5941 
    5942 > save 214_side1.png supersample 3 transparentBackground true
    5943 
    5944 > ~ribbon
    5945 
    5946 > ~ribbon
    5947 
    5948 > ribbon #13/R/P/M
    5949 
    5950 > view #13/R/P/M
    5951 
    5952 > set bgColor white
    5953 
    5954 > ribbon #13/N/O
    5955 
    5956 > view name hub_side1
    5957 
    5958 > ribbon #13/R/M/P/N/O
    5959 
    5960 > view hub_side1
    5961 
    5962 > set bgColor black
    5963 
    5964 > save hub_side1.png supersample 3 transparentBackground true
    5965 
    5966 > ligthing intensity 2
    5967 
    5968 Unknown command: ligthing intensity 2 
    5969 
    5970 > lighting intensity 2
    5971 
    5972 > lighting intensity 1.8
    5973 
    5974 > save hub_side1.png supersample 3 transparentBackground true
    5975 
    5976 > lighting intensity 1.5
    5977 
    5978 > save hub_side1.png supersample 3 transparentBackground true
    5979 
    5980 > lighting intensity 2
    5981 
    5982 > save hub_side1.png supersample 3 transparentBackground true
    5983 
    5984 > color /M #6a00d4
    5985 
    5986 > color /M #6900d4
    5987 
    5988 > color /M #6300d4
    5989 
    5990 > set bgColor white
    5991 
    5992 > color /M #7F00FF
    5993 
    5994 > color /N #b4e400
    5995 
    5996 > color /N #81c73c
    5997 
    5998 > color /N #71ad36
    5999 
    6000 > color /N #6fa638
    6001 
    6002 > save hub_side1.png supersample 3 transparentBackground false
    6003 
    6004 > ribbon #13/Q
    6005 
    6006 > color /R #159493
    6007 
    6008 > color /R #136e6d
    6009 
    6010 > color /R #126b6a
    6011 
    6012 > color /M #532bba
    6013 
    6014 > color /Q cyan
    6015 
    6016 > color /P #d46246
    6017 
    6018 > color /P #ad4e36
    6019 
    6020 > set bgColor black
    6021 
    6022 > save hub_side1.png supersample 3 transparentBackground true
    6023 
    6024 > ribbon #13/S
    6025 
    6026 > ribbon #13/S/L/K
    6027 
    6028 > set bgColor white
    6029 
    6030 > color /K blue
    6031 
    6032 > color /K purple
    6033 
    6034 > show #!7 models
    6035 
    6036 > hide #!7 models
    6037 
    6038 > show #!6 models
    6039 
    6040 > color /L #FF8853
    6041 
    6042 > color /L #b5613c
    6043 
    6044 > color /L #b57f3c
    6045 
    6046 > view name Y_side1
    6047 
    6048 > save Y_side1.png supersample 3 transparentBackground true
    6049 
    6050 > view name Y_side1
    6051 
    6052 > save Y_side1.png supersample 3 transparentBackground true
    6053 
    6054 > view hub_side1
    6055 
    6056 Drag select of 1 pore_whole_resample.mrc , 2 residues 
    6057 
    6058 > select clear
    6059 
    6060 Drag select of 1 pore_whole_resample.mrc , 3 residues 
    6061 
    6062 > view hub_side1
    6063 
    6064 > select clear
    6065 
    6066 Drag select of 1 pore_whole_resample.mrc , 2 residues 
    6067 
    6068 > select clear
    6069 
    6070 > save hub_side1.png supersample 3 transparentBackground true
    6071 
    6072 > color /M #4f3299
    6073 
    6074 > color /M #8f67f5
    6075 
    6076 > color /M #533c8c
    6077 
    6078 > color /M #533c8c
    6079 
    6080 > color /R #126b6a
    6081 
    6082 > color /N #6fa638
    6083 
    6084 > color /P #ad4e36
    6085 
    6086 > ribbon #13/R/M/P/N/O
    6087 
    6088 > view hub_side1
    6089 
    6090 > set bgColor black
    6091 
    6092 > save hub_side1.png supersample 3 transparentBackground true
    6093 
    6094 > save hub_side1_dark.png supersample 3 transparentBackground true
    6095 
    6096 > volume #1 color #808080
    6097 
    6098 > measure symmetry #1
    6099 
    6100 Symmetry pore_whole_resample.mrc: C8, center 288 288 300 
    6101 
    6102 > sym #9-21 symmetry #1
    6103 
    6104 > color #9-21 white
    6105 
    6106 > volume #1 color #808080
    6107 
    6108 > volume #1 transparency 0.8
    6109 
    6110 > graphics silhouettes color white
    6111 
    6112 > graphics silhouettes true width 3
    6113 
    6114 > view hub_side1
    6115 
    6116 > save hub_side1_back.png supersample 3 transparentBackground false
    6117 
    6118 > save hub_side1_back.png supersample 3 transparentBackground true
    6119 
    6120 > ribbon
    6121 
    6122 > color #9-21 white
    6123 
    6124 > view hib_side1
    6125 
    6126 Expected an objects specifier or a view name or a keyword 
    6127 
    6128 > view hub_side1
    6129 
    6130 > color #9-23 white
    6131 
    6132 > view hub_side1
    6133 
    6134 > sym #9-23 symmetry #1 copies true
    6135 
    6136 > view hub_side1
    6137 
    6138 > save hub_side1_back.png supersample 3 transparentBackground true
    6139 
    6140 > volume #1 color white
    6141 
    6142 > save hub_side1_back.png supersample 3 transparentBackground true
    6143 
    6144 > volume #1 color white
    6145 
    6146 > volume #1 transparency 0.8
    6147 
    6148 > save hub_side1_back.png supersample 3 transparentBackground true
    6149 
    6150 > graphics silhouettes true width 0
    6151 
    6152 > save hub_side1_back.png supersample 3 transparentBackground true
    6153 
    6154 > lighting intensity 1
    6155 
    6156 > lighting intensity 5
    6157 
    6158 > lighting intensity 4
    6159 
    6160 > save hub_side1_back.png supersample 3 transparentBackground true
    6161 
    6162 > lighting intensity 10
    6163 
    6164 > save hub_side1_back.png supersample 3 transparentBackground true
    6165 
    6166 > material ambientReflectivity 0.8
    6167 
    6168 > lighting direction -1,-1,-1
    6169 
    6170 > lighting direction 1,-1,-1
    6171 
    6172 > hide #!1 models
    6173 
    6174 > show #!1 models
    6175 
    6176 > save hub_side1_back.png supersample 3 transparentBackground true
    6177 
    6178 > lighting direction -1,-1,-1
    6179 
    6180 > lighting direction -1,-1,1
    6181 
    6182 > lighting direction 1,1,1
    6183 
    6184 > lighting direction -1,-1,-1
    6185 
    6186 > lighting intensity 1
    6187 
    6188 > save hub_side1_back.png supersample 3 transparentBackground true
    6189 
    6190 > hide #!1 models
    6191 
    6192 > save hub_side1_back.png supersample 3 transparentBackground true
    6193 
    6194 > transparency #9-23 0.7
    6195 
    6196 > ribbon #9-23 trans 0.7
    6197 
    6198 > cartoon #9-23 trans 0.7
    6199 
    6200 Expected a keyword 
    6201 
    6202 > ribbon #9-23 trans 0.7
    6203 
    6204 > cartoon #9-23 trans 0.7
    6205 
    6206 Expected a keyword 
    6207 
    6208 > transparency #9-23 0.7
    6209 
    6210 > save hub_side1_back.png supersample 3 transparentBackground true
    6211 
    6212 > transparency #9-24 0.7
    6213 
    6214 > view hub_side1
    6215 
    6216 > transparency #9-23,r 0.7
    6217 
    6218 Missing or invalid "percent" argument: Expected a number 
    6219 
    6220 > transparency #9-23 0.7 target r
    6221 
    6222 > view hub_side1
    6223 
    6224 > transparency #9-23 70 target r
    6225 
    6226 > transparency #9-24 70 target r
    6227 
    6228 > view hub_side1
    6229 
    6230 > save hub_side1_back.png supersample 3 transparentBackground true
    6231 
    6232 > set bgColor white
    6233 
    6234 > save hub_side1_back.png supersample 3 transparentBackground true
    6235 
    6236 > transparency #9-24 0 target r
    6237 
    6238 > save hub_side1_back.png supersample 3 transparentBackground true
    6239 
    6240 > save hub_side1_back.png supersample 3 transparentBackground true
    6241 
    6242 > transparency #9-24 50 target r
    6243 
    6244 > save hub_side1_back.png supersample 3 transparentBackground true
    6245 
    6246 > transparency #9-24 40 target r
    6247 
    6248 > save hub_side1_back.png supersample 3 transparentBackground true
    6249 
    6250 > sym #22-23 symmetry #1
    6251 
    6252 > hide #1
    6253 
    6254 > measure symmetry
    6255 
    6256 Missing or invalid "volumes" argument: empty atom specifier 
    6257 
    6258 > sym #9-23 symmetry #1
    6259 
    6260 > color #9-24 white
    6261 
    6262 > graphics silhouettes false
    6263 
    6264 > transparency #9-24 50 target r
    6265 
    6266 > set bgColor white
    6267 
    6268 > view hub_side1
    6269 
    6270 > save hub_side1_back.png supersample 3 transparentBackground true
    6271 
    6272 > view 205_side1
    6273 
    6274 Expected an objects specifier or a view name or a keyword 
    6275 
    6276 > save 205_side1_back.png supersample 3 transparentBackground true
    6277 
    6278 > view 205_side2
    6279 
    6280 Expected an objects specifier or a view name or a keyword 
    6281 
    6282 > save 205_side2_back.png supersample 3 transparentBackground true
    6283 
    6284 > view 214_side2
    6285 
    6286 > save 214_side2_back.png supersample 3 transparentBackground true
    6287 
    6288 > view 214_top
    6289 
    6290 Expected an objects specifier or a view name or a keyword 
    6291 
    6292 > save 214_top_back.png supersample 3 transparentBackground true
    6293 
    6294 > view 358_top
    6295 
    6296 > save 358_top_back.png supersample 3 transparentBackground true
    6297 
    6298 > view 358_side1
    6299 
    6300 > save 358_side1_back.png supersample 3 transparentBackground true
    6301 
    6302 > view 358_side2
    6303 
    6304 > save 358_side2_back.png supersample 3 transparentBackground true
    6305 
    6306 > windowsize 1920 1080
    6307 
    6308 > windowsize 1040 920
    6309 
    6310 > windowsize 1440 810
    6311 
    6312 > close #17#9-16,18-24#24.1-8
    6313 
    6314 > windowsize 1440 810view 214_side1
    6315 
    6316 Expected an integer >= 1 or a keyword 
    6317 
    6318 > view 214_side1
    6319 
    6320 > view 205_side2
    6321 
    6322 Expected an objects specifier or a view name or a keyword 
    6323 
    6324 > view 205_side1
    6325 
    6326 Expected an objects specifier or a view name or a keyword 
    6327 
    6328 > view 205_CRinner_side1
    6329 
    6330 > save /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview3.cxs
    6331 
    6332 opened ChimeraX session 
    6333 
    6334 > open
    6335 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
    6336 
    6337 Summary of feedback from opening
    6338 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb 
    6339 --- 
    6340 warnings | Duplicate atom serial number found: 272408 
    6341 Duplicate atom serial number found: 272409 
    6342 Duplicate atom serial number found: 272410 
    6343 Duplicate atom serial number found: 272411 
    6344 Duplicate atom serial number found: 272412 
    6345 44904 messages similar to the above omitted 
    6346  
    6347 Chain information for IRcyt_outer.pdb #9 
    6348 --- 
    6349 Chain | Description 
    6350 4 | No description available 
    6351 A | No description available 
    6352 B | No description available 
    6353 D | No description available 
    6354 E | No description available 
    6355 F | No description available 
    6356 H | No description available 
    6357 I | No description available 
    6358 J | No description available 
    6359 U | No description available 
    6360  
    6361 
    6362 > open
    6363 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
    6364 
    6365 Summary of feedback from opening
    6366 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb 
    6367 --- 
    6368 warnings | Duplicate atom serial number found: 616953 
    6369 Duplicate atom serial number found: 616954 
    6370 Duplicate atom serial number found: 616955 
    6371 Duplicate atom serial number found: 616956 
    6372 Duplicate atom serial number found: 616957 
    6373 130 messages similar to the above omitted 
    6374  
    6375 Chain information for IRcyt_inner.pdb #10 
    6376 --- 
    6377 Chain | Description 
    6378 A | No description available 
    6379 C | No description available 
    6380 D | No description available 
    6381 F | No description available 
    6382 H | No description available 
    6383 I | No description available 
    6384 J | No description available 
    6385 U | No description available 
    6386  
    6387 
    6388 > open
    6389 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
    6390 
    6391 Summary of feedback from opening
    6392 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb 
    6393 --- 
    6394 warnings | Duplicate atom serial number found: 652149 
    6395 Duplicate atom serial number found: 652150 
    6396 Duplicate atom serial number found: 652151 
    6397 Duplicate atom serial number found: 652152 
    6398 Duplicate atom serial number found: 652153 
    6399 130 messages similar to the above omitted 
    6400  
    6401 Chain information for IRnuc_inner.pdb #11 
    6402 --- 
    6403 Chain | Description 
    6404 A | No description available 
    6405 C | No description available 
    6406 D | No description available 
    6407 F | No description available 
    6408 H | No description available 
    6409 I | No description available 
    6410 J | No description available 
    6411 U | No description available 
    6412  
    6413 
    6414 > open
    6415 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
    6416 
    6417 Summary of feedback from opening
    6418 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb 
    6419 --- 
    6420 warnings | Duplicate atom serial number found: 687345 
    6421 Duplicate atom serial number found: 687346 
    6422 Duplicate atom serial number found: 687347 
    6423 Duplicate atom serial number found: 687348 
    6424 Duplicate atom serial number found: 687349 
    6425 130 messages similar to the above omitted 
    6426  
    6427 Chain information for IRnuc_outer.pdb #12 
    6428 --- 
    6429 Chain | Description 
    6430 4 | No description available 
    6431 A | No description available 
    6432 B | No description available 
    6433 D | No description available 
    6434 E | No description available 
    6435 F | No description available 
    6436 H | No description available 
    6437 I | No description available 
    6438 J | No description available 
    6439 U | No description available 
    6440  
    6441 
    6442 > open
    6443 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
    6444 
    6445 Summary of feedback from opening
    6446 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb 
    6447 --- 
    6448 warnings | Duplicate atom serial number found: 848673 
    6449 Duplicate atom serial number found: 848674 
    6450 Duplicate atom serial number found: 848675 
    6451 Duplicate atom serial number found: 848676 
    6452 Duplicate atom serial number found: 848677 
    6453 6155 messages similar to the above omitted 
    6454  
    6455 Chain information for Y.CRouter.pdb #13 
    6456 --- 
    6457 Chain | Description 
    6458 A | No description available 
    6459 C | No description available 
    6460 J | No description available 
    6461 K | No description available 
    6462 L | No description available 
    6463 M | No description available 
    6464 N | No description available 
    6465 O | No description available 
    6466 P | No description available 
    6467 Q | No description available 
    6468 R | No description available 
    6469 S | No description available 
    6470 U | No description available 
    6471 V | No description available 
    6472 W | No description available 
    6473  
    6474 
    6475 > open
    6476 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
    6477 
    6478 Summary of feedback from opening
    6479 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb 
    6480 --- 
    6481 warnings | Duplicate atom serial number found: 811728 
    6482 Duplicate atom serial number found: 811729 
    6483 Duplicate atom serial number found: 811730 
    6484 Duplicate atom serial number found: 811731 
    6485 Duplicate atom serial number found: 811732 
    6486 6155 messages similar to the above omitted 
    6487  
    6488 Chain information for Y.CRinner.pdb #14 
    6489 --- 
    6490 Chain | Description 
    6491 A | No description available 
    6492 C | No description available 
    6493 K | No description available 
    6494 L | No description available 
    6495 M | No description available 
    6496 N | No description available 
    6497 O | No description available 
    6498 P | No description available 
    6499 Q | No description available 
    6500 R | No description available 
    6501 S | No description available 
    6502 U | No description available 
    6503  
    6504 
    6505 > open
    6506 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
    6507 
    6508 Summary of feedback from opening
    6509 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb 
    6510 --- 
    6511 warnings | Duplicate atom serial number found: 885606 
    6512 Duplicate atom serial number found: 885607 
    6513 Duplicate atom serial number found: 885608 
    6514 Duplicate atom serial number found: 885609 
    6515 Duplicate atom serial number found: 885610 
    6516 6155 messages similar to the above omitted 
    6517  
    6518 Chain information for Y.NRinner.pdb #15 
    6519 --- 
    6520 Chain | Description 
    6521 K | No description available 
    6522 L | No description available 
    6523 M | No description available 
    6524 N | No description available 
    6525 O | No description available 
    6526 P | No description available 
    6527 Q | No description available 
    6528 R | No description available 
    6529 S | No description available 
    6530 T | No description available 
    6531  
    6532 
    6533 > open
    6534 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
    6535 
    6536 Summary of feedback from opening
    6537 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb 
    6538 --- 
    6539 warnings | Duplicate atom serial number found: 922551 
    6540 Duplicate atom serial number found: 922552 
    6541 Duplicate atom serial number found: 922553 
    6542 Duplicate atom serial number found: 922554 
    6543 Duplicate atom serial number found: 922555 
    6544 6155 messages similar to the above omitted 
    6545  
    6546 Chain information for Y.NRouter.pdb #16 
    6547 --- 
    6548 Chain | Description 
    6549 A | No description available 
    6550 C | No description available 
    6551 F | No description available 
    6552 K | No description available 
    6553 L | No description available 
    6554 M | No description available 
    6555 N | No description available 
    6556 O | No description available 
    6557 P | No description available 
    6558 Q | No description available 
    6559 R | No description available 
    6560 S | No description available 
    6561 T | No description available 
    6562 U | No description available 
    6563  
    6564 
    6565 > open
    6566 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
    6567 
    6568 Summary of feedback from opening
    6569 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb 
    6570 --- 
    6571 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    6572 THR A 20 1 14 
    6573 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    6574 17 
    6575 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    6576 15 
    6577 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    6578 13 
    6579 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    6580 53 
    6581 10570 messages similar to the above omitted 
    6582  
    6583 Chain information for hNup358_1_CRouter.pdb #17 
    6584 --- 
    6585 Chain | Description 
    6586 0 | No description available 
    6587  
    6588 
    6589 > open
    6590 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
    6591 
    6592 Summary of feedback from opening
    6593 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb 
    6594 --- 
    6595 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    6596 THR A 20 1 14 
    6597 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    6598 17 
    6599 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    6600 15 
    6601 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    6602 13 
    6603 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    6604 53 
    6605 10570 messages similar to the above omitted 
    6606  
    6607 Chain information for hNup358_2_CRouter.pdb #18 
    6608 --- 
    6609 Chain | Description 
    6610 0 | No description available 
    6611  
    6612 
    6613 > open
    6614 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
    6615 
    6616 Summary of feedback from opening
    6617 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb 
    6618 --- 
    6619 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    6620 THR A 20 1 14 
    6621 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    6622 17 
    6623 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    6624 15 
    6625 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    6626 13 
    6627 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    6628 53 
    6629 10570 messages similar to the above omitted 
    6630  
    6631 Chain information for hNup358_1_CRinner.pdb #19 
    6632 --- 
    6633 Chain | Description 
    6634 0 | No description available 
    6635  
    6636 
    6637 > open
    6638 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
    6639 
    6640 Summary of feedback from opening
    6641 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb 
    6642 --- 
    6643 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    6644 THR A 20 1 14 
    6645 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    6646 17 
    6647 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    6648 15 
    6649 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    6650 13 
    6651 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    6652 53 
    6653 10570 messages similar to the above omitted 
    6654  
    6655 Chain information for hNup358_2_CRinner.pdb #20 
    6656 --- 
    6657 Chain | Description 
    6658 0 | No description available 
    6659  
    6660 
    6661 > open
    6662 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
    6663 
    6664 Summary of feedback from opening
    6665 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb 
    6666 --- 
    6667 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    6668 THR A 20 1 14 
    6669 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    6670 17 
    6671 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    6672 15 
    6673 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    6674 13 
    6675 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    6676 53 
    6677 10570 messages similar to the above omitted 
    6678  
    6679 Chain information for hNup358_CRmiddle.pdb #21 
    6680 --- 
    6681 Chain | Description 
    6682 0 | No description available 
    6683  
    6684 
    6685 > open
    6686 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
    6687 
    6688 Summary of feedback from opening
    6689 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb 
    6690 --- 
    6691 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    6692 THR A 20 1 14 
    6693 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    6694 17 
    6695 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    6696 15 
    6697 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    6698 13 
    6699 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    6700 53 
    6701 9610 messages similar to the above omitted 
    6702  
    6703 Chain information for hNup155_CRconnector.pdb #22 
    6704 --- 
    6705 Chain | Description 
    6706 D | No description available 
    6707 F | No description available 
    6708 U | No description available 
    6709  
    6710 
    6711 > open
    6712 > /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
    6713 
    6714 Summary of feedback from opening
    6715 /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb 
    6716 --- 
    6717 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
    6718 THR A 20 1 14 
    6719 Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
    6720 17 
    6721 Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
    6722 15 
    6723 Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
    6724 13 
    6725 Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
    6726 53 
    6727 9610 messages similar to the above omitted 
    6728  
    6729 Chain information for hNup155_NRconnector.pdb #23 
    6730 --- 
    6731 Chain | Description 
    6732 D | No description available 
    6733 F | No description available 
    6734 U | No description available 
    6735  
    6736 
    6737 > ribbon style #9-23 width 2.5 thickness 0.6
    6738 
    6739 > volume #1 color #808080
    6740 
    6741 > volume #1 transparency 0.75
    6742 
    6743 > material ambientReflectivity 0
    6744 
    6745 > material specularReflectivity 0
    6746 
    6747 > lighting intensity 2.2
    6748 
    6749 > lighting fillDirection 1,-1,-1
    6750 
    6751 > lighting direction 1,-1,-2
    6752 
    6753 > graphics silhouettes true color black
    6754 
    6755 > hide atoms
    6756 
    6757 > ~ribbon
     1595
     1596[lots of this log deleted to fit within ticket length limit]
    67581597
    67591598> ribbon #13/A:170-2000#17-21