Changes between Initial Version and Version 1 of Ticket #8834


Ignore:
Timestamp:
Apr 14, 2023, 10:25:19 AM (3 years ago)
Author:
Eric Pettersen
Comment:

Reported by Leonardo Lima

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #8834

    • Property Component Unassigned → Third Party
    • Property Owner set to Tristan Croll
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → AdaptiveDihedralRestraintMgr creation for closed structure

  • Ticket #8834 – Description

    initial v1  
    15901590> select clear
    15911591
    1592 [Repeated 1 time(s)]
    1593 
    1594 > isolde pepflip sel
    1595 
    1596 Flipping the peptide bond for 1 residues 
    1597 
    1598 > isolde pepflip sel
    1599 
    1600 Flipping the peptide bond for 1 residues 
    1601 
    1602 > isolde pepflip sel
    1603 
    1604 Flipping the peptide bond for 1 residues 
    1605 
    1606 > isolde pepflip sel
    1607 
    1608 Flipping the peptide bond for 1 residues 
    1609 
    1610 > isolde pepflip sel
    1611 
    1612 Flipping the peptide bond for 1 residues 
    1613 
    1614 > select clear
    1615 
    1616 [Repeated 3 time(s)]
    1617 
    1618 > isolde pepflip sel
    1619 
    1620 Flipping the peptide bond for 1 residues 
    1621 
    1622 > isolde pepflip sel
    1623 
    1624 Flipping the peptide bond for 1 residues 
    1625 
    1626 > isolde sim pause
    1627 
    1628 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    1629 > mut8-no-C-ter/-KSRP-no-C-ter-Step1-FourthSubsteps.cxs
    1630 
    1631 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    1632 
    1633 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    1634 > mut8-no-C-ter/5-KSRP-no-C-ter-Step1-FifthSubsteps.pdb
    1635 
    1636 [Repeated 1 time(s)]
    1637 
    1638 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    1639 > mut8-no-C-ter/5-KSRP-no-C-ter-Step1-FifthSubsteps.cxs
    1640 
    1641 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    1642 
    1643 > isolde sim start sel
    1644 
    1645 Simulation already running! 
    1646 
    1647 > isolde sim resume
    1648 
    1649 > isolde cisflip sel
    1650 
    1651 Performing cis<\-->trans flip for 1 residues 
    1652 
    1653 > isolde cisflip sel
    1654 
    1655 Performing cis<\-->trans flip for 1 residues 
    1656 
    1657 > isolde pepflip sel
    1658 
    1659 Flipping the peptide bond for 1 residues 
    1660 
    1661 > isolde cisflip sel
    1662 
    1663 Performing cis<\-->trans flip for 1 residues 
    1664 
    1665 > isolde cisflip sel
    1666 
    1667 Performing cis<\-->trans flip for 1 residues 
    1668 
    1669 > isolde pepflip sel
    1670 
    1671 Flipping the peptide bond for 1 residues 
    1672 
    1673 > isolde pepflip sel
    1674 
    1675 Flipping the peptide bond for 1 residues 
    1676 
    1677 > isolde pepflip sel
    1678 
    1679 Flipping the peptide bond for 1 residues 
    1680 
    1681 > isolde pepflip sel
    1682 
    1683 Flipping the peptide bond for 1 residues 
    1684 
    1685 > isolde pepflip sel
    1686 
    1687 Flipping the peptide bond for 1 residues 
    1688 
    1689 > select clear
    1690 
    1691 [Repeated 1 time(s)]
    1692 
    1693 > isolde pepflip sel
    1694 
    1695 Flipping the peptide bond for 1 residues 
    1696 
    1697 > isolde pepflip sel
    1698 
    1699 Flipping the peptide bond for 1 residues 
    1700 Unable to flip peptide bond after 50 rounds. Giving up. 
    1701 
    1702 > select clear
    1703 
    1704 > isolde pepflip sel
    1705 
    1706 Flipping the peptide bond for 1 residues 
    1707 
    1708 > isolde pepflip sel
    1709 
    1710 Flipping the peptide bond for 1 residues 
    1711 
    1712 > isolde pepflip sel
    1713 
    1714 Flipping the peptide bond for 1 residues 
    1715 
    1716 > isolde pepflip sel
    1717 
    1718 Flipping the peptide bond for 1 residues 
    1719 
    1720 > select clear
    1721 
    1722 > hide #!1.2 models
    1723 
    1724 > show #!1.2 models
    1725 
    1726 > hide #!1.2 models
    1727 
    1728 > show #!1.2 models
    1729 
    1730 > hide #!1.2 models
    1731 
    1732 > show #!1.2 models
    1733 
    1734 > select clear
    1735 
    1736 > isolde pepflip sel
    1737 
    1738 Flipping the peptide bond for 1 residues 
    1739 
    1740 > isolde pepflip sel
    1741 
    1742 Flipping the peptide bond for 1 residues 
    1743 
    1744 > isolde pepflip sel
    1745 
    1746 Flipping the peptide bond for 1 residues 
    1747 
    1748 > isolde pepflip sel
    1749 
    1750 Flipping the peptide bond for 1 residues 
    1751 Unable to flip peptide bond after 50 rounds. Giving up. 
    1752 
    1753 > isolde pepflip sel
    1754 
    1755 Flipping the peptide bond for 1 residues 
    1756 Unable to flip peptide bond after 50 rounds. Giving up. 
    1757 
    1758 > isolde pepflip sel
    1759 
    1760 Flipping the peptide bond for 1 residues 
    1761 
    1762 > isolde sim pause
    1763 
    1764 > select #1
    1765 
    1766 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    1767 
    1768 > select #1/Q:40-46
    1769 
    1770 132 atoms, 133 bonds, 7 residues, 1 model selected 
    1771 
    1772 > isolde sim resume
    1773 
    1774 > isolde pepflip sel
    1775 
    1776 Flipping the peptide bond for 1 residues 
    1777 
    1778 > isolde pepflip sel
    1779 
    1780 Flipping the peptide bond for 1 residues 
    1781 
    1782 > isolde sim stop
    1783 
    1784 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1785 chains... 
    1786 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    1787 standards. 
    1788 ISOLDE: stopped sim 
    1789 
    1790 > isolde sim start sel
    1791 
    1792 ISOLDE: started sim 
    1793 
    1794 > select clear
    1795 
    1796 [Repeated 2 time(s)]
    1797 
    1798 > select #1/Q:37
    1799 
    1800 22 atoms, 21 bonds, 1 residue, 1 model selected 
    1801 
    1802 > select #1
    1803 
    1804 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    1805 
    1806 > select #1/Q:37
    1807 
    1808 22 atoms, 21 bonds, 1 residue, 1 model selected 
    1809 
    1810 > select #1/Q:43-44
    1811 
    1812 33 atoms, 33 bonds, 2 residues, 1 model selected 
    1813 
    1814 > isolde sim pause
    1815 
    1816 > select #1
    1817 
    1818 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    1819 
    1820 > select #1/Q:42
    1821 
    1822 17 atoms, 16 bonds, 1 residue, 1 model selected 
    1823 
    1824 > isolde sim resume
    1825 
    1826 > isolde cisflip sel
    1827 
    1828 Performing cis<\-->trans flip for 1 residues 
    1829 
    1830 > isolde cisflip sel
    1831 
    1832 Performing cis<\-->trans flip for 1 residues 
    1833 
    1834 > select #1/Q:42
    1835 
    1836 17 atoms, 16 bonds, 1 residue, 1 model selected 
    1837 
    1838 > isolde pepflip sel
    1839 
    1840 Flipping the peptide bond for 1 residues 
    1841 Unable to flip peptide bond after 50 rounds. Giving up. 
    1842 
    1843 > select clear
    1844 
    1845 > isolde pepflip sel
    1846 
    1847 Flipping the peptide bond for 1 residues 
    1848 
    1849 > isolde cisflip sel
    1850 
    1851 Performing cis<\-->trans flip for 1 residues 
    1852 
    1853 > isolde pepflip sel
    1854 
    1855 Flipping the peptide bond for 1 residues 
    1856 
    1857 > isolde pepflip sel
    1858 
    1859 Flipping the peptide bond for 1 residues 
    1860 Unable to flip peptide bond after 50 rounds. Giving up. 
    1861 
    1862 > select clear
    1863 
    1864 [Repeated 1 time(s)]
    1865 
    1866 > isolde cisflip sel
    1867 
    1868 Performing cis<\-->trans flip for 1 residues 
    1869 
    1870 > select clear
    1871 
    1872 [Repeated 1 time(s)]
    1873 
    1874 > ui tool show "Ramachandran Plot"
    1875 
    1876 > select clear
    1877 
    1878 > isolde sim stop
    1879 
    1880 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1881 chains... 
    1882 ISOLDE: stopped sim 
    1883 
    1884 > isolde sim start sel
    1885 
    1886 ISOLDE: started sim 
    1887 
    1888 > isolde sim stop
    1889 
    1890 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1891 chains... 
    1892 ISOLDE: stopped sim 
    1893 
    1894 > isolde sim start sel
    1895 
    1896 ISOLDE: started sim 
    1897 
    1898 > ui tool show "Ramachandran Plot"
    1899 
    1900 > select clear
    1901 
    1902 > isolde pepflip sel
    1903 
    1904 Flipping the peptide bond for 1 residues 
    1905 
    1906 > isolde pepflip sel
    1907 
    1908 Flipping the peptide bond for 1 residues 
    1909 
    1910 > isolde pepflip sel
    1911 
    1912 Flipping the peptide bond for 1 residues 
    1913 
    1914 > select clear
    1915 
    1916 [Repeated 1 time(s)]
    1917 
    1918 > isolde pepflip sel
    1919 
    1920 Flipping the peptide bond for 1 residues 
    1921 
    1922 > isolde pepflip sel
    1923 
    1924 Flipping the peptide bond for 1 residues 
    1925 
    1926 > select clear
    1927 
    1928 > isolde sim stop discardTo start
    1929 
    1930 reverting to start 
    1931 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1932 chains... 
    1933 ISOLDE: stopped sim 
    1934 
    1935 > isolde sim start sel
    1936 
    1937 ISOLDE: started sim 
    1938 
    1939 > isolde sim stop
    1940 
    1941 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1942 chains... 
    1943 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    1944 standards. 
    1945 ISOLDE: stopped sim 
    1946 
    1947 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    1948 > mut8-no-C-ter/6-KSRP-no-C-ter-Step1-SixthSubsteps.cxs
    1949 
    1950 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    1951 
    1952 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    1953 > mut8-no-C-ter/6-KSRP-no-C-ter-Step1-SixthSubsteps.pdb
    1954 
    1955 > isolde sim start sel
    1956 
    1957 ISOLDE: started sim 
    1958 
    1959 > isolde sim stop
    1960 
    1961 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1962 chains... 
    1963 ISOLDE: stopped sim 
    1964 
    1965 > isolde sim start sel
    1966 
    1967 ISOLDE: started sim 
    1968 
    1969 > select clear
    1970 
    1971 [Repeated 1 time(s)]
    1972 
    1973 > isolde pepflip sel
    1974 
    1975 Flipping the peptide bond for 1 residues 
    1976 
    1977 > select clear
    1978 
    1979 > isolde pepflip sel
    1980 
    1981 Flipping the peptide bond for 1 residues 
    1982 
    1983 > isolde pepflip sel
    1984 
    1985 Flipping the peptide bond for 1 residues 
    1986 
    1987 > select clear
    1988 
    1989 > isolde pepflip sel
    1990 
    1991 Flipping the peptide bond for 1 residues 
    1992 
    1993 > isolde pepflip sel
    1994 
    1995 Flipping the peptide bond for 1 residues 
    1996 
    1997 > select clear
    1998 
    1999 [Repeated 2 time(s)]
    2000 
    2001 > isolde pepflip sel
    2002 
    2003 Flipping the peptide bond for 1 residues 
    2004 
    2005 > isolde pepflip sel
    2006 
    2007 Flipping the peptide bond for 1 residues 
    2008 
    2009 > select clear
    2010 
    2011 [Repeated 2 time(s)]
    2012 
    2013 > isolde sim stop
    2014 
    2015 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2016 chains... 
    2017 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    2018 standards. 
    2019 ISOLDE: stopped sim 
    2020 
    2021 > isolde sim start sel
    2022 
    2023 ISOLDE: started sim 
    2024 
    2025 > isolde pepflip sel
    2026 
    2027 Flipping the peptide bond for 1 residues 
    2028 
    2029 > isolde pepflip sel
    2030 
    2031 Flipping the peptide bond for 1 residues 
    2032 
    2033 > select clear
    2034 
    2035 > isolde pepflip sel
    2036 
    2037 Flipping the peptide bond for 1 residues 
    2038 
    2039 > select clear
    2040 
    2041 > isolde pepflip sel
    2042 
    2043 Flipping the peptide bond for 1 residues 
    2044 
    2045 > isolde pepflip sel
    2046 
    2047 Flipping the peptide bond for 1 residues 
    2048 
    2049 > isolde pepflip sel
    2050 
    2051 Flipping the peptide bond for 1 residues 
    2052 
    2053 > select clear
    2054 
    2055 > isolde sim stop
    2056 
    2057 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2058 chains... 
    2059 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2060 standards. 
    2061 ISOLDE: stopped sim 
    2062 
    2063 > select clear
    2064 
    2065 > isolde sim start sel
    2066 
    2067 ISOLDE: started sim 
    2068 
    2069 > select clear
    2070 
    2071 > isolde pepflip sel
    2072 
    2073 Flipping the peptide bond for 1 residues 
    2074 
    2075 > isolde pepflip sel
    2076 
    2077 Flipping the peptide bond for 1 residues 
    2078 
    2079 > select clear
    2080 
    2081 > isolde pepflip sel
    2082 
    2083 Flipping the peptide bond for 1 residues 
    2084 
    2085 > select clear
    2086 
    2087 > isolde sim stop
    2088 
    2089 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2090 chains... 
    2091 ISOLDE: stopped sim 
    2092 
    2093 > isolde sim start sel
    2094 
    2095 ISOLDE: started sim 
    2096 
    2097 > select clear
    2098 
    2099 > isolde sim stop
    2100 
    2101 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2102 chains... 
    2103 ISOLDE: stopped sim 
    2104 
    2105 > isolde sim start sel
    2106 
    2107 ISOLDE: started sim 
    2108 
    2109 > select clear
    2110 
    2111 > isolde sim stop
    2112 
    2113 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2114 chains... 
    2115 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2116 standards. 
    2117 ISOLDE: stopped sim 
    2118 
    2119 > isolde sim start sel
    2120 
    2121 ISOLDE: started sim 
    2122 
    2123 > isolde pepflip sel
    2124 
    2125 Flipping the peptide bond for 1 residues 
    2126 
    2127 > select clear
    2128 
    2129 [Repeated 1 time(s)]
    2130 
    2131 > isolde pepflip sel
    2132 
    2133 Flipping the peptide bond for 1 residues 
    2134 
    2135 > isolde pepflip sel
    2136 
    2137 Flipping the peptide bond for 1 residues 
    2138 
    2139 > isolde pepflip sel
    2140 
    2141 Flipping the peptide bond for 1 residues 
    2142 
    2143 > isolde pepflip sel
    2144 
    2145 Flipping the peptide bond for 1 residues 
    2146 
    2147 > select clear
    2148 
    2149 [Repeated 3 time(s)]
    2150 
    2151 > isolde pepflip sel
    2152 
    2153 Flipping the peptide bond for 1 residues 
    2154 
    2155 > select clear
    2156 
    2157 > isolde pepflip sel
    2158 
    2159 Flipping the peptide bond for 1 residues 
    2160 
    2161 > isolde pepflip sel
    2162 
    2163 Flipping the peptide bond for 1 residues 
    2164 
    2165 > select clear
    2166 
    2167 > isolde pepflip sel
    2168 
    2169 Flipping the peptide bond for 1 residues 
    2170 
    2171 > isolde pepflip sel
    2172 
    2173 Flipping the peptide bond for 1 residues 
    2174 
    2175 > select clear
    2176 
    2177 [Repeated 4 time(s)]
    2178 
    2179 > isolde sim stop
    2180 
    2181 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2182 chains... 
    2183 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2184 standards. 
    2185 ISOLDE: stopped sim 
    2186 
    2187 > isolde sim start sel
    2188 
    2189 ISOLDE: started sim 
    2190 
    2191 > isolde sim stop discardTo start
    2192 
    2193 reverting to start 
    2194 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2195 chains... 
    2196 ISOLDE: stopped sim 
    2197 
    2198 > isolde sim start sel
    2199 
    2200 ISOLDE: started sim 
    2201 
    2202 > ui tool show "Ramachandran Plot"
    2203 
    2204 > select clear
    2205 
    2206 [Repeated 7 time(s)]
    2207 
    2208 > isolde sim stop discardTo start
    2209 
    2210 reverting to start 
    2211 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2212 chains... 
    2213 ISOLDE: stopped sim 
    2214 
    2215 > isolde sim start sel
    2216 
    2217 ISOLDE: started sim 
    2218 
    2219 > isolde sim stop
    2220 
    2221 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2222 chains... 
    2223 ISOLDE: stopped sim 
    2224 
    2225 > isolde sim start sel
    2226 
    2227 ISOLDE: started sim 
    2228 
    2229 > select #1
    2230 
    2231 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    2232 
    2233 > select clear
    2234 
    2235 > isolde pepflip sel
    2236 
    2237 Flipping the peptide bond for 1 residues 
    2238 
    2239 > select clear
    2240 
    2241 > isolde pepflip sel
    2242 
    2243 Flipping the peptide bond for 1 residues 
    2244 
    2245 > select clear
    2246 
    2247 [Repeated 2 time(s)]
    2248 
    2249 > isolde pepflip sel
    2250 
    2251 Flipping the peptide bond for 1 residues 
    2252 
    2253 > isolde pepflip sel
    2254 
    2255 Flipping the peptide bond for 1 residues 
    2256 
    2257 > select clear
    2258 
    2259 > isolde cisflip sel
    2260 
    2261 Performing cis<\-->trans flip for 1 residues 
    2262 
    2263 > isolde cisflip sel
    2264 
    2265 Performing cis<\-->trans flip for 1 residues 
    2266 
    2267 > select clear
    2268 
    2269 [Repeated 1 time(s)]
    2270 
    2271 > isolde pepflip sel
    2272 
    2273 Flipping the peptide bond for 1 residues 
    2274 
    2275 > isolde pepflip sel
    2276 
    2277 Flipping the peptide bond for 1 residues 
    2278 
    2279 > isolde pepflip sel
    2280 
    2281 Flipping the peptide bond for 1 residues 
    2282 
    2283 > isolde pepflip sel
    2284 
    2285 Flipping the peptide bond for 1 residues 
    2286 
    2287 > isolde pepflip sel
    2288 
    2289 Flipping the peptide bond for 1 residues 
    2290 
    2291 > isolde pepflip sel
    2292 
    2293 Flipping the peptide bond for 1 residues 
    2294 
    2295 > select clear
    2296 
    2297 [Repeated 3 time(s)]
    2298 
    2299 > isolde pepflip sel
    2300 
    2301 Flipping the peptide bond for 1 residues 
    2302 
    2303 > select clear
    2304 
    2305 [Repeated 3 time(s)]
    2306 
    2307 > isolde pepflip sel
    2308 
    2309 Flipping the peptide bond for 1 residues 
    2310 
    2311 > select clear
    2312 
    2313 > select #1
    2314 
    2315 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    2316 
    2317 > isolde pepflip sel
    2318 
    2319 Flipping the peptide bond for 1 residues 
    2320 
    2321 > isolde pepflip sel
    2322 
    2323 Flipping the peptide bond for 1 residues 
    2324 
    2325 > isolde pepflip sel
    2326 
    2327 Flipping the peptide bond for 1 residues 
    2328 
    2329 > isolde pepflip sel
    2330 
    2331 Flipping the peptide bond for 1 residues 
    2332 
    2333 > select clear
    2334 
    2335 [Repeated 4 time(s)]
    2336 
    2337 > isolde sim pause
    2338 
    2339 > select #1
    2340 
    2341 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    2342 
    2343 > isolde sim resume
    2344 
    2345 > select clear
    2346 
    2347 > isolde pepflip sel
    2348 
    2349 Flipping the peptide bond for 1 residues 
    2350 
    2351 > isolde pepflip sel
    2352 
    2353 Flipping the peptide bond for 1 residues 
    2354 
    2355 > isolde pepflip sel
    2356 
    2357 Flipping the peptide bond for 1 residues 
    2358 
    2359 > select clear
    2360 
    2361 > isolde pepflip sel
    2362 
    2363 Flipping the peptide bond for 1 residues 
    2364 
    2365 > isolde pepflip sel
    2366 
    2367 Flipping the peptide bond for 1 residues 
    2368 
    2369 > select clear
    2370 
    2371 > isolde pepflip sel
    2372 
    2373 Flipping the peptide bond for 1 residues 
    2374 
    2375 > select clear
    2376 
    2377 [Repeated 1 time(s)]
    2378 
    2379 > isolde pepflip sel
    2380 
    2381 Flipping the peptide bond for 1 residues 
    2382 
    2383 > select clear
    2384 
    2385 > isolde pepflip sel
    2386 
    2387 Flipping the peptide bond for 1 residues 
    2388 
    2389 > ui tool show "Ramachandran Plot"
    2390 
    2391 > select clear
    2392 
    2393 > ui tool show "Ramachandran Plot"
    2394 
    2395 > select clear
    2396 
    2397 [Repeated 3 time(s)]
    2398 
    2399 > isolde pepflip sel
    2400 
    2401 Flipping the peptide bond for 1 residues 
    2402 
    2403 > select #1
    2404 
    2405 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    2406 
    2407 > select #1/o:60
    2408 
    2409 24 atoms, 23 bonds, 1 residue, 1 model selected 
    2410 
    2411 > select clear
    2412 
    2413 > ui tool show "Ramachandran Plot"
    2414 
    2415 > select clear
    2416 
    2417 [Repeated 1 time(s)]
    2418 
    2419 > ui tool show "Ramachandran Plot"
    2420 
    2421 > select clear
    2422 
    2423 [Repeated 1 time(s)]
    2424 
    2425 > isolde pepflip sel
    2426 
    2427 Flipping the peptide bond for 1 residues 
    2428 Peptide bond must be mobile in the simulation! 
    2429 
    2430 > ui tool show "Ramachandran Plot"
    2431 
    2432 > select clear
    2433 
    2434 > ui tool show "Ramachandran Plot"
    2435 
    2436 > select #1
    2437 
    2438 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    2439 
    2440 > isolde pepflip sel
    2441 
    2442 Flipping the peptide bond for 1 residues 
    2443 
    2444 > select clear
    2445 
    2446 > isolde pepflip sel
    2447 
    2448 Flipping the peptide bond for 1 residues 
    2449 
    2450 > select clear
    2451 
    2452 > ui tool show "Ramachandran Plot"
    2453 
    2454 Traceback (most recent call last): 
    2455 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    2456 packages/matplotlib/cbook/__init__.py", line 287, in process 
    2457 func(*args, **kwargs) 
    2458 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    2459 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    2460 on_resize 
    2461 c.draw() 
    2462 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    2463 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    2464 self.figure.draw(self.renderer) 
    2465 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    2466 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    2467 result = draw(artist, renderer, *args, **kwargs) 
    2468 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    2469 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    2470 return draw(artist, renderer) 
    2471 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    2472 packages/matplotlib/figure.py", line 2796, in draw 
    2473 artists = self._get_draw_artists(renderer) 
    2474 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    2475 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    2476 ax.apply_aspect() 
    2477 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    2478 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    2479 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    2480 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    2481 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    2482 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    2483 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    2484 
    2485 > ui tool show "Ramachandran Plot"
    2486 
    2487 > select clear
    2488 
    2489 > isolde pepflip sel
    2490 
    2491 Flipping the peptide bond for 1 residues 
    2492 
    2493 > isolde pepflip sel
    2494 
    2495 Flipping the peptide bond for 1 residues 
    2496 
    2497 > isolde pepflip sel
    2498 
    2499 Flipping the peptide bond for 1 residues 
    2500 
    2501 > isolde pepflip sel
    2502 
    2503 Flipping the peptide bond for 1 residues 
    2504 
    2505 > isolde pepflip sel
    2506 
    2507 Flipping the peptide bond for 1 residues 
    2508 
    2509 > select clear
    2510 
    2511 [Repeated 4 time(s)]
    2512 
    2513 > ui tool show "Ramachandran Plot"
    2514 
    2515 [Repeated 1 time(s)]
    2516 
    2517 > select clear
    2518 
    2519 > isolde sim stop
    2520 
    2521 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2522 chains... 
    2523 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    2524 standards. 
    2525 ISOLDE: stopped sim 
    2526 
    2527 > select #1/a:47
    2528 
    2529 16 atoms, 15 bonds, 1 residue, 1 model selected 
    2530 
    2531 > view #1/a:47
    2532 
    2533 > view #1/o:63
    2534 
    2535 [Repeated 1 time(s)]
    2536 
    2537 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    2538 > mut8-no-C-ter/7-KSRP-no-C-ter-Step1-SeventhSubsteps.cxs
    2539 
    2540 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    2541 
    2542 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    2543 > mut8-no-C-ter/7-KSRP-no-C-ter-Step1-SeventhSubsteps.pdb
    2544 
    2545 > isolde sim start sel
    2546 
    2547 ISOLDE: started sim 
    2548 
    2549 > select clear
    2550 
    2551 [Repeated 1 time(s)]
    2552 
    2553 > isolde pepflip sel
    2554 
    2555 Flipping the peptide bond for 1 residues 
    2556 
    2557 > isolde pepflip sel
    2558 
    2559 Flipping the peptide bond for 1 residues 
    2560 Peptide bond must be mobile in the simulation! 
    2561 
    2562 > isolde pepflip sel
    2563 
    2564 Flipping the peptide bond for 1 residues 
    2565 
    2566 > select clear
    2567 
    2568 > isolde sim stop
    2569 
    2570 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2571 chains... 
    2572 ISOLDE: stopped sim 
    2573 
    2574 > isolde sim start sel
    2575 
    2576 ISOLDE: started sim 
    2577 
    2578 > isolde pepflip sel
    2579 
    2580 Flipping the peptide bond for 1 residues 
    2581 
    2582 > select clear
    2583 
    2584 [Repeated 1 time(s)]
    2585 
    2586 > isolde sim stop
    2587 
    2588 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2589 chains... 
    2590 ISOLDE: stopped sim 
    2591 
    2592 > select #1/p:43
    2593 
    2594 24 atoms, 25 bonds, 1 residue, 1 model selected 
    2595 
    2596 > isolde sim start sel
    2597 
    2598 ISOLDE: started sim 
    2599 
    2600 > view sel
    2601 
    2602 > select clear
    2603 
    2604 > isolde sim start sel
    2605 
    2606 Simulation already running! 
    2607 
    2608 > isolde sim stop
    2609 
    2610 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2611 chains... 
    2612 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2613 standards. 
    2614 ISOLDE: stopped sim 
    2615 
    2616 > isolde sim start sel
    2617 
    2618 ISOLDE: started sim 
    2619 
    2620 > isolde pepflip sel
    2621 
    2622 Flipping the peptide bond for 1 residues 
    2623 
    2624 > select clear
    2625 
    2626 > isolde sim stop
    2627 
    2628 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2629 chains... 
    2630 ISOLDE: stopped sim 
    2631 
    2632 > select #1/p:43
    2633 
    2634 24 atoms, 25 bonds, 1 residue, 1 model selected 
    2635 
    2636 > view #1/p:43
    2637 
    2638 > select #1/p:43
    2639 
    2640 24 atoms, 25 bonds, 1 residue, 1 model selected 
    2641 
    2642 > isolde sim start sel
    2643 
    2644 ISOLDE: started sim 
    2645 
    2646 > select clear
    2647 
    2648 > isolde sim stop
    2649 
    2650 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2651 chains... 
    2652 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2653 standards. 
    2654 ISOLDE: stopped sim 
    2655 
    2656 > isolde sim start sel
    2657 
    2658 ISOLDE: started sim 
    2659 
    2660 > isolde sim stop
    2661 
    2662 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2663 chains... 
    2664 ISOLDE: stopped sim 
    2665 
    2666 > isolde sim start sel
    2667 
    2668 ISOLDE: started sim 
    2669 
    2670 > isolde sim stop
    2671 
    2672 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2673 chains... 
    2674 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    2675 standards. 
    2676 ISOLDE: stopped sim 
    2677 
    2678 > view #1/p:111
    2679 
    2680 > select #1/p:111
    2681 
    2682 12 atoms, 11 bonds, 1 residue, 1 model selected 
    2683 
    2684 > isolde sim start sel
    2685 
    2686 ISOLDE: started sim 
    2687 
    2688 > select clear
    2689 
    2690 > view sele
    2691 
    2692 Expected an objects specifier or a view name or a keyword 
    2693 
    2694 > view sel
    2695 
    2696 > isolde sim stop
    2697 
    2698 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2699 chains... 
    2700 ISOLDE: stopped sim 
    2701 
    2702 > isolde sim start sel
    2703 
    2704 ISOLDE: started sim 
    2705 
    2706 > isolde pepflip sel
    2707 
    2708 Flipping the peptide bond for 1 residues 
    2709 
    2710 > isolde pepflip sel
    2711 
    2712 Flipping the peptide bond for 1 residues 
    2713 
    2714 > isolde sim stop
    2715 
    2716 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2717 chains... 
    2718 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2719 standards. 
    2720 ISOLDE: stopped sim 
    2721 
    2722 > isolde sim start sel
    2723 
    2724 ISOLDE: started sim 
    2725 
    2726 > isolde pepflip sel
    2727 
    2728 Flipping the peptide bond for 1 residues 
    2729 
    2730 > isolde pepflip sel
    2731 
    2732 Flipping the peptide bond for 1 residues 
    2733 
    2734 > select clear
    2735 
    2736 > ui tool show "Ramachandran Plot"
    2737 
    2738 > select clear
    2739 
    2740 [Repeated 6 time(s)]
    2741 
    2742 > ui tool show "Ramachandran Plot"
    2743 
    2744 > select clear
    2745 
    2746 [Repeated 1 time(s)]
    2747 
    2748 > ui tool show "Ramachandran Plot"
    2749 
    2750 > select clear
    2751 
    2752 [Repeated 1 time(s)]
    2753 
    2754 > ui tool show "Ramachandran Plot"
    2755 
    2756 > select clear
    2757 
    2758 > isolde pepflip sel
    2759 
    2760 Flipping the peptide bond for 1 residues 
    2761 
    2762 > isolde pepflip sel
    2763 
    2764 Flipping the peptide bond for 1 residues 
    2765 
    2766 > select clear
    2767 
    2768 [Repeated 1 time(s)]
    2769 
    2770 > isolde sim stop
    2771 
    2772 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2773 chains... 
    2774 ISOLDE: stopped sim 
    2775 
    2776 > view #1/p:64
    2777 
    2778 > isolde sim start sel
    2779 
    2780 ISOLDE: started sim 
    2781 
    2782 > isolde pepflip sel
    2783 
    2784 Flipping the peptide bond for 1 residues 
    2785 
    2786 > isolde pepflip sel
    2787 
    2788 Flipping the peptide bond for 1 residues 
    2789 
    2790 > isolde pepflip sel
    2791 
    2792 Flipping the peptide bond for 1 residues 
    2793 
    2794 > isolde pepflip sel
    2795 
    2796 Flipping the peptide bond for 1 residues 
    2797 
    2798 > select clear
    2799 
    2800 > isolde sim stop
    2801 
    2802 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2803 chains... 
    2804 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2805 standards. 
    2806 ISOLDE: stopped sim 
    2807 
    2808 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    2809 > mut8-no-C-ter/8-KSRP-no-C-ter-Step1-EightenthSubsteps.cxs
    2810 
    2811 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    2812 
    2813 ——— End of log from Mon Mar 6 10:45:08 2023 ———
    2814 
    2815 opened ChimeraX session 
    2816 
    2817 > isolde start
    2818 
    2819 > set selectionWidth 4
    2820 
    2821 > select clear
    2822 
    2823 > view #1/p:118
    2824 
    2825 > view #1/p:161
    2826 
    2827 > select #1/p:161
    2828 
    2829 11 atoms, 10 bonds, 1 residue, 1 model selected 
    2830 
    2831 > select #1/p:158-161|/p:167-171
    2832 
    2833 150 atoms, 150 bonds, 9 residues, 1 model selected 
    2834 
    2835 > isolde sim start sel
    2836 
    2837 Launching using CUDA failed with the below message. Falling back to using
    2838 OpenCL. 
    2839  
    2840 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    2841 (-arch) 
    2842  
    2843 
    2844 ISOLDE: started sim 
    2845 
    2846 > isolde sim stop discardTo start
    2847 
    2848 reverting to start 
    2849 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2850 chains... 
    2851 ISOLDE: stopped sim 
    2852 
    2853 > select #1/p:158-161|/p:167-171
    2854 
    2855 150 atoms, 150 bonds, 9 residues, 1 model selected 
    2856 
    2857 > isolde sim start sel
    2858 
    2859 ISOLDE: started sim 
    2860 
    2861 > ui tool show "Ramachandran Plot"
    2862 
    2863 > isolde pepflip sel
    2864 
    2865 Flipping the peptide bond for 1 residues 
    2866 
    2867 > isolde pepflip sel
    2868 
    2869 Flipping the peptide bond for 1 residues 
    2870 
    2871 > isolde pepflip sel
    2872 
    2873 Flipping the peptide bond for 1 residues 
    2874 
    2875 > select #1/p:158-161|/p:167-171
    2876 
    2877 150 atoms, 150 bonds, 9 residues, 1 model selected 
    2878 
    2879 > select #1/p:158-171
    2880 
    2881 223 atoms, 225 bonds, 14 residues, 1 model selected 
    2882 
    2883 > ui tool show "Ramachandran Plot"
    2884 
    2885 > select clear
    2886 
    2887 [Repeated 5 time(s)]
    2888 
    2889 > show target m
    2890 
    2891 > isolde sim stop
    2892 
    2893 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2894 chains... 
    2895 ISOLDE: stopped sim 
    2896 
    2897 > isolde start
    2898 
    2899 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    2900 > mut8-no-C-ter/9-KSRP-no-C-ter-Step1-NinthSubsteps.cxs
    2901 
    2902 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    2903 
    2904 ——— End of log from Wed Mar 8 06:50:37 2023 ———
    2905 
    2906 opened ChimeraX session 
    2907 
    2908 > isolde start
    2909 
    2910 > set selectionWidth 4
    2911 
    2912 > isolde sim start sel
    2913 
    2914 Launching using CUDA failed with the below message. Falling back to using
    2915 OpenCL. 
    2916  
    2917 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    2918 (-arch) 
    2919  
    2920 
    2921 ISOLDE: started sim 
    2922 
    2923 > isolde sim stop discardTo start
    2924 
    2925 reverting to start 
    2926 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2927 chains... 
    2928 ISOLDE: stopped sim 
    2929 
    2930 > isolde sim start sel
    2931 
    2932 ISOLDE: started sim 
    2933 
    2934 > ui tool show "Ramachandran Plot"
    2935 
    2936 > isolde sim stop
    2937 
    2938 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2939 chains... 
    2940 ISOLDE: stopped sim 
    2941 
    2942 > isolde sim start sel
    2943 
    2944 ISOLDE: started sim 
    2945 
    2946 > select clear
    2947 
    2948 [Repeated 2 time(s)]
    2949 
    2950 > isolde pepflip sel
    2951 
    2952 Flipping the peptide bond for 1 residues 
    2953 
    2954 > select clear
    2955 
    2956 > isolde pepflip sel
    2957 
    2958 Flipping the peptide bond for 1 residues 
    2959 
    2960 > select clear
    2961 
    2962 [Repeated 1 time(s)]
    2963 
    2964 > isolde pepflip sel
    2965 
    2966 Flipping the peptide bond for 1 residues 
    2967 
    2968 > isolde pepflip sel
    2969 
    2970 Flipping the peptide bond for 1 residues 
    2971 
    2972 > select clear
    2973 
    2974 [Repeated 3 time(s)]
    2975 
    2976 > isolde pepflip sel
    2977 
    2978 Flipping the peptide bond for 1 residues 
    2979 
    2980 > isolde sim stop
    2981 
    2982 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2983 chains... 
    2984 ISOLDE: stopped sim 
    2985 
    2986 > isolde sim start sel
    2987 
    2988 ISOLDE: started sim 
    2989 
    2990 > ui tool show "Ramachandran Plot"
    2991 
    2992 > style #1/r:116|/r:112 sphere
    2993 
    2994 Changed 41 atom styles 
    2995 
    2996 > style #1/r:116|/r:112|/r:113 sphere
    2997 
    2998 Changed 53 atom styles 
    2999 
    3000 > select clear
    3001 
    3002 > style #1/r:116|/r:112|/r:113 stick
    3003 
    3004 Changed 53 atom styles 
    3005 
    3006 > select clear
    3007 
    3008 [Repeated 1 time(s)]
    3009 
    3010 > ui tool show "Ramachandran Plot"
    3011 
    3012 > isolde pepflip sel
    3013 
    3014 Flipping the peptide bond for 1 residues 
    3015 
    3016 > select clear
    3017 
    3018 > isolde pepflip sel
    3019 
    3020 Flipping the peptide bond for 1 residues 
    3021 
    3022 > select clear
    3023 
    3024 > ui tool show "Ramachandran Plot"
    3025 
    3026 [Repeated 1 time(s)]
    3027 
    3028 > isolde pepflip sel
    3029 
    3030 Flipping the peptide bond for 1 residues 
    3031 
    3032 > select clear
    3033 
    3034 > isolde pepflip sel
    3035 
    3036 Flipping the peptide bond for 1 residues 
    3037 
    3038 > select clear
    3039 
    3040 > ui tool show "Ramachandran Plot"
    3041 
    3042 > select clear
    3043 
    3044 > ui tool show "Ramachandran Plot"
    3045 
    3046 [Repeated 1 time(s)]
    3047 
    3048 > select clear
    3049 
    3050 > isolde sim stop
    3051 
    3052 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3053 chains... 
    3054 ISOLDE: stopped sim 
    3055 
    3056 > isolde sim start sel
    3057 
    3058 ISOLDE: started sim 
    3059 
    3060 > isolde sim stop
    3061 
    3062 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3063 chains... 
    3064 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    3065 standards. 
    3066 ISOLDE: stopped sim 
    3067 
    3068 > view #1/r:121
    3069 
    3070 > select #1/r:121
    3071 
    3072 21 atoms, 21 bonds, 1 residue, 1 model selected 
    3073 
    3074 > isolde sim start sel
    3075 
    3076 ISOLDE: started sim 
    3077 
    3078 > select clear
    3079 
    3080 [Repeated 3 time(s)]
    3081 
    3082 > isolde pepflip sel
    3083 
    3084 Flipping the peptide bond for 1 residues 
    3085 
    3086 > isolde pepflip sel
    3087 
    3088 Flipping the peptide bond for 1 residues 
    3089 
    3090 > select clear
    3091 
    3092 Unable to flip peptide bond after 50 rounds. Giving up. 
    3093 
    3094 > isolde pepflip sel
    3095 
    3096 Flipping the peptide bond for 1 residues 
    3097 
    3098 > isolde pepflip sel
    3099 
    3100 Flipping the peptide bond for 1 residues 
    3101 
    3102 > select clear
    3103 
    3104 > isolde pepflip sel
    3105 
    3106 Flipping the peptide bond for 1 residues 
    3107 
    3108 > isolde pepflip sel
    3109 
    3110 Flipping the peptide bond for 1 residues 
    3111 
    3112 > select clear
    3113 
    3114 [Repeated 2 time(s)]
    3115 
    3116 > ui tool show "Ramachandran Plot"
    3117 
    3118 > isolde pepflip sel
    3119 
    3120 Flipping the peptide bond for 1 residues 
    3121 
    3122 > select clear
    3123 
    3124 [Repeated 2 time(s)]
    3125 
    3126 > isolde pepflip sel
    3127 
    3128 Flipping the peptide bond for 1 residues 
    3129 
    3130 > select clear
    3131 
    3132 > isolde pepflip sel
    3133 
    3134 Flipping the peptide bond for 1 residues 
    3135 
    3136 > isolde pepflip sel
    3137 
    3138 Flipping the peptide bond for 1 residues 
    3139 
    3140 > select clear
    3141 
    3142 > ui tool show "Ramachandran Plot"
    3143 
    3144 [Repeated 2 time(s)]
    3145 
    3146 > isolde sim stop
    3147 
    3148 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3149 chains... 
    3150 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    3151 standards. 
    3152 ISOLDE: stopped sim 
    3153 
    3154 > isolde sim start sel
    3155 
    3156 ISOLDE: started sim 
    3157 
    3158 > select clear
    3159 
    3160 > isolde pepflip sel
    3161 
    3162 Flipping the peptide bond for 1 residues 
    3163 
    3164 > select clear
    3165 
    3166 > isolde sim stop
    3167 
    3168 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3169 chains... 
    3170 ISOLDE: stopped sim 
    3171 
    3172 > view #1/r:121
    3173 
    3174 > select #1/r:121
    3175 
    3176 21 atoms, 21 bonds, 1 residue, 1 model selected 
    3177 
    3178 > isolde sim start sel
    3179 
    3180 ISOLDE: started sim 
    3181 
    3182 > ui tool show "Ramachandran Plot"
    3183 
    3184 > isolde sim stop
    3185 
    3186 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3187 chains... 
    3188 ISOLDE: stopped sim 
    3189 
    3190 > isolde sim start sel
    3191 
    3192 ISOLDE: started sim 
    3193 
    3194 > isolde sim stop
    3195 
    3196 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3197 chains... 
    3198 ISOLDE: stopped sim 
    3199 
    3200 > isolde pepflip sel
    3201 
    3202 Flipping the peptide bond for 1 residues 
    3203 ISOLDE: started sim 
    3204 
    3205 > isolde pepflip sel
    3206 
    3207 Flipping the peptide bond for 1 residues 
    3208 
    3209 > isolde pepflip sel
    3210 
    3211 Flipping the peptide bond for 1 residues 
    3212 
    3213 > isolde pepflip sel
    3214 
    3215 Flipping the peptide bond for 1 residues 
    3216 
    3217 > isolde pepflip sel
    3218 
    3219 Flipping the peptide bond for 1 residues 
    3220 
    3221 > isolde pepflip sel
    3222 
    3223 Flipping the peptide bond for 1 residues 
    3224 
    3225 > isolde pepflip sel
    3226 
    3227 Flipping the peptide bond for 1 residues 
    3228 
    3229 > select clear
    3230 
    3231 > ui tool show "Ramachandran Plot"
    3232 
    3233 > select #1/O:9
    3234 
    3235 20 atoms, 20 bonds, 1 residue, 1 model selected 
    3236 
    3237 > ui tool show "Ramachandran Plot"
    3238 
    3239 > select clear
    3240 
    3241 [Repeated 2 time(s)]
    3242 
    3243 > isolde pepflip sel
    3244 
    3245 Flipping the peptide bond for 1 residues 
    3246 
    3247 > select clear
    3248 
    3249 > isolde pepflip sel
    3250 
    3251 Flipping the peptide bond for 1 residues 
    3252 
    3253 > isolde pepflip sel
    3254 
    3255 Flipping the peptide bond for 1 residues 
    3256 
    3257 > select clear
    3258 
    3259 [Repeated 3 time(s)]
    3260 
    3261 > isolde pepflip sel
    3262 
    3263 Flipping the peptide bond for 1 residues 
    3264 
    3265 > select clear
    3266 
    3267 > ui tool show "Ramachandran Plot"
    3268 
    3269 [Repeated 1 time(s)]
    3270 
    3271 > select clear
    3272 
    3273 [Repeated 1 time(s)]
    3274 
    3275 > isolde pepflip sel
    3276 
    3277 Flipping the peptide bond for 1 residues 
    3278 
    3279 > select clear
    3280 
    3281 > ui tool show "Ramachandran Plot"
    3282 
    3283 > isolde pepflip sel
    3284 
    3285 Flipping the peptide bond for 1 residues 
    3286 
    3287 > isolde pepflip sel
    3288 
    3289 Flipping the peptide bond for 1 residues 
    3290 
    3291 > isolde pepflip sel
    3292 
    3293 Flipping the peptide bond for 1 residues 
    3294 
    3295 > isolde pepflip sel
    3296 
    3297 Flipping the peptide bond for 1 residues 
    3298 
    3299 > select clear
    3300 
    3301 > isolde pepflip sel
    3302 
    3303 Flipping the peptide bond for 1 residues 
    3304 
    3305 > isolde pepflip sel
    3306 
    3307 Flipping the peptide bond for 1 residues 
    3308 
    3309 > select clear
    3310 
    3311 > isolde pepflip sel
    3312 
    3313 Flipping the peptide bond for 1 residues 
    3314 
    3315 > isolde pepflip sel
    3316 
    3317 Flipping the peptide bond for 1 residues 
    3318 
    3319 > select clear
    3320 
    3321 [Repeated 1 time(s)]
    3322 
    3323 > isolde pepflip sel
    3324 
    3325 Flipping the peptide bond for 1 residues 
    3326 
    3327 > isolde pepflip sel
    3328 
    3329 Flipping the peptide bond for 1 residues 
    3330 
    3331 > isolde pepflip sel
    3332 
    3333 Flipping the peptide bond for 1 residues 
    3334 
    3335 > isolde pepflip sel
    3336 
    3337 Flipping the peptide bond for 1 residues 
    3338 
    3339 > isolde pepflip sel
    3340 
    3341 Flipping the peptide bond for 1 residues 
    3342 
    3343 > isolde pepflip sel
    3344 
    3345 Flipping the peptide bond for 1 residues 
    3346 
    3347 > isolde pepflip sel
    3348 
    3349 Flipping the peptide bond for 1 residues 
    3350 
    3351 > isolde sim stop
    3352 
    3353 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3354 chains... 
    3355 ISOLDE: stopped sim 
    3356 
    3357 > select #1
    3358 
    3359 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    3360 
    3361 > select #1>O8-13
    3362 
    3363 Expected an objects specifier or a keyword 
    3364 
    3365 > select #1/O:8-13
    3366 
    3367 110 atoms, 112 bonds, 6 residues, 1 model selected 
    3368 
    3369 > select #1/O:10-11
    3370 
    3371 36 atoms, 35 bonds, 2 residues, 1 model selected 
    3372 
    3373 > isolde sim start sel
    3374 
    3375 ISOLDE: started sim 
    3376 
    3377 > isolde pepflip sel
    3378 
    3379 Flipping the peptide bond for 1 residues 
    3380 
    3381 > isolde pepflip sel
    3382 
    3383 Flipping the peptide bond for 1 residues 
    3384 
    3385 > isolde pepflip sel
    3386 
    3387 Flipping the peptide bond for 1 residues 
    3388 
    3389 > isolde pepflip sel
    3390 
    3391 Flipping the peptide bond for 1 residues 
    3392 
    3393 > select clear
    3394 
    3395 > isolde pepflip sel
    3396 
    3397 Flipping the peptide bond for 1 residues 
    3398 
    3399 > isolde pepflip sel
    3400 
    3401 Flipping the peptide bond for 1 residues 
    3402 
    3403 > isolde sim stop
    3404 
    3405 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3406 chains... 
    3407 ISOLDE: stopped sim 
    3408 
    3409 > select #1
    3410 
    3411 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    3412 
    3413 > select #1/r:58-64|/O:1-15
    3414 
    3415 358 atoms, 361 bonds, 22 residues, 1 model selected 
    3416 
    3417 > isolde sim start sel
    3418 
    3419 ISOLDE: started sim 
    3420 
    3421 > select clear
    3422 
    3423 > isolde pepflip sel
    3424 
    3425 Flipping the peptide bond for 1 residues 
    3426 
    3427 > isolde pepflip sel
    3428 
    3429 Flipping the peptide bond for 1 residues 
    3430 
    3431 > isolde pepflip sel
    3432 
    3433 Flipping the peptide bond for 1 residues 
    3434 
    3435 > isolde pepflip sel
    3436 
    3437 Flipping the peptide bond for 1 residues 
    3438 
    3439 > isolde pepflip sel
    3440 
    3441 Flipping the peptide bond for 1 residues 
    3442 
    3443 > isolde pepflip sel
    3444 
    3445 Flipping the peptide bond for 1 residues 
    3446 
    3447 > select clear
    3448 
    3449 > isolde pepflip sel
    3450 
    3451 Flipping the peptide bond for 1 residues 
    3452 
    3453 > isolde pepflip sel
    3454 
    3455 Flipping the peptide bond for 1 residues 
    3456 
    3457 > select clear
    3458 
    3459 Unable to flip peptide bond after 50 rounds. Giving up. 
    3460 
    3461 > ui tool show "Ramachandran Plot"
    3462 
    3463 > select clear
    3464 
    3465 > isolde pepflip sel
    3466 
    3467 Flipping the peptide bond for 1 residues 
    3468 
    3469 > select clear
    3470 
    3471 [Repeated 1 time(s)]
    3472 
    3473 > ui tool show "Ramachandran Plot"
    3474 
    3475 > view sel
    3476 
    3477 > isolde sim stop
    3478 
    3479 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3480 chains... 
    3481 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    3482 standards. 
    3483 ISOLDE: stopped sim 
    3484 
    3485 > isolde sim start sel
    3486 
    3487 ISOLDE: started sim 
    3488 
    3489 > select clear
    3490 
    3491 > isolde pepflip sel
    3492 
    3493 Flipping the peptide bond for 1 residues 
    3494 
    3495 > isolde pepflip sel
    3496 
    3497 Flipping the peptide bond for 1 residues 
    3498 
    3499 > isolde pepflip sel
    3500 
    3501 Flipping the peptide bond for 1 residues 
    3502 
    3503 > isolde pepflip sel
    3504 
    3505 Flipping the peptide bond for 1 residues 
    3506 
    3507 > select clear
    3508 
    3509 > isolde pepflip sel
    3510 
    3511 Flipping the peptide bond for 1 residues 
    3512 
    3513 > isolde pepflip sel
    3514 
    3515 Flipping the peptide bond for 1 residues 
    3516 
    3517 > isolde pepflip sel
    3518 
    3519 Flipping the peptide bond for 1 residues 
    3520 
    3521 > isolde sim stop
    3522 
    3523 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3524 chains... 
    3525 ISOLDE: stopped sim 
    3526 
    3527 > isolde sim start sel
    3528 
    3529 ISOLDE: started sim 
    3530 
    3531 > select clear
    3532 
    3533 > isolde pepflip sel
    3534 
    3535 Flipping the peptide bond for 1 residues 
    3536 
    3537 > isolde pepflip sel
    3538 
    3539 Flipping the peptide bond for 1 residues 
    3540 
    3541 > select clear
    3542 
    3543 > select #1/r:58-64|/O:1-15
    3544 
    3545 358 atoms, 361 bonds, 22 residues, 1 model selected 
    3546 
    3547 > select #1/r:42
    3548 
    3549 16 atoms, 15 bonds, 1 residue, 1 model selected 
    3550 
    3551 > ui tool show "Ramachandran Plot"
    3552 
    3553 > isolde sim stop
    3554 
    3555 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3556 chains... 
    3557 ISOLDE: stopped sim 
    3558 
    3559 > view #1/r:42
    3560 
    3561 > select #1/r:42
    3562 
    3563 16 atoms, 15 bonds, 1 residue, 1 model selected 
    3564 
    3565 > isolde sim start sel
    3566 
    3567 ISOLDE: started sim 
    3568 
    3569 > ui tool show "Ramachandran Plot"
    3570 
    3571 > isolde sim stop
    3572 
    3573 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3574 chains... 
    3575 ISOLDE: stopped sim 
    3576 
    3577 > view #1/r:58-64|/O:1-15
    3578 
    3579 > select #1/r:58-64|/O:1-15
    3580 
    3581 358 atoms, 361 bonds, 22 residues, 1 model selected 
    3582 
    3583 > isolde sim start sel
    3584 
    3585 ISOLDE: started sim 
    3586 
    3587 > ui tool show "Ramachandran Plot"
    3588 
    3589 > select clear
    3590 
    3591 > isolde sim stop
    3592 
    3593 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3594 chains... 
    3595 ISOLDE: stopped sim 
    3596 
    3597 > view #1/O:10
    3598 
    3599 > select#1/O:10
    3600 
    3601 Unknown command: select#1/O:10 
    3602 
    3603 > select #1/O:10
    3604 
    3605 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3606 
    3607 > select #1/O:10
    3608 
    3609 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3610 
    3611 > isolde sim start sel
    3612 
    3613 ISOLDE: started sim 
    3614 
    3615 > ui tool show "Ramachandran Plot"
    3616 
    3617 > select clear
    3618 
    3619 > isolde sim stop
    3620 
    3621 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3622 chains... 
    3623 ISOLDE: stopped sim 
    3624 
    3625 > select #1/O:10
    3626 
    3627 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3628 
    3629 > isolde sim start sel
    3630 
    3631 ISOLDE: started sim 
    3632 
    3633 > isolde sim stop
    3634 
    3635 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3636 chains... 
    3637 ISOLDE: stopped sim 
    3638 
    3639 > isolde sim start sel
    3640 
    3641 ISOLDE: started sim 
    3642 
    3643 > select clear
    3644 
    3645 > ui tool show "Ramachandran Plot"
    3646 
    3647 [Repeated 1 time(s)]
    3648 
    3649 > select clear
    3650 
    3651 [Repeated 6 time(s)]
    3652 
    3653 > ui tool show "Ramachandran Plot"
    3654 
    3655 > isolde sim stop
    3656 
    3657 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3658 chains... 
    3659 ISOLDE: stopped sim 
    3660 
    3661 > isolde sim start sel
    3662 
    3663 ISOLDE: started sim 
    3664 
    3665 > isolde pepflip sel
    3666 
    3667 Flipping the peptide bond for 1 residues 
    3668 
    3669 > select clear
    3670 
    3671 > isolde pepflip sel
    3672 
    3673 Flipping the peptide bond for 1 residues 
    3674 
    3675 > isolde pepflip sel
    3676 
    3677 Flipping the peptide bond for 1 residues 
    3678 
    3679 > select clear
    3680 
    3681 [Repeated 1 time(s)]
    3682 
    3683 > ui tool show "Ramachandran Plot"
    3684 
    3685 [Repeated 1 time(s)]
    3686 
    3687 > select clear
    3688 
    3689 [Repeated 1 time(s)]
    3690 
    3691 > isolde pepflip sel
    3692 
    3693 Flipping the peptide bond for 1 residues 
    3694 
    3695 > isolde pepflip sel
    3696 
    3697 Flipping the peptide bond for 1 residues 
    3698 
    3699 > select clear
    3700 
    3701 > isolde sim pause
    3702 
    3703 > select #1
    3704 
    3705 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    3706 
    3707 > select #1/u:8-9
    3708 
    3709 34 atoms, 33 bonds, 2 residues, 1 model selected 
    3710 
    3711 > isolde sim resume
    3712 
    3713 > isolde pepflip sel
    3714 
    3715 Flipping the peptide bond for 1 residues 
    3716 
    3717 > select clear
    3718 
    3719 > select #1
    3720 
    3721 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    3722 
    3723 > isolde sim stop
    3724 
    3725 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3726 chains... 
    3727 ISOLDE: stopped sim 
    3728 
    3729 > select #1/u:60-65|/u:8-12
    3730 
    3731 180 atoms, 180 bonds, 11 residues, 1 model selected 
    3732 
    3733 > isolde sim start sel
    3734 
    3735 ISOLDE: started sim 
    3736 
    3737 > isolde pepflip sel
    3738 
    3739 Flipping the peptide bond for 1 residues 
    3740 
    3741 > isolde pepflip sel
    3742 
    3743 Flipping the peptide bond for 1 residues 
    3744 
    3745 > isolde pepflip sel
    3746 
    3747 Flipping the peptide bond for 1 residues 
    3748 
    3749 > isolde pepflip sel
    3750 
    3751 Flipping the peptide bond for 1 residues 
    3752 
    3753 > isolde pepflip sel
    3754 
    3755 Flipping the peptide bond for 1 residues 
    3756 
    3757 > select clear
    3758 
    3759 [Repeated 1 time(s)]
    3760 
    3761 > isolde pepflip sel
    3762 
    3763 Flipping the peptide bond for 1 residues 
    3764 
    3765 > isolde pepflip sel
    3766 
    3767 Flipping the peptide bond for 1 residues 
    3768 Unable to flip peptide bond after 50 rounds. Giving up. 
    3769 
    3770 > isolde pepflip sel
    3771 
    3772 Flipping the peptide bond for 1 residues 
    3773 
    3774 > isolde pepflip sel
    3775 
    3776 Flipping the peptide bond for 1 residues 
    3777 
    3778 > select clear
    3779 
    3780 [Repeated 1 time(s)]
    3781 
    3782 > isolde sim stop
    3783 
    3784 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3785 chains... 
    3786 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    3787 standards. 
    3788 ISOLDE: stopped sim 
    3789 
    3790 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    3791 > mut8-no-C-ter/10-KSRP-no-C-ter-Step1-tenthSubsteps.cxs
    3792 
    3793 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    3794 
    3795 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    3796 > mut8-no-C-ter/10-KSRP-no-C-ter-Step1-tenthSubsteps.pdb
    3797 
    3798 > select #1/u:47-54
    3799 
    3800 123 atoms, 122 bonds, 8 residues, 1 model selected 
    3801 
    3802 > select clear
    3803 
    3804 > select #1/u:57-67
    3805 
    3806 162 atoms, 161 bonds, 11 residues, 1 model selected 
    3807 
    3808 > isolde sim start sel
    3809 
    3810 ISOLDE: started sim 
    3811 
    3812 > select #1/u:57-67
    3813 
    3814 162 atoms, 161 bonds, 11 residues, 1 model selected 
    3815 
    3816 > hide #!1.2 models
    3817 
    3818 > show #!1.2 models
    3819 
    3820 > hide #!1.2 models
    3821 
    3822 > show #!1.2 models
    3823 
    3824 > hide #!1.2 models
    3825 
    3826 > show #!1.2 models
    3827 
    3828 > isolde sim stop
    3829 
    3830 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3831 chains... 
    3832 ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB
    3833 standards. 
    3834 ISOLDE: stopped sim 
    3835 
    3836 > select #1/u:57-67
    3837 
    3838 162 atoms, 161 bonds, 11 residues, 1 model selected 
    3839 
    3840 > select #1/u:57-71
    3841 
    3842 223 atoms, 222 bonds, 15 residues, 1 model selected 
    3843 
    3844 > isolde sim start sel
    3845 
    3846 ISOLDE: started sim 
    3847 
    3848 > isolde pepflip sel
    3849 
    3850 Flipping the peptide bond for 1 residues 
    3851 
    3852 > isolde pepflip sel
    3853 
    3854 Flipping the peptide bond for 1 residues 
    3855 
    3856 > isolde pepflip sel
    3857 
    3858 Flipping the peptide bond for 1 residues 
    3859 
    3860 > isolde pepflip sel
    3861 
    3862 Flipping the peptide bond for 1 residues 
    3863 
    3864 > isolde pepflip sel
    3865 
    3866 Flipping the peptide bond for 1 residues 
    3867 
    3868 > isolde pepflip sel
    3869 
    3870 Flipping the peptide bond for 1 residues 
    3871 
    3872 > isolde pepflip sel
    3873 
    3874 Flipping the peptide bond for 1 residues 
    3875 
    3876 > isolde pepflip sel
    3877 
    3878 Flipping the peptide bond for 1 residues 
    3879 
    3880 > isolde pepflip sel
    3881 
    3882 Flipping the peptide bond for 1 residues 
    3883 
    3884 > isolde pepflip sel
    3885 
    3886 Flipping the peptide bond for 1 residues 
    3887 
    3888 > isolde sim start sel
    3889 
    3890 Simulation already running! 
    3891 
    3892 > isolde sim stop
    3893 
    3894 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3895 chains... 
    3896 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    3897 standards. 
    3898 ISOLDE: stopped sim 
    3899 
    3900 > isolde sim start sel
    3901 
    3902 ISOLDE: started sim 
    3903 
    3904 > isolde sim stop discardTo start
    3905 
    3906 reverting to start 
    3907 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3908 chains... 
    3909 ISOLDE: stopped sim 
    3910 
    3911 > isolde sim start sel
    3912 
    3913 ISOLDE: started sim 
    3914 
    3915 > isolde pepflip sel
    3916 
    3917 Flipping the peptide bond for 1 residues 
    3918 
    3919 > isolde pepflip sel
    3920 
    3921 Flipping the peptide bond for 1 residues 
    3922 
    3923 > isolde sim pause
    3924 
    3925 > isolde sim resume
    3926 
    3927 > isolde pepflip sel
    3928 
    3929 Flipping the peptide bond for 1 residues 
    3930 
    3931 > select clear
    3932 
    3933 [Repeated 2 time(s)]
    3934 
    3935 > isolde pepflip sel
    3936 
    3937 Flipping the peptide bond for 1 residues 
    3938 
    3939 > isolde sim stop
    3940 
    3941 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3942 chains... 
    3943 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    3944 standards. 
    3945 ISOLDE: stopped sim 
    3946 
    3947 > isolde sim start sel
    3948 
    3949 ISOLDE: started sim 
    3950 
    3951 > select clear
    3952 
    3953 [Repeated 5 time(s)]
    3954 
    3955 > isolde sim stop
    3956 
    3957 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3958 chains... 
    3959 ISOLDE: stopped sim 
    3960 
    3961 > select clear
    3962 
    3963 [Repeated 1 time(s)]
    3964 
    3965 > isolde sim start sel
    3966 
    3967 ISOLDE: started sim 
    3968 
    3969 > isolde sim stop
    3970 
    3971 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3972 chains... 
    3973 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    3974 standards. 
    3975 ISOLDE: stopped sim 
    3976 
    3977 > isolde sim start sel
    3978 
    3979 ISOLDE: started sim 
    3980 
    3981 > isolde pepflip sel
    3982 
    3983 Flipping the peptide bond for 1 residues 
    3984 
    3985 > isolde pepflip sel
    3986 
    3987 Flipping the peptide bond for 1 residues 
    3988 Unable to flip peptide bond after 50 rounds. Giving up. 
    3989 
    3990 > select clear
    3991 
    3992 [Repeated 2 time(s)]
    3993 
    3994 > isolde pepflip sel
    3995 
    3996 Flipping the peptide bond for 1 residues 
    3997 Peptide bond must be mobile in the simulation! 
    3998 
    3999 > select clear
    4000 
    4001 > isolde pepflip sel
    4002 
    4003 Flipping the peptide bond for 1 residues 
    4004 
    4005 > isolde pepflip sel
    4006 
    4007 Flipping the peptide bond for 1 residues 
    4008 
    4009 > select clear
    4010 
    4011 [Repeated 1 time(s)]
    4012 
    4013 > isolde pepflip sel
    4014 
    4015 Flipping the peptide bond for 1 residues 
    4016 
    4017 > isolde pepflip sel
    4018 
    4019 Flipping the peptide bond for 1 residues 
    4020 
    4021 > select clear
    4022 
    4023 [Repeated 1 time(s)]
    4024 
    4025 > isolde pepflip sel
    4026 
    4027 Flipping the peptide bond for 1 residues 
    4028 
    4029 > isolde pepflip sel
    4030 
    4031 Flipping the peptide bond for 1 residues 
    4032 
    4033 > isolde pepflip sel
    4034 
    4035 Flipping the peptide bond for 1 residues 
    4036 
    4037 > isolde pepflip sel
    4038 
    4039 Flipping the peptide bond for 1 residues 
    4040 
    4041 > select clear
    4042 
    4043 [Repeated 2 time(s)]
    4044 
    4045 > isolde pepflip sel
    4046 
    4047 Flipping the peptide bond for 1 residues 
    4048 
    4049 > isolde pepflip sel
    4050 
    4051 Flipping the peptide bond for 1 residues 
    4052 
    4053 > isolde pepflip sel
    4054 
    4055 Flipping the peptide bond for 1 residues 
    4056 
    4057 > select clear
    4058 
    4059 > ui tool show "Ramachandran Plot"
    4060 
    4061 > select clear
    4062 
    4063 > isolde pepflip sel
    4064 
    4065 Flipping the peptide bond for 1 residues 
    4066 
    4067 > ui tool show "Ramachandran Plot"
    4068 
    4069 > isolde pepflip sel
    4070 
    4071 Flipping the peptide bond for 1 residues 
    4072 
    4073 > select clear
    4074 
    4075 > isolde sim start sel
    4076 
    4077 No atoms selected! 
    4078 
    4079 > ui tool show "Ramachandran Plot"
    4080 
    4081 > isolde pepflip sel
    4082 
    4083 Flipping the peptide bond for 1 residues 
    4084 
    4085 > ui tool show "Ramachandran Plot"
    4086 
    4087 Traceback (most recent call last): 
    4088 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4089 packages/matplotlib/cbook/__init__.py", line 287, in process 
    4090 func(*args, **kwargs) 
    4091 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    4092 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    4093 on_resize 
    4094 c.draw() 
    4095 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4096 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    4097 self.figure.draw(self.renderer) 
    4098 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4099 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    4100 result = draw(artist, renderer, *args, **kwargs) 
    4101 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4102 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    4103 return draw(artist, renderer) 
    4104 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4105 packages/matplotlib/figure.py", line 2796, in draw 
    4106 artists = self._get_draw_artists(renderer) 
    4107 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4108 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    4109 ax.apply_aspect() 
    4110 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4111 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    4112 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    4113 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4114 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    4115 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    4116 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    4117 
    4118 > select clear
    4119 
    4120 [Repeated 1 time(s)]
    4121 
    4122 > isolde pepflip sel
    4123 
    4124 Flipping the peptide bond for 1 residues 
    4125 
    4126 > isolde pepflip sel
    4127 
    4128 Flipping the peptide bond for 1 residues 
    4129 
    4130 > select clear
    4131 
    4132 [Repeated 1 time(s)]
    4133 
    4134 > isolde pepflip sel
    4135 
    4136 Flipping the peptide bond for 1 residues 
    4137 
    4138 > isolde pepflip sel
    4139 
    4140 Flipping the peptide bond for 1 residues 
    4141 
    4142 > select clear
    4143 
    4144 [Repeated 3 time(s)]
    4145 
    4146 > isolde pepflip sel
    4147 
    4148 Flipping the peptide bond for 1 residues 
    4149 
    4150 > isolde pepflip sel
    4151 
    4152 Flipping the peptide bond for 1 residues 
    4153 
    4154 > isolde pepflip sel
    4155 
    4156 Flipping the peptide bond for 1 residues 
    4157 
    4158 > isolde pepflip sel
    4159 
    4160 Flipping the peptide bond for 1 residues 
    4161 
    4162 > isolde pepflip sel
    4163 
    4164 Flipping the peptide bond for 1 residues 
    4165 
    4166 > select clear
    4167 
    4168 [Repeated 2 time(s)]
    4169 
    4170 > select #1/u:57-71
    4171 
    4172 223 atoms, 222 bonds, 15 residues, 1 model selected 
    4173 
    4174 > select #1/u:57-71
    4175 
    4176 223 atoms, 222 bonds, 15 residues, 1 model selected 
    4177 
    4178 > select #1/u:57-67
    4179 
    4180 162 atoms, 161 bonds, 11 residues, 1 model selected 
    4181 
    4182 > select clear
    4183 
    4184 > select #1/u:25
    4185 
    4186 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4187 
    4188 > view #1/u:25
    4189 
    4190 > select clear
    4191 
    4192 [Repeated 1 time(s)]
    4193 
    4194 > ui tool show "Ramachandran Plot"
    4195 
    4196 > isolde sim stop
    4197 
    4198 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4199 chains... 
    4200 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    4201 standards. 
    4202 ISOLDE: stopped sim 
    4203 
    4204 > isolde sim start sel
    4205 
    4206 ISOLDE: started sim 
    4207 
    4208 > isolde pepflip sel
    4209 
    4210 Flipping the peptide bond for 1 residues 
    4211 
    4212 > isolde pepflip sel
    4213 
    4214 Flipping the peptide bond for 1 residues 
    4215 
    4216 > select clear
    4217 
    4218 [Repeated 4 time(s)]
    4219 
    4220 > isolde pepflip sel
    4221 
    4222 Flipping the peptide bond for 1 residues 
    4223 
    4224 > isolde pepflip sel
    4225 
    4226 Flipping the peptide bond for 1 residues 
    4227 
    4228 > select clear
    4229 
    4230 [Repeated 1 time(s)]
    4231 
    4232 > select #1/u:57-67
    4233 
    4234 162 atoms, 161 bonds, 11 residues, 1 model selected 
    4235 
    4236 > select #1/u:28-42
    4237 
    4238 245 atoms, 247 bonds, 15 residues, 1 model selected 
    4239 
    4240 > isolde sim stop
    4241 
    4242 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4243 chains... 
    4244 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4245 standards. 
    4246 ISOLDE: stopped sim 
    4247 
    4248 > style #1 ribbon
    4249 
    4250 Expected a keyword 
    4251 
    4252 > select #1/u:57-67
    4253 
    4254 162 atoms, 161 bonds, 11 residues, 1 model selected 
    4255 
    4256 > select #1/u:28-42
    4257 
    4258 245 atoms, 247 bonds, 15 residues, 1 model selected 
    4259 
    4260 > isolde sim start sel
    4261 
    4262 ISOLDE: started sim 
    4263 
    4264 > select #1/u:28-42
    4265 
    4266 245 atoms, 247 bonds, 15 residues, 1 model selected 
    4267 
    4268 > select #1/o:53-56
    4269 
    4270 68 atoms, 67 bonds, 4 residues, 1 model selected 
    4271 
    4272 > isolde sim stop
    4273 
    4274 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4275 chains... 
    4276 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    4277 standards. 
    4278 ISOLDE: stopped sim 
    4279 
    4280 > select #1/u:28-42|/o:53-56|/u:43-47
    4281 
    4282 400 atoms, 402 bonds, 24 residues, 1 model selected 
    4283 
    4284 > select #1/u:28-42|/o:53-56|/u:43-47
    4285 
    4286 400 atoms, 402 bonds, 24 residues, 1 model selected 
    4287 
    4288 > isolde sim start sel
    4289 
    4290 ISOLDE: started sim 
    4291 
    4292 > select clear
    4293 
    4294 > isolde pepflip sel
    4295 
    4296 Flipping the peptide bond for 1 residues 
    4297 
    4298 > isolde pepflip sel
    4299 
    4300 Flipping the peptide bond for 1 residues 
    4301 
    4302 > isolde pepflip sel
    4303 
    4304 Flipping the peptide bond for 1 residues 
    4305 
    4306 > select clear
    4307 
    4308 > isolde pepflip sel
    4309 
    4310 Flipping the peptide bond for 1 residues 
    4311 
    4312 > select clear
    4313 
    4314 > isolde pepflip sel
    4315 
    4316 Flipping the peptide bond for 1 residues 
    4317 
    4318 > isolde pepflip sel
    4319 
    4320 Flipping the peptide bond for 1 residues 
    4321 
    4322 > select clear
    4323 
    4324 Unable to flip peptide bond after 50 rounds. Giving up. 
    4325 
    4326 > select clear
    4327 
    4328 > isolde pepflip sel
    4329 
    4330 Flipping the peptide bond for 1 residues 
    4331 
    4332 > isolde pepflip sel
    4333 
    4334 Flipping the peptide bond for 1 residues 
    4335 
    4336 > select clear
    4337 
    4338 Unable to flip peptide bond after 50 rounds. Giving up. 
    4339 
    4340 > isolde pepflip sel
    4341 
    4342 Flipping the peptide bond for 1 residues 
    4343 
    4344 > select clear
    4345 
    4346 > hide #!1.2 models
    4347 
    4348 > show #!1.2 models
    4349 
    4350 > hide #!1.2 models
    4351 
    4352 > show #!1.2 models
    4353 
    4354 > hide #!1.2 models
    4355 
    4356 > show #!1.2 models
    4357 
    4358 > isolde pepflip sel
    4359 
    4360 Flipping the peptide bond for 1 residues 
    4361 
    4362 > isolde pepflip sel
    4363 
    4364 Flipping the peptide bond for 1 residues 
    4365 
    4366 > isolde sim stop discardTo start
    4367 
    4368 [Repeated 1 time(s)]reverting to start 
    4369 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4370 chains... 
    4371 ISOLDE: stopped sim 
    4372 
    4373 > select #1
    4374 
    4375 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    4376 
    4377 > select clear
    4378 
    4379 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    4380 > mut8-no-C-ter/11-KSRP-no-C-ter-Step1-EleventhSubsteps.cxs
    4381 
    4382 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    4383 
    4384 ——— End of log from Thu Mar 9 08:50:34 2023 ———
    4385 
    4386 opened ChimeraX session 
    4387 
    4388 > select #1/u:28-42|/o:53-56|/u:43-47
    4389 
    4390 400 atoms, 402 bonds, 24 residues, 1 model selected 
    4391 
    4392 > isolde sim start sel
    4393 
    4394 Launching using CUDA failed with the below message. Falling back to using
    4395 OpenCL. 
    4396  
    4397 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    4398 (-arch) 
    4399  
    4400 
    4401 ISOLDE: started sim 
    4402 ISOLDE: created disulfide bonds between the following residues: 
    4403 T78-T81 
    4404 
    4405 > isolde sim stop discardTo start
    4406 
    4407 reverting to start 
    4408 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4409 chains... 
    4410 ISOLDE: stopped sim 
    4411 
    4412 > select #1/u:28-42|/o:53-56|/u:43-47
    4413 
    4414 400 atoms, 402 bonds, 24 residues, 1 model selected 
    4415 
    4416 > isolde sim start sel
    4417 
    4418 ISOLDE: started sim 
    4419 
    4420 > select #1/u:36-50
    4421 
    4422 229 atoms, 230 bonds, 15 residues, 1 model selected 
    4423 
    4424 > isolde sim stop
    4425 
    4426 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4427 chains... 
    4428 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    4429 standards. 
    4430 ISOLDE: stopped sim 
    4431 
    4432 > select #1/u:12
    4433 
    4434 17 atoms, 17 bonds, 1 residue, 1 model selected 
    4435 
    4436 > view #1/u:12
    4437 
    4438 > select #1/u:12
    4439 
    4440 17 atoms, 17 bonds, 1 residue, 1 model selected 
    4441 
    4442 > isolde sim start sel
    4443 
    4444 ISOLDE: started sim 
    4445 
    4446 > isolde sim stop
    4447 
    4448 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4449 chains... 
    4450 ISOLDE: stopped sim 
    4451 
    4452 > isolde sim start sel
    4453 
    4454 ISOLDE: started sim 
    4455 
    4456 > isolde pepflip sel
    4457 
    4458 Flipping the peptide bond for 1 residues 
    4459 
    4460 > isolde pepflip sel
    4461 
    4462 Flipping the peptide bond for 1 residues 
    4463 
    4464 > select clear
    4465 
    4466 > ui tool show "Ramachandran Plot"
    4467 
    4468 > isolde sim stop
    4469 
    4470 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4471 chains... 
    4472 ISOLDE: stopped sim 
    4473 
    4474 > isolde sim start sel
    4475 
    4476 ISOLDE: started sim 
    4477 
    4478 > isolde pepflip sel
    4479 
    4480 Flipping the peptide bond for 1 residues 
    4481 
    4482 > select clear
    4483 
    4484 > isolde pepflip sel
    4485 
    4486 Flipping the peptide bond for 1 residues 
    4487 
    4488 > isolde pepflip sel
    4489 
    4490 Flipping the peptide bond for 1 residues 
    4491 
    4492 > select clear
    4493 
    4494 > isolde pepflip sel
    4495 
    4496 Flipping the peptide bond for 1 residues 
    4497 
    4498 > isolde pepflip sel
    4499 
    4500 Flipping the peptide bond for 1 residues 
    4501 
    4502 > isolde pepflip sel
    4503 
    4504 Flipping the peptide bond for 1 residues 
    4505 
    4506 > select clear
    4507 
    4508 > isolde pepflip sel
    4509 
    4510 Flipping the peptide bond for 1 residues 
    4511 
    4512 > select clear
    4513 
    4514 > ui tool show "Ramachandran Plot"
    4515 
    4516 [Repeated 1 time(s)]
    4517 
    4518 > isolde sim stop
    4519 
    4520 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4521 chains... 
    4522 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4523 standards. 
    4524 ISOLDE: stopped sim 
    4525 
    4526 > select #1/o:55
    4527 
    4528 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4529 
    4530 > isolde sim start sel
    4531 
    4532 ISOLDE: started sim 
    4533 
    4534 > select clear
    4535 
    4536 [Repeated 5 time(s)]
    4537 
    4538 > isolde pepflip sel
    4539 
    4540 Flipping the peptide bond for 1 residues 
    4541 
    4542 > isolde pepflip sel
    4543 
    4544 Flipping the peptide bond for 1 residues 
    4545 
    4546 > isolde pepflip sel
    4547 
    4548 Flipping the peptide bond for 1 residues 
    4549 
    4550 > isolde pepflip sel
    4551 
    4552 Flipping the peptide bond for 1 residues 
    4553 
    4554 > isolde pepflip sel
    4555 
    4556 Flipping the peptide bond for 1 residues 
    4557 
    4558 > isolde pepflip sel
    4559 
    4560 Flipping the peptide bond for 1 residues 
    4561 
    4562 > select clear
    4563 
    4564 [Repeated 3 time(s)]
    4565 
    4566 > isolde pepflip sel
    4567 
    4568 Flipping the peptide bond for 1 residues 
    4569 
    4570 > isolde pepflip sel
    4571 
    4572 Flipping the peptide bond for 1 residues 
    4573 
    4574 > isolde pepflip sel
    4575 
    4576 Flipping the peptide bond for 1 residues 
    4577 
    4578 > select clear
    4579 
    4580 > isolde pepflip sel
    4581 
    4582 Flipping the peptide bond for 1 residues 
    4583 
    4584 > isolde pepflip sel
    4585 
    4586 Flipping the peptide bond for 1 residues 
    4587 
    4588 > select clear
    4589 
    4590 > isolde pepflip sel
    4591 
    4592 Flipping the peptide bond for 1 residues 
    4593 
    4594 > select clear
    4595 
    4596 > ui tool show "Ramachandran Plot"
    4597 
    4598 [Repeated 1 time(s)]
    4599 
    4600 > isolde pepflip sel
    4601 
    4602 Flipping the peptide bond for 1 residues 
    4603 
    4604 > isolde pepflip sel
    4605 
    4606 Flipping the peptide bond for 1 residues 
    4607 
    4608 > select clear
    4609 
    4610 > view #1/o:55
    4611 
    4612 > isolde pepflip sel
    4613 
    4614 Flipping the peptide bond for 1 residues 
    4615 
    4616 > isolde pepflip sel
    4617 
    4618 Flipping the peptide bond for 1 residues 
    4619 
    4620 > select clear
    4621 
    4622 > isolde pepflip sel
    4623 
    4624 Flipping the peptide bond for 1 residues 
    4625 
    4626 > isolde pepflip sel
    4627 
    4628 Flipping the peptide bond for 1 residues 
    4629 
    4630 > select clear
    4631 
    4632 > isolde pepflip sel
    4633 
    4634 Flipping the peptide bond for 1 residues 
    4635 
    4636 > isolde pepflip sel
    4637 
    4638 Flipping the peptide bond for 1 residues 
    4639 
    4640 > isolde pepflip sel
    4641 
    4642 Flipping the peptide bond for 1 residues 
    4643 
    4644 > isolde pepflip sel
    4645 
    4646 Flipping the peptide bond for 1 residues 
    4647 
    4648 > isolde pepflip sel
    4649 
    4650 Flipping the peptide bond for 1 residues 
    4651 
    4652 > isolde pepflip sel
    4653 
    4654 Flipping the peptide bond for 1 residues 
    4655 
    4656 > isolde sim stop
    4657 
    4658 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4659 chains... 
    4660 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4661 standards. 
    4662 ISOLDE: stopped sim 
    4663 
    4664 > select #1/o:55|/o:37
    4665 
    4666 39 atoms, 37 bonds, 2 residues, 1 model selected 
    4667 
    4668 > select #1/o:55|/o:37
    4669 
    4670 39 atoms, 37 bonds, 2 residues, 1 model selected 
    4671 
    4672 > select #1/o:37
    4673 
    4674 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4675 
    4676 > select #1/u:37A/o:55
    4677 
    4678 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4679 
    4680 > select #1/u:37/o:55
    4681 
    4682 38 atoms, 36 bonds, 2 residues, 1 model selected 
    4683 
    4684 > isolde sim start sel
    4685 
    4686 ISOLDE: started sim 
    4687 
    4688 > select clear
    4689 
    4690 > isolde pepflip sel
    4691 
    4692 Flipping the peptide bond for 1 residues 
    4693 
    4694 > select clear
    4695 
    4696 [Repeated 2 time(s)]
    4697 
    4698 > isolde pepflip sel
    4699 
    4700 Flipping the peptide bond for 1 residues 
    4701 
    4702 > isolde pepflip sel
    4703 
    4704 Flipping the peptide bond for 1 residues 
    4705 
    4706 > isolde pepflip sel
    4707 
    4708 Flipping the peptide bond for 1 residues 
    4709 
    4710 > select clear
    4711 
    4712 [Repeated 3 time(s)]
    4713 
    4714 > isolde pepflip sel
    4715 
    4716 Flipping the peptide bond for 1 residues 
    4717 
    4718 > select clear
    4719 
    4720 [Repeated 1 time(s)]
    4721 
    4722 > isolde pepflip sel
    4723 
    4724 Flipping the peptide bond for 1 residues 
    4725 
    4726 > isolde pepflip sel
    4727 
    4728 Flipping the peptide bond for 1 residues 
    4729 
    4730 > isolde pepflip sel
    4731 
    4732 Flipping the peptide bond for 1 residues 
    4733 
    4734 > select clear
    4735 
    4736 [Repeated 1 time(s)]
    4737 
    4738 > isolde pepflip sel
    4739 
    4740 Flipping the peptide bond for 1 residues 
    4741 
    4742 > isolde pepflip sel
    4743 
    4744 Flipping the peptide bond for 1 residues 
    4745 
    4746 > isolde cisflip sel
    4747 
    4748 Performing cis<\-->trans flip for 1 residues 
    4749 
    4750 > isolde cisflip sel
    4751 
    4752 Performing cis<\-->trans flip for 1 residues 
    4753 
    4754 > isolde cisflip sel
    4755 
    4756 Performing cis<\-->trans flip for 1 residues 
    4757 
    4758 > isolde pepflip sel
    4759 
    4760 Flipping the peptide bond for 1 residues 
    4761 
    4762 > isolde pepflip sel
    4763 
    4764 Flipping the peptide bond for 1 residues 
    4765 
    4766 > isolde pepflip sel
    4767 
    4768 Flipping the peptide bond for 1 residues 
    4769 
    4770 > isolde pepflip sel
    4771 
    4772 Flipping the peptide bond for 1 residues 
    4773 
    4774 > isolde pepflip sel
    4775 
    4776 Flipping the peptide bond for 1 residues 
    4777 
    4778 > isolde pepflip sel
    4779 
    4780 Flipping the peptide bond for 1 residues 
    4781 
    4782 > isolde pepflip sel
    4783 
    4784 Flipping the peptide bond for 1 residues 
    4785 
    4786 > isolde pepflip sel
    4787 
    4788 Flipping the peptide bond for 1 residues 
    4789 
    4790 > select clear
    4791 
    4792 > isolde pepflip sel
    4793 
    4794 Flipping the peptide bond for 1 residues 
    4795 
    4796 > isolde pepflip sel
    4797 
    4798 Flipping the peptide bond for 1 residues 
    4799 Unable to flip peptide bond after 50 rounds. Giving up. 
    4800 
    4801 > isolde sim pause
    4802 
    4803 > select #1
    4804 
    4805 144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    4806 
    4807 > select clear
    4808 
    4809 [Repeated 2 time(s)]
    4810 
    4811 > isolde sim resume
    4812 
    4813 > select clear
    4814 
    4815 > isolde pepflip sel
    4816 
    4817 Flipping the peptide bond for 1 residues 
    4818 
    4819 > select clear
    4820 
    4821 > isolde pepflip sel
    4822 
    4823 Flipping the peptide bond for 1 residues 
    4824 
    4825 > select clear
    4826 
    4827 > isolde pepflip sel
    4828 
    4829 Flipping the peptide bond for 1 residues 
    4830 
    4831 > isolde pepflip sel
    4832 
    4833 Flipping the peptide bond for 1 residues 
    4834 
    4835 > isolde pepflip sel
    4836 
    4837 Flipping the peptide bond for 1 residues 
    4838 
    4839 > isolde pepflip sel
    4840 
    4841 Flipping the peptide bond for 1 residues 
    4842 
    4843 > isolde pepflip sel
    4844 
    4845 Flipping the peptide bond for 1 residues 
    4846 
    4847 > isolde pepflip sel
    4848 
    4849 Flipping the peptide bond for 1 residues 
    4850 
    4851 > isolde sim pause
    4852 
    4853 > isolde sim resume
    4854 
    4855 > isolde pepflip sel
    4856 
    4857 Flipping the peptide bond for 1 residues 
    4858 
    4859 > select clear
    4860 
    4861 [Repeated 1 time(s)]
    4862 
    4863 > isolde pepflip sel
    4864 
    4865 Flipping the peptide bond for 1 residues 
    4866 
    4867 > isolde pepflip sel
    4868 
    4869 Flipping the peptide bond for 1 residues 
    4870 
    4871 > isolde sim pause
    4872 
    4873 > select #1
    4874 
    4875 144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    4876 
    4877 > isolde sim resume
    4878 
    4879 > select clear
    4880 
    4881 > isolde pepflip sel
    4882 
    4883 Flipping the peptide bond for 1 residues 
    4884 
    4885 > isolde pepflip sel
    4886 
    4887 Flipping the peptide bond for 1 residues 
    4888 
    4889 > select clear
    4890 
    4891 [Repeated 3 time(s)]
    4892 
    4893 > isolde pepflip sel
    4894 
    4895 Flipping the peptide bond for 1 residues 
    4896 
    4897 > isolde pepflip sel
    4898 
    4899 Flipping the peptide bond for 1 residues 
    4900 
    4901 > select clear
    4902 
    4903 Unable to flip peptide bond after 50 rounds. Giving up. 
    4904 
    4905 > isolde pepflip sel
    4906 
    4907 Flipping the peptide bond for 1 residues 
    4908 
    4909 > select clear
    4910 
    4911 > isolde pepflip sel
    4912 
    4913 Flipping the peptide bond for 1 residues 
    4914 
    4915 > isolde pepflip sel
    4916 
    4917 Flipping the peptide bond for 1 residues 
    4918 
    4919 > isolde pepflip sel
    4920 
    4921 Flipping the peptide bond for 1 residues 
    4922 
    4923 > select clear
    4924 
    4925 [Repeated 1 time(s)]
    4926 
    4927 > ui tool show "Ramachandran Plot"
    4928 
    4929 > isolde pepflip sel
    4930 
    4931 Flipping the peptide bond for 1 residues 
    4932 
    4933 > isolde pepflip sel
    4934 
    4935 Flipping the peptide bond for 1 residues 
    4936 
    4937 > select clear
    4938 
    4939 > isolde pepflip sel
    4940 
    4941 Flipping the peptide bond for 1 residues 
    4942 
    4943 > select clear
    4944 
    4945 > isolde pepflip sel
    4946 
    4947 Flipping the peptide bond for 1 residues 
    4948 
    4949 > isolde pepflip sel
    4950 
    4951 Flipping the peptide bond for 1 residues 
    4952 
    4953 > select clear
    4954 
    4955 > isolde pepflip sel
    4956 
    4957 Flipping the peptide bond for 1 residues 
    4958 
    4959 > select clear
    4960 
    4961 > ui tool show "Ramachandran Plot"
    4962 
    4963 > isolde pepflip sel
    4964 
    4965 Flipping the peptide bond for 1 residues 
    4966 
    4967 > select clear
    4968 
    4969 > isolde pepflip sel
    4970 
    4971 Flipping the peptide bond for 1 residues 
    4972 
    4973 > isolde pepflip sel
    4974 
    4975 Flipping the peptide bond for 1 residues 
    4976 
    4977 > select clear
    4978 
    4979 [Repeated 4 time(s)]
    4980 
    4981 > ui tool show "Ramachandran Plot"
    4982 
    4983 > isolde pepflip sel
    4984 
    4985 Flipping the peptide bond for 1 residues 
    4986 
    4987 > select clear
    4988 
    4989 > isolde pepflip sel
    4990 
    4991 Flipping the peptide bond for 1 residues 
    4992 
    4993 > ui tool show "Ramachandran Plot"
    4994 
    4995 > isolde pepflip sel
    4996 
    4997 Flipping the peptide bond for 1 residues 
    4998 
    4999 > isolde pepflip sel
    5000 
    5001 Flipping the peptide bond for 1 residues 
    5002 
    5003 > isolde pepflip sel
    5004 
    5005 Flipping the peptide bond for 1 residues 
    5006 
    5007 > ui tool show "Ramachandran Plot"
    5008 
    5009 > isolde pepflip sel
    5010 
    5011 Flipping the peptide bond for 1 residues 
    5012 
    5013 > isolde pepflip sel
    5014 
    5015 Flipping the peptide bond for 1 residues 
    5016 
    5017 > select clear
    5018 
    5019 [Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up. 
    5020 
    5021 > ui tool show "Ramachandran Plot"
    5022 
    5023 Traceback (most recent call last): 
    5024 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5025 packages/matplotlib/cbook/__init__.py", line 287, in process 
    5026 func(*args, **kwargs) 
    5027 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    5028 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    5029 on_resize 
    5030 c.draw() 
    5031 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5032 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    5033 self.figure.draw(self.renderer) 
    5034 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5035 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    5036 result = draw(artist, renderer, *args, **kwargs) 
    5037 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5038 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    5039 return draw(artist, renderer) 
    5040 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5041 packages/matplotlib/figure.py", line 2796, in draw 
    5042 artists = self._get_draw_artists(renderer) 
    5043 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5044 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    5045 ax.apply_aspect() 
    5046 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5047 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    5048 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    5049 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5050 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    5051 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    5052 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    5053 
    5054 > isolde pepflip sel
    5055 
    5056 Flipping the peptide bond for 1 residues 
    5057 
    5058 > isolde pepflip sel
    5059 
    5060 Flipping the peptide bond for 1 residues 
    5061 
    5062 > isolde pepflip sel
    5063 
    5064 Flipping the peptide bond for 1 residues 
    5065 
    5066 > select clear
    5067 
    5068 > ui tool show "Ramachandran Plot"
    5069 
    5070 > isolde pepflip sel
    5071 
    5072 Flipping the peptide bond for 1 residues 
    5073 
    5074 > select clear
    5075 
    5076 [Repeated 1 time(s)]
    5077 
    5078 > ui tool show "Ramachandran Plot"
    5079 
    5080 > view #1/u:37
    5081 
    5082 > ui tool show "Ramachandran Plot"
    5083 
    5084 > isolde pepflip sel
    5085 
    5086 Flipping the peptide bond for 1 residues 
    5087 
    5088 > select clear
    5089 
    5090 > ui tool show "Ramachandran Plot"
    5091 
    5092 > isolde pepflip sel
    5093 
    5094 Flipping the peptide bond for 1 residues 
    5095 
    5096 > isolde pepflip sel
    5097 
    5098 Flipping the peptide bond for 1 residues 
    5099 
    5100 > ui tool show "Ramachandran Plot"
    5101 
    5102 > select clear
    5103 
    5104 > ui tool show "Ramachandran Plot"
    5105 
    5106 [Repeated 1 time(s)]
    5107 
    5108 > isolde pepflip sel
    5109 
    5110 Flipping the peptide bond for 1 residues 
    5111 
    5112 > select clear
    5113 
    5114 > ui tool show "Ramachandran Plot"
    5115 
    5116 > ui tool show ISOLDE
    5117 
    5118 > ui tool show "Ramachandran Plot"
    5119 
    5120 > isolde pepflip sel
    5121 
    5122 Flipping the peptide bond for 1 residues 
    5123 
    5124 > isolde pepflip sel
    5125 
    5126 Flipping the peptide bond for 1 residues 
    5127 
    5128 > select clear
    5129 
    5130 > ui tool show "Ramachandran Plot"
    5131 
    5132 [Repeated 2 time(s)]
    5133 
    5134 > isolde pepflip sel
    5135 
    5136 Flipping the peptide bond for 1 residues 
    5137 
    5138 > ui tool show "Ramachandran Plot"
    5139 
    5140 > select clear
    5141 
    5142 > ui tool show "Ramachandran Plot"
    5143 
    5144 > isolde pepflip sel
    5145 
    5146 Flipping the peptide bond for 1 residues 
    5147 
    5148 > select clear
    5149 
    5150 > isolde pepflip sel
    5151 
    5152 Flipping the peptide bond for 1 residues 
    5153 
    5154 > isolde pepflip sel
    5155 
    5156 Flipping the peptide bond for 1 residues 
    5157 
    5158 > ui tool show "Ramachandran Plot"
    5159 
    5160 > isolde pepflip sel
    5161 
    5162 Flipping the peptide bond for 1 residues 
    5163 
    5164 > isolde pepflip sel
    5165 
    5166 Flipping the peptide bond for 1 residues 
    5167 
    5168 > select clear
    5169 
    5170 [Repeated 1 time(s)]
    5171 
    5172 > isolde pepflip sel
    5173 
    5174 Flipping the peptide bond for 1 residues 
    5175 
    5176 > isolde pepflip sel
    5177 
    5178 Flipping the peptide bond for 1 residues 
    5179 
    5180 > select clear
    5181 
    5182 > isolde pepflip sel
    5183 
    5184 Flipping the peptide bond for 1 residues 
    5185 
    5186 > isolde pepflip sel
    5187 
    5188 Flipping the peptide bond for 1 residues 
    5189 
    5190 > ui tool show "Ramachandran Plot"
    5191 
    5192 > isolde pepflip sel
    5193 
    5194 Flipping the peptide bond for 1 residues 
    5195 
    5196 > select clear
    5197 
    5198 [Repeated 1 time(s)]
    5199 
    5200 > ui tool show "Ramachandran Plot"
    5201 
    5202 [Repeated 1 time(s)]
    5203 
    5204 > select clear
    5205 
    5206 [Repeated 3 time(s)]
    5207 
    5208 > ui tool show "Ramachandran Plot"
    5209 
    5210 [Repeated 2 time(s)]
    5211 
    5212 > isolde pepflip sel
    5213 
    5214 Flipping the peptide bond for 1 residues 
    5215 
    5216 > isolde pepflip sel
    5217 
    5218 Flipping the peptide bond for 1 residues 
    5219 
    5220 > isolde pepflip sel
    5221 
    5222 Flipping the peptide bond for 1 residues 
    5223 
    5224 > isolde pepflip sel
    5225 
    5226 Flipping the peptide bond for 1 residues 
    5227 
    5228 > select clear
    5229 
    5230 Unable to flip peptide bond after 50 rounds. Giving up. 
    5231 
    5232 > ui tool show "Ramachandran Plot"
    5233 
    5234 > select clear
    5235 
    5236 > ui tool show "Ramachandran Plot"
    5237 
    5238 > isolde pepflip sel
    5239 
    5240 Flipping the peptide bond for 1 residues 
    5241 
    5242 > isolde pepflip sel
    5243 
    5244 Flipping the peptide bond for 1 residues 
    5245 
    5246 > select clear
    5247 
    5248 [Repeated 1 time(s)]
    5249 
    5250 > ui tool show "Ramachandran Plot"
    5251 
    5252 > hide #!1.2 models
    5253 
    5254 > show #!1.2 models
    5255 
    5256 > ui tool show "Ramachandran Plot"
    5257 
    5258 > select clear
    5259 
    5260 [Repeated 3 time(s)]
    5261 
    5262 > ui tool show "Ramachandran Plot"
    5263 
    5264 > isolde pepflip sel
    5265 
    5266 Flipping the peptide bond for 1 residues 
    5267 
    5268 > isolde pepflip sel
    5269 
    5270 Flipping the peptide bond for 1 residues 
    5271 
    5272 > isolde pepflip sel
    5273 
    5274 Flipping the peptide bond for 1 residues 
    5275 
    5276 > isolde pepflip sel
    5277 
    5278 Flipping the peptide bond for 1 residues 
    5279 
    5280 > isolde pepflip sel
    5281 
    5282 Flipping the peptide bond for 1 residues 
    5283 
    5284 > isolde pepflip sel
    5285 
    5286 Flipping the peptide bond for 1 residues 
    5287 
    5288 > isolde pepflip sel
    5289 
    5290 Flipping the peptide bond for 1 residues 
    5291 
    5292 > isolde pepflip sel
    5293 
    5294 Flipping the peptide bond for 1 residues 
    5295 
    5296 > select clear
    5297 
    5298 > isolde pepflip sel
    5299 
    5300 Flipping the peptide bond for 1 residues 
    5301 
    5302 > isolde pepflip sel
    5303 
    5304 Flipping the peptide bond for 1 residues 
    5305 
    5306 > isolde pepflip sel
    5307 
    5308 Flipping the peptide bond for 1 residues 
    5309 
    5310 > ui tool show "Ramachandran Plot"
    5311 
    5312 > select clear
    5313 
    5314 > isolde pepflip sel
    5315 
    5316 Flipping the peptide bond for 1 residues 
    5317 
    5318 > isolde pepflip sel
    5319 
    5320 Flipping the peptide bond for 1 residues 
    5321 
    5322 > select clear
    5323 
    5324 [Repeated 1 time(s)]
    5325 
    5326 > isolde pepflip sel
    5327 
    5328 Flipping the peptide bond for 1 residues 
    5329 
    5330 > isolde pepflip sel
    5331 
    5332 Flipping the peptide bond for 1 residues 
    5333 
    5334 > select clear
    5335 
    5336 > isolde pepflip sel
    5337 
    5338 Flipping the peptide bond for 1 residues 
    5339 
    5340 > isolde pepflip sel
    5341 
    5342 Flipping the peptide bond for 1 residues 
    5343 
    5344 > isolde pepflip sel
    5345 
    5346 Flipping the peptide bond for 1 residues 
    5347 
    5348 > isolde pepflip sel
    5349 
    5350 Flipping the peptide bond for 1 residues 
    5351 
    5352 > select clear
    5353 
    5354 > isolde pepflip sel
    5355 
    5356 Flipping the peptide bond for 1 residues 
    5357 
    5358 > select clear
    5359 
    5360 > ui tool show "Ramachandran Plot"
    5361 
    5362 > isolde pepflip sel
    5363 
    5364 Flipping the peptide bond for 1 residues 
    5365 
    5366 > select clear
    5367 
    5368 [Repeated 1 time(s)]
    5369 
    5370 > isolde pepflip sel
    5371 
    5372 Flipping the peptide bond for 1 residues 
    5373 
    5374 > isolde pepflip sel
    5375 
    5376 Flipping the peptide bond for 1 residues 
    5377 
    5378 > isolde pepflip sel
    5379 
    5380 Flipping the peptide bond for 1 residues 
    5381 
    5382 > isolde pepflip sel
    5383 
    5384 Flipping the peptide bond for 1 residues 
    5385 
    5386 > isolde pepflip sel
    5387 
    5388 Flipping the peptide bond for 1 residues 
    5389 
    5390 > select clear
    5391 
    5392 > ui tool show "Ramachandran Plot"
    5393 
    5394 > isolde pepflip sel
    5395 
    5396 Flipping the peptide bond for 1 residues 
    5397 
    5398 > select clear
    5399 
    5400 > ui tool show "Ramachandran Plot"
    5401 
    5402 > isolde pepflip sel
    5403 
    5404 Flipping the peptide bond for 1 residues 
    5405 Unable to flip peptide bond after 50 rounds. Giving up. 
    5406 
    5407 > select clear
    5408 
    5409 > isolde pepflip sel
    5410 
    5411 Flipping the peptide bond for 1 residues 
    5412 
    5413 > isolde pepflip sel
    5414 
    5415 Flipping the peptide bond for 1 residues 
    5416 
    5417 > ui tool show "Ramachandran Plot"
    5418 
    5419 > isolde sim pause
    5420 
    5421 > ui tool show "Ramachandran Plot"
    5422 
    5423 > isolde sim resume
    5424 
    5425 > ui tool show "Ramachandran Plot"
    5426 
    5427 > isolde sim pause
    5428 
    5429 > isolde sim stop
    5430 
    5431 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5432 chains... 
    5433 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    5434 standards. 
    5435 ISOLDE: stopped sim 
    5436 
    5437 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    5438 > mut8-no-C-ter/12-KSRP-no-C-ter-Step1-twelventhSubsteps-
    5439 > simulatedAnnealingIn-u37-o55-region.csx.cxs
    5440 
    5441 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    5442 
    5443 ——— End of log from Fri Mar 17 17:24:40 2023 ———
    5444 
    5445 opened ChimeraX session 
    5446 
    5447 > isolde start
    5448 
    5449 > set selectionWidth 4
    5450 
    5451 > select clear
    5452 
    5453 > view #1/o:55
    5454 
    5455 > select #1/o:55
    5456 
    5457 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5458 
    5459 > isolde sim start sel
    5460 
    5461 Launching using CUDA failed with the below message. Falling back to using
    5462 OpenCL. 
    5463  
    5464 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    5465 (-arch) 
    5466  
    5467 
    5468 ISOLDE: started sim 
    5469 
    5470 > isolde sim stop discardTo start
    5471 
    5472 reverting to start 
    5473 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5474 chains... 
    5475 ISOLDE: stopped sim 
    5476 
    5477 > select #1/o:55
    5478 
    5479 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5480 
    5481 > isolde sim start sel
    5482 
    5483 ISOLDE: started sim 
    5484 
    5485 > ui tool show "Ramachandran Plot"
    5486 
    5487 > select clear
    5488 
    5489 > isolde sim stop
    5490 
    5491 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5492 chains... 
    5493 ISOLDE: stopped sim 
    5494 
    5495 > view #1/u:49
    5496 
    5497 > select #1/u:49
    5498 
    5499 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5500 
    5501 > isolde sim start sel
    5502 
    5503 ISOLDE: started sim 
    5504 
    5505 > isolde sim stop discardTo start
    5506 
    5507 reverting to start 
    5508 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5509 chains... 
    5510 ISOLDE: stopped sim 
    5511 
    5512 > select #1/u:49
    5513 
    5514 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5515 
    5516 > isolde sim start sel
    5517 
    5518 ISOLDE: started sim 
    5519 
    5520 > ui tool show "Ramachandran Plot"
    5521 
    5522 > select clear
    5523 
    5524 > isolde pepflip sel
    5525 
    5526 Flipping the peptide bond for 1 residues 
    5527 
    5528 > select clear
    5529 
    5530 > ui tool show "Ramachandran Plot"
    5531 
    5532 > isolde sim pause
    5533 
    5534 > isolde sim resume
    5535 
    5536 > isolde sim pause
    5537 
    5538 3 models selected 
    5539 [Repeated 1 time(s)]
    5540 
    5541 > view #1
    5542 
    5543 > view #1/u:49
    5544 
    5545 > view #1/P
    5546 
    5547 > ui tool show "Ramachandran Plot"
    5548 
    5549 > view #1/u:49
    5550 
    5551 > isolde sim resume
    5552 
    5553 > ui tool show "Ramachandran Plot"
    5554 
    5555 [Repeated 2 time(s)]
    5556 
    5557 > isolde sim stop
    5558 
    5559 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5560 chains... 
    5561 ISOLDE: stopped sim 
    5562 
    5563 > view #1/u:63
    5564 
    5565 > select #1/u:63
    5566 
    5567 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5568 
    5569 > isolde sim start sel
    5570 
    5571 ISOLDE: started sim 
    5572 
    5573 > ui tool show "Ramachandran Plot"
    5574 
    5575 > isolde pepflip sel
    5576 
    5577 Flipping the peptide bond for 1 residues 
    5578 
    5579 > isolde pepflip sel
    5580 
    5581 Flipping the peptide bond for 1 residues 
    5582 
    5583 > isolde pepflip sel
    5584 
    5585 Flipping the peptide bond for 1 residues 
    5586 
    5587 > ui tool show "Ramachandran Plot"
    5588 
    5589 [Repeated 1 time(s)]
    5590 
    5591 > select clear
    5592 
    5593 [Repeated 1 time(s)]
    5594 
    5595 > isolde pepflip sel
    5596 
    5597 Flipping the peptide bond for 1 residues 
    5598 
    5599 > isolde pepflip sel
    5600 
    5601 Flipping the peptide bond for 1 residues 
    5602 
    5603 > isolde pepflip sel
    5604 
    5605 Flipping the peptide bond for 1 residues 
    5606 
    5607 > ui tool show "Ramachandran Plot"
    5608 
    5609 > select clear
    5610 
    5611 > ui tool show "Ramachandran Plot"
    5612 
    5613 > select clear
    5614 
    5615 > isolde sim stop
    5616 
    5617 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5618 chains... 
    5619 ISOLDE: stopped sim 
    5620 
    5621 > view #1/u:49
    5622 
    5623 > select #1/u:49
    5624 
    5625 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5626 
    5627 > isolde sim start sel
    5628 
    5629 ISOLDE: started sim 
    5630 
    5631 > ui tool show "Ramachandran Plot"
    5632 
    5633 > isolde sim stop
    5634 
    5635 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5636 chains... 
    5637 ISOLDE: stopped sim 
    5638 
    5639 > view #1/u:43
    5640 
    5641 > select #1/u:43
    5642 
    5643 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5644 
    5645 > isolde sim start sel
    5646 
    5647 ISOLDE: started sim 
    5648 
    5649 > ui tool show "Ramachandran Plot"
    5650 
    5651 > select clear
    5652 
    5653 > isolde pepflip sel
    5654 
    5655 Flipping the peptide bond for 1 residues 
    5656 
    5657 > select clear
    5658 
    5659 > ui tool show "Ramachandran Plot"
    5660 
    5661 > view #1/u:43
    5662 
    5663 > ui tool show "Ramachandran Plot"
    5664 
    5665 > select clear
    5666 
    5667 > ui tool show "Ramachandran Plot"
    5668 
    5669 > select clear
    5670 
    5671 [Repeated 1 time(s)]
    5672 
    5673 > isolde pepflip sel
    5674 
    5675 Flipping the peptide bond for 1 residues 
    5676 
    5677 > select clear
    5678 
    5679 > isolde pepflip sel
    5680 
    5681 Flipping the peptide bond for 1 residues 
    5682 
    5683 > select clear
    5684 
    5685 [Repeated 1 time(s)]
    5686 
    5687 > isolde pepflip sel
    5688 
    5689 Flipping the peptide bond for 1 residues 
    5690 
    5691 > select clear
    5692 
    5693 [Repeated 1 time(s)]
    5694 
    5695 > hide #!1.1 models
    5696 
    5697 > show #!1.1 models
    5698 
    5699 > hide #!1.2 models
    5700 
    5701 > show #!1.2 models
    5702 
    5703 > hide #!1.2 models
    5704 
    5705 > show #!1.2 models
    5706 
    5707 > hide #!1.2 models
    5708 
    5709 > show #!1.2 models
    5710 
    5711 > hide #!1.2 models
    5712 
    5713 > show #!1.2 models
    5714 
    5715 > ui tool show "Ramachandran Plot"
    5716 
    5717 > select clear
    5718 
    5719 > view #1/u:43
    5720 
    5721 > isolde sim stop
    5722 
    5723 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5724 chains... 
    5725 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5726 standards. 
    5727 ISOLDE: stopped sim 
    5728 
    5729 > isolde sim start sel
    5730 
    5731 ISOLDE: started sim 
    5732 
    5733 > select clear
    5734 
    5735 [Repeated 1 time(s)]
    5736 
    5737 > isolde sim stop
    5738 
    5739 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5740 chains... 
    5741 ISOLDE: stopped sim 
    5742 
    5743 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    5744 > mut8-no-C-ter/13-KSRP-no-C-ter-Step1-thirtenthSubsteps.pdb
    5745 
    5746 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    5747 > mut8-no-C-ter/13-KSRP-no-C-ter-Step1-thirtenthSubsteps.cxs
    5748 
    5749 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    5750 
    5751 > view #1/u:42|u:55
    5752 
    5753 Expected an objects specifier or a view name or a keyword 
    5754 
    5755 > view #1/u:42|/u:55
    5756 
    5757 > select #1/u:42|/u:55
    5758 
    5759 34 atoms, 32 bonds, 2 residues, 1 model selected 
    5760 
    5761 > isolde sim start sel
    5762 
    5763 ISOLDE: started sim 
    5764 
    5765 > isolde sim stop discardTo start
    5766 
    5767 reverting to start 
    5768 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5769 chains... 
    5770 ISOLDE: stopped sim 
    5771 
    5772 > select #1/u:42|/u:55
    5773 
    5774 34 atoms, 32 bonds, 2 residues, 1 model selected 
    5775 
    5776 > isolde sim start sel
    5777 
    5778 ISOLDE: started sim 
    5779 
    5780 > ui tool show "Ramachandran Plot"
    5781 
    5782 > select clear
    5783 
    5784 [Repeated 2 time(s)]
    5785 
    5786 > isolde pepflip sel
    5787 
    5788 Flipping the peptide bond for 1 residues 
    5789 
    5790 > isolde pepflip sel
    5791 
    5792 Flipping the peptide bond for 1 residues 
    5793 
    5794 > select clear
    5795 
    5796 > ui tool show "Ramachandran Plot"
    5797 
    5798 Unable to flip peptide bond after 50 rounds. Giving up. 
    5799 
    5800 > ui tool show "Ramachandran Plot"
    5801 
    5802 > isolde sim stop
    5803 
    5804 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5805 chains... 
    5806 ISOLDE: stopped sim 
    5807 
    5808 > view #1/u:43
    5809 
    5810 > select #1/u:43
    5811 
    5812 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5813 
    5814 > isolde sim start sel
    5815 
    5816 ISOLDE: started sim 
    5817 
    5818 > ui tool show "Ramachandran Plot"
    5819 
    5820 > select clear
    5821 
    5822 > isolde sim stop
    5823 
    5824 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5825 chains... 
    5826 ISOLDE: stopped sim 
    5827 
    5828 > view #1/u:63
    5829 
    5830 > select #1/u:63
    5831 
    5832 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5833 
    5834 > select #1/u:63
    5835 
    5836 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5837 
    5838 > isolde sim start sel
    5839 
    5840 ISOLDE: started sim 
    5841 
    5842 > ui tool show "Ramachandran Plot"
    5843 
    5844 > isolde sim stop
    5845 
    5846 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5847 chains... 
    5848 ISOLDE: stopped sim 
    5849 
    5850 > ui tool show "Ramachandran Plot"
    5851 
    5852 > select #1/u:49
    5853 
    5854 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5855 
    5856 > view #1/u:49
    5857 
    5858 > select #1/u:49
    5859 
    5860 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5861 
    5862 > isolde sim start sel
    5863 
    5864 ISOLDE: started sim 
    5865 
    5866 > ui tool show "Ramachandran Plot"
    5867 
    5868 [Repeated 1 time(s)]
    5869 
    5870 > isolde sim stop
    5871 
    5872 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5873 chains... 
    5874 ISOLDE: stopped sim 
    5875 
    5876 > view #1/o:55
    5877 
    5878 > select #1/o:55
    5879 
    5880 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5881 
    5882 > isolde sim start sel
    5883 
    5884 ISOLDE: started sim 
    5885 
    5886 > ui tool show "Ramachandran Plot"
    5887 
    5888 > isolde sim stop
    5889 
    5890 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5891 chains... 
    5892 ISOLDE: stopped sim 
    5893 
    5894 > view #1/u:12
    5895 
    5896 > select #1/u:12
    5897 
    5898 17 atoms, 17 bonds, 1 residue, 1 model selected 
    5899 
    5900 > isolde sim start sel
    5901 
    5902 ISOLDE: started sim 
    5903 
    5904 > ui tool show "Ramachandran Plot"
    5905 
    5906 > select clear
    5907 
    5908 > isolde sim stop
    5909 
    5910 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5911 chains... 
    5912 ISOLDE: stopped sim 
    5913 
    5914 > view #1/u:28-42|/o:53-56|/u:43-47
    5915 
    5916 > select #1/u:28-42|/o:53-56|/u:43-47
    5917 
    5918 400 atoms, 402 bonds, 24 residues, 1 model selected 
    5919 
    5920 > isolde sim start sel
    5921 
    5922 ISOLDE: started sim 
    5923 
    5924 > ui tool show "Ramachandran Plot"
    5925 
    5926 > isolde sim pause
    5927 
    5928 > ui tool show "Ramachandran Plot"
    5929 
    5930 [Repeated 2 time(s)]
    5931 
    5932 > isolde sim resume
    5933 
    5934 > isolde sim stop
    5935 
    5936 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5937 chains... 
    5938 ISOLDE: stopped sim 
    5939 
    5940 > select #1/u:35
    5941 
    5942 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5943 
    5944 > view #1/u:35
    5945 
    5946 > select #1/u:35
    5947 
    5948 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5949 
    5950 > select #1/u:35
    5951 
    5952 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5953 
    5954 > isolde sim start sel
    5955 
    5956 ISOLDE: started sim 
    5957 
    5958 > ui tool show "Ramachandran Plot"
    5959 
    5960 > isolde sim stop
    5961 
    5962 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5963 chains... 
    5964 ISOLDE: stopped sim 
    5965 
    5966 > view #1/u:25
    5967 
    5968 > select #1/u:25
    5969 
    5970 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5971 
    5972 > isolde sim start sel
    5973 
    5974 ISOLDE: started sim 
    5975 
    5976 > ui tool show "Ramachandran Plot"
    5977 
    5978 > select clear
    5979 
    5980 > isolde sim stop
    5981 
    5982 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5983 chains... 
    5984 ISOLDE: stopped sim 
    5985 
    5986 > view #1/u:60-65|/u:8-12
    5987 
    5988 > select #1/u:60-65|/u:8-12
    5989 
    5990 180 atoms, 180 bonds, 11 residues, 1 model selected 
    5991 
    5992 > isolde sim start sel
    5993 
    5994 ISOLDE: started sim 
    5995 
    5996 > ui tool show "Ramachandran Plot"
    5997 
    5998 > isolde sim stop
    5999 
    6000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6001 chains... 
    6002 ISOLDE: stopped sim 
    6003 
    6004 > view #1/u:12
    6005 
    6006 > select sim start sel
    6007 
    6008 Expected an objects specifier or a keyword 
    6009 
    6010 > view #1/u:12
    6011 
    6012 > select #1/u:12
    6013 
    6014 17 atoms, 17 bonds, 1 residue, 1 model selected 
    6015 
    6016 > isolde sim start sel
    6017 
    6018 ISOLDE: started sim 
    6019 
    6020 > ui tool show "Ramachandran Plot"
    6021 
    6022 > isolde sim stop
    6023 
    6024 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6025 chains... 
    6026 ISOLDE: stopped sim 
    6027 
    6028 > isolde sim start sel
    6029 
    6030 ISOLDE: started sim 
    6031 
    6032 > ui tool show "Ramachandran Plot"
    6033 
    6034 [Repeated 1 time(s)]
    6035 
    6036 > select clear
    6037 
    6038 > isolde sim stop
    6039 
    6040 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6041 chains... 
    6042 ISOLDE: stopped sim 
    6043 
    6044 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6045 > mut8-no-C-ter/4-KSRP-no-C-ter-Step1-FourtenthSubsteps-End1d1db.cxs
    6046 
    6047 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6048 
    6049 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6050 > mut8-no-C-ter/14-KSRP-no-C-ter-Step1-FourtenthSubsteps-End1d1db.pdb
    6051 
    6052 > isolde cisflip #1.2/Q:137
    6053 
    6054 Performing cis<\-->trans flip for 1 residues 
    6055 ISOLDE: started sim 
    6056 
    6057 > isolde sim stop discardTo start
    6058 
    6059 reverting to start 
    6060 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6061 chains... 
    6062 ISOLDE: stopped sim 
    6063 
    6064 > isolde sim start sel
    6065 
    6066 ISOLDE: started sim 
    6067 
    6068 > isolde sim stop discardTo start
    6069 
    6070 reverting to start 
    6071 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6072 chains... 
    6073 ISOLDE: stopped sim 
    6074 
    6075 > isolde sim start sel
    6076 
    6077 ISOLDE: started sim 
    6078 
    6079 > isolde cisflip sel
    6080 
    6081 Performing cis<\-->trans flip for 1 residues 
    6082 
    6083 > isolde cisflip #1.2/Q:137
    6084 
    6085 Performing cis<\-->trans flip for 1 residues 
    6086 
    6087 > isolde pepflip sel
    6088 
    6089 Flipping the peptide bond for 1 residues 
    6090 
    6091 > select clear
    6092 
    6093 [Repeated 2 time(s)]
    6094 
    6095 > ui tool show "Ramachandran Plot"
    6096 
    6097 > select clear
    6098 
    6099 > ui tool show "Ramachandran Plot"
    6100 
    6101 > view #1/Q:137
    6102 
    6103 > isolde sim pause
    6104 
    6105 > isolde sim stop
    6106 
    6107 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6108 chains... 
    6109 ISOLDE: stopped sim 
    6110 
    6111 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6112 > mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FifttenthSubsteps.pdb
    6113 
    6114 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6115 > mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FifttenthSubsteps.cxs
    6116 
    6117 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6118 
    6119 > view #1/Q:137
    6120 
    6121 > select #1/Q:137
    6122 
    6123 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6124 
    6125 > isolde sim start sel
    6126 
    6127 ISOLDE: started sim 
    6128 
    6129 > ui tool show "Ramachandran Plot"
    6130 
    6131 > isolde pepflip sel
    6132 
    6133 Flipping the peptide bond for 1 residues 
    6134 
    6135 > ui tool show "Ramachandran Plot"
    6136 
    6137 > isolde pepflip sel
    6138 
    6139 Flipping the peptide bond for 1 residues 
    6140 
    6141 > select clear
    6142 
    6143 > isolde pepflip sel
    6144 
    6145 Flipping the peptide bond for 1 residues 
    6146 
    6147 > select clear
    6148 
    6149 [Repeated 1 time(s)]
    6150 
    6151 > ui tool show "Ramachandran Plot"
    6152 
    6153 [Repeated 1 time(s)]
    6154 
    6155 > isolde sim stop
    6156 
    6157 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6158 chains... 
    6159 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6160 standards. 
    6161 ISOLDE: stopped sim 
    6162 
    6163 > isolde sim start sel
    6164 
    6165 ISOLDE: started sim 
    6166 
    6167 > isolde sim stop discardTo start
    6168 
    6169 reverting to start 
    6170 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6171 chains... 
    6172 ISOLDE: stopped sim 
    6173 
    6174 > select #1/Q:181
    6175 
    6176 19 atoms, 18 bonds, 1 residue, 1 model selected 
    6177 
    6178 > isolde sim start sel
    6179 
    6180 ISOLDE: started sim 
    6181 
    6182 > ui tool show "Ramachandran Plot"
    6183 
    6184 > isolde sim stop
    6185 
    6186 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6187 chains... 
    6188 ISOLDE: stopped sim 
    6189 
    6190 > view #1/Q:137
    6191 
    6192 > select #1/Q:137
    6193 
    6194 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6195 
    6196 > isolde sim start sel
    6197 
    6198 ISOLDE: started sim 
    6199 
    6200 > ui tool show "Ramachandran Plot"
    6201 
    6202 > select clear
    6203 
    6204 > isolde sim stop
    6205 
    6206 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6207 chains... 
    6208 ISOLDE: stopped sim 
    6209 
    6210 > isolde sim start sel
    6211 
    6212 ISOLDE: started sim 
    6213 
    6214 > isolde cisflip #1.2/O:156
    6215 
    6216 Performing cis<\-->trans flip for 1 residues 
    6217 
    6218 > isolde pepflip sel
    6219 
    6220 Flipping the peptide bond for 1 residues 
    6221 
    6222 > isolde pepflip sel
    6223 
    6224 Flipping the peptide bond for 1 residues 
    6225 
    6226 > select clear
    6227 
    6228 > isolde pepflip sel
    6229 
    6230 Flipping the peptide bond for 1 residues 
    6231 
    6232 > isolde pepflip sel
    6233 
    6234 Flipping the peptide bond for 1 residues 
    6235 
    6236 > isolde sim stop discardTo start
    6237 
    6238 reverting to start 
    6239 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6240 chains... 
    6241 ISOLDE: stopped sim 
    6242 
    6243 > view #1/Q:137
    6244 
    6245 [Repeated 1 time(s)]
    6246 
    6247 > view #1/Q:156
    6248 
    6249 > select #1/Q:156
    6250 
    6251 22 atoms, 21 bonds, 1 residue, 1 model selected 
    6252 
    6253 > select #1/O:156
    6254 
    6255 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6256 
    6257 > view #1/O:156
    6258 
    6259 > select clear
    6260 
    6261 > isolde sim start sel
    6262 
    6263 ISOLDE: started sim 
    6264 
    6265 > isolde cisflip #1.2/Q:44
    6266 
    6267 Performing cis<\-->trans flip for 1 residues 
    6268 
    6269 > isolde pepflip sel
    6270 
    6271 Flipping the peptide bond for 1 residues 
    6272 
    6273 > isolde pepflip sel
    6274 
    6275 Flipping the peptide bond for 1 residues 
    6276 
    6277 > isolde pepflip sel
    6278 
    6279 Flipping the peptide bond for 1 residues 
    6280 
    6281 > isolde pepflip sel
    6282 
    6283 Flipping the peptide bond for 1 residues 
    6284 
    6285 > select clear
    6286 
    6287 > isolde pepflip sel
    6288 
    6289 Flipping the peptide bond for 1 residues 
    6290 
    6291 > isolde pepflip sel
    6292 
    6293 Flipping the peptide bond for 1 residues 
    6294 
    6295 > ui tool show "Ramachandran Plot"
    6296 
    6297 > isolde sim stop discardTo start
    6298 
    6299 reverting to start 
    6300 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6301 chains... 
    6302 ISOLDE: stopped sim 
    6303 
    6304 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6305 > mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FivetenthSubsteps-Final-of-PART-1d1.cxs
    6306 
    6307 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6308 
    6309 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6310 > mut8-no-C-ter/16-KSRP-no-C-ter-Step1-FivetenthSubsteps-Final-of-PART-1d1.pdb
    6311 
    6312 > ui tool show "Ramachandran Plot"
    6313 
    6314 [Repeated 1 time(s)]
    6315 
    6316 > isolde sim start sel
    6317 
    6318 ISOLDE: started sim 
    6319 
    6320 > ui tool show "Ramachandran Plot"
    6321 
    6322 > select clear
    6323 
    6324 > isolde pepflip sel
    6325 
    6326 Flipping the peptide bond for 1 residues 
    6327 
    6328 > isolde pepflip sel
    6329 
    6330 Flipping the peptide bond for 1 residues 
    6331 
    6332 > select clear
    6333 
    6334 [Repeated 1 time(s)]
    6335 
    6336 > isolde sim pause
    6337 
    6338 > isolde sim resume
    6339 
    6340 > isolde pepflip sel
    6341 
    6342 Flipping the peptide bond for 1 residues 
    6343 
    6344 > isolde pepflip sel
    6345 
    6346 Flipping the peptide bond for 1 residues 
    6347 
    6348 > select clear
    6349 
    6350 3 models selected 
    6351 
    6352 > select clear
    6353 
    6354 > ui tool show "Ramachandran Plot"
    6355 
    6356 > isolde sim pause
    6357 
    6358 > ui tool show "Ramachandran Plot"
    6359 
    6360 > view #1/h:163
    6361 
    6362 > ui tool show "Ramachandran Plot"
    6363 
    6364 > isolde sim stop
    6365 
    6366 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6367 chains... 
    6368 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6369 standards. 
    6370 ISOLDE: stopped sim 
    6371 
    6372 > ui tool show "Ramachandran Plot"
    6373 
    6374 > view #1/h:163
    6375 
    6376 > isolde sim start sel
    6377 
    6378 ISOLDE: started sim 
    6379 
    6380 > ui tool show "Ramachandran Plot"
    6381 
    6382 Traceback (most recent call last): 
    6383 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6384 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6385 func(*args, **kwargs) 
    6386 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6387 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6388 on_resize 
    6389 c.draw() 
    6390 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6391 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6392 self.figure.draw(self.renderer) 
    6393 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6394 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6395 result = draw(artist, renderer, *args, **kwargs) 
    6396 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6397 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6398 return draw(artist, renderer) 
    6399 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6400 packages/matplotlib/figure.py", line 2796, in draw 
    6401 artists = self._get_draw_artists(renderer) 
    6402 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6403 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6404 ax.apply_aspect() 
    6405 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6406 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6407 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6408 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6409 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6410 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6411 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6412 
    6413 > select clear
    6414 
    6415 [Repeated 3 time(s)]
    6416 
    6417 > isolde pepflip sel
    6418 
    6419 Flipping the peptide bond for 1 residues 
    6420 
    6421 > isolde pepflip sel
    6422 
    6423 Flipping the peptide bond for 1 residues 
    6424 
    6425 > isolde pepflip sel
    6426 
    6427 Flipping the peptide bond for 1 residues 
    6428 
    6429 > select clear
    6430 
    6431 > isolde pepflip sel
    6432 
    6433 Flipping the peptide bond for 1 residues 
    6434 
    6435 > isolde pepflip sel
    6436 
    6437 Flipping the peptide bond for 1 residues 
    6438 
    6439 > select clear
    6440 
    6441 > ui tool show "Ramachandran Plot"
    6442 
    6443 Unable to flip peptide bond after 50 rounds. Giving up. 
    6444 
    6445 > isolde pepflip sel
    6446 
    6447 Flipping the peptide bond for 1 residues 
    6448 
    6449 > isolde pepflip sel
    6450 
    6451 Flipping the peptide bond for 1 residues 
    6452 
    6453 > select clear
    6454 
    6455 Unable to flip peptide bond after 50 rounds. Giving up. 
    6456 
    6457 > isolde sim pause
    6458 
    6459 > select #1/h:180|/h:184
    6460 
    6461 28 atoms, 26 bonds, 2 residues, 1 model selected 
    6462 
    6463 > isolde sim start sel
    6464 
    6465 Simulation already running! 
    6466 
    6467 > isolde sim stop
    6468 
    6469 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6470 chains... 
    6471 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6472 standards. 
    6473 ISOLDE: stopped sim 
    6474 
    6475 > isolde sim start sel
    6476 
    6477 ISOLDE: started sim 
    6478 
    6479 > select clear
    6480 
    6481 > isolde pepflip sel
    6482 
    6483 Flipping the peptide bond for 1 residues 
    6484 
    6485 > isolde pepflip sel
    6486 
    6487 Flipping the peptide bond for 1 residues 
    6488 
    6489 > isolde pepflip sel
    6490 
    6491 Flipping the peptide bond for 1 residues 
    6492 
    6493 > select clear
    6494 
    6495 [Repeated 1 time(s)]
    6496 
    6497 > isolde pepflip sel
    6498 
    6499 Flipping the peptide bond for 1 residues 
    6500 
    6501 > select clear
    6502 
    6503 > isolde pepflip sel
    6504 
    6505 Flipping the peptide bond for 1 residues 
    6506 
    6507 > select clear
    6508 
    6509 > isolde sim pause
    6510 
    6511 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6512 > mut8-no-C-ter/17-KSRP-no-C-ter-Step1-SevententhSubstep.pdb
    6513 
    6514 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6515 > mut8-no-C-ter/17-KSRP-no-C-ter-Step1-SevententhSubstep.cxs
    6516 
    6517 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6518 
    6519 > isolde sim start sel
    6520 
    6521 Simulation already running! 
    6522 
    6523 > isolde sim resume
    6524 
    6525 > select clear
    6526 
    6527 [Repeated 4 time(s)]
    6528 
    6529 > isolde pepflip sel
    6530 
    6531 Flipping the peptide bond for 1 residues 
    6532 
    6533 > isolde pepflip sel
    6534 
    6535 Flipping the peptide bond for 1 residues 
    6536 
    6537 > select clear
    6538 
    6539 > isolde pepflip sel
    6540 
    6541 Flipping the peptide bond for 1 residues 
    6542 
    6543 > select #1/h
    6544 
    6545 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6546 
    6547 > select clear
    6548 
    6549 > ui tool show "Ramachandran Plot"
    6550 
    6551 > view #1/h:N183
    6552 
    6553 No objects specified. 
    6554 
    6555 > view #1/h:183
    6556 
    6557 > isolde sim pause
    6558 
    6559 > isolde sim resume
    6560 
    6561 > select clear
    6562 
    6563 [Repeated 2 time(s)]
    6564 
    6565 > isolde pepflip sel
    6566 
    6567 Flipping the peptide bond for 1 residues 
    6568 
    6569 > isolde pepflip sel
    6570 
    6571 Flipping the peptide bond for 1 residues 
    6572 
    6573 > isolde pepflip sel
    6574 
    6575 Flipping the peptide bond for 1 residues 
    6576 Unable to flip peptide bond after 50 rounds. Giving up. 
    6577 [Repeated 1 time(s)]
    6578 
    6579 > select clear
    6580 
    6581 > isolde sim stop
    6582 
    6583 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6584 chains... 
    6585 ISOLDE: stopped sim 
    6586 
    6587 > view #1/h
    6588 
    6589 > select #1/h
    6590 
    6591 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6592 
    6593 > isolde sim start sel
    6594 
    6595 ISOLDE: started sim 
    6596 
    6597 > ui tool show "Ramachandran Plot"
    6598 
    6599 > isolde pepflip sel
    6600 
    6601 Flipping the peptide bond for 1 residues 
    6602 
    6603 > select clear
    6604 
    6605 > isolde sim pause
    6606 
    6607 > isolde sim resume
    6608 
    6609 > select clear
    6610 
    6611 > isolde pepflip sel
    6612 
    6613 Flipping the peptide bond for 1 residues 
    6614 
    6615 > select clear
    6616 
    6617 > isolde sim stop
    6618 
    6619 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6620 chains... 
    6621 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6622 standards. 
    6623 ISOLDE: stopped sim 
    6624 
    6625 > select #1/h
    6626 
    6627 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6628 
    6629 > isolde sim start sel
    6630 
    6631 ISOLDE: started sim 
    6632 
    6633 > select clear
    6634 
    6635 > isolde pepflip sel
    6636 
    6637 Flipping the peptide bond for 1 residues 
    6638 
    6639 > isolde pepflip sel
    6640 
    6641 Flipping the peptide bond for 1 residues 
    6642 
    6643 > isolde sim pause
    6644 
    6645 > ui tool show "Ramachandran Plot"
    6646 
    6647 > isolde sim resume
    6648 
    6649 > isolde pepflip sel
    6650 
    6651 Flipping the peptide bond for 1 residues 
    6652 
    6653 > isolde pepflip sel
    6654 
    6655 Flipping the peptide bond for 1 residues 
    6656 
    6657 > select #1/h:115-119
    6658 
    6659 85 atoms, 84 bonds, 5 residues, 1 model selected 
    6660 
    6661 > select clear
    6662 
    6663 > select #1/h:215-219
    6664 
    6665 70 atoms, 69 bonds, 5 residues, 1 model selected 
    6666 
    6667 > select #1/h:152-155
    6668 
    6669 61 atoms, 62 bonds, 4 residues, 1 model selected 
    6670 
    6671 > select #1/h:152-156
    6672 
    6673 80 atoms, 81 bonds, 5 residues, 1 model selected 
    6674 
    6675 > select #1/h
    6676 
    6677 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6678 
    6679 > select clear
    6680 
    6681 [Repeated 1 time(s)]
    6682 
    6683 > isolde pepflip sel
    6684 
    6685 Flipping the peptide bond for 1 residues 
    6686 
    6687 > select clear
    6688 
    6689 > isolde pepflip sel
    6690 
    6691 Flipping the peptide bond for 1 residues 
    6692 
    6693 > isolde pepflip sel
    6694 
    6695 Flipping the peptide bond for 1 residues 
    6696 Unable to flip peptide bond after 50 rounds. Giving up. 
    6697 
    6698 > select clear
    6699 
    6700 [Repeated 1 time(s)]
    6701 
    6702 > isolde pepflip sel
    6703 
    6704 Flipping the peptide bond for 1 residues 
    6705 
    6706 > select clear
    6707 
    6708 > isolde sim pause
    6709 
    6710 > isolde sim resume
    6711 
    6712 > ui tool show "Ramachandran Plot"
    6713 
    6714 > isolde sim pause
    6715 
    6716 > isolde sim resume
    6717 
    6718 > view #1/P:244
    6719 
    6720 > view #1/h
    6721 
    6722 > ui tool show "Ramachandran Plot"
    6723 
    6724 3 models selected 
    6725 [Repeated 2 time(s)]
    6726 
    6727 > isolde sim pause
    6728 
    6729 > isolde sim resume
    6730 
    6731 > isolde sim pause
    6732 
    6733 > isolde sim resume
    6734 
    6735 > select clear
    6736 
    6737 3 models selected 
    6738 
    6739 > select clear
    6740 
    6741 > ui tool show "Ramachandran Plot"
    6742 
    6743 [Repeated 1 time(s)]
    6744 
    6745 > isolde sim pause
    6746 
    6747 > isolde sim resume
    6748 
    6749 > isolde sim pause
    6750 
    6751 > ui tool show "Ramachandran Plot"
    6752 
    6753 > isolde sim resume
    6754 
    6755 > select clear
    6756 
    6757 > isolde pepflip sel
    6758 
    6759 Flipping the peptide bond for 1 residues 
    6760 
    6761 > select clear
    6762 
    6763 > isolde pepflip sel
    6764 
    6765 Flipping the peptide bond for 1 residues 
    6766 
    6767 > select clear
    6768 
    6769 Unable to flip peptide bond after 50 rounds. Giving up. 
    6770 
    6771 > ui tool show "Ramachandran Plot"
    6772 
    6773 > isolde sim pause
    6774 
    6775 > isolde sim resume
    6776 
    6777 > select clear
    6778 
    6779 [Repeated 2 time(s)]
    6780 
    6781 > isolde pepflip sel
    6782 
    6783 Flipping the peptide bond for 1 residues 
    6784 
    6785 > select clear
    6786 
    6787 > isolde pepflip sel
    6788 
    6789 Flipping the peptide bond for 1 residues 
    6790 Unable to flip peptide bond after 50 rounds. Giving up. 
    6791 
    6792 > select clear
    6793 
    6794 > ui tool show "Ramachandran Plot"
    6795 
    6796 > isolde pepflip sel
    6797 
    6798 Flipping the peptide bond for 1 residues 
    6799 
    6800 > select clear
    6801 
    6802 > isolde pepflip sel
    6803 
    6804 Flipping the peptide bond for 1 residues 
    6805 
    6806 > select clear
    6807 
    6808 > ui tool show "Ramachandran Plot"
    6809 
    6810 > select clear
    6811 
    6812 [Repeated 3 time(s)]
    6813 
    6814 > ui tool show "Ramachandran Plot"
    6815 
    6816 > isolde sim pause
    6817 
    6818 > isolde sim resume
    6819 
    6820 > ui tool show "Ramachandran Plot"
    6821 
    6822 > select clear
    6823 
    6824 [Repeated 1 time(s)]
    6825 
    6826 > ui tool show "Ramachandran Plot"
    6827 
    6828 [Repeated 5 time(s)]
    6829 
    6830 > isolde pepflip sel
    6831 
    6832 Flipping the peptide bond for 1 residues 
    6833 
    6834 > select clear
    6835 
    6836 > isolde pepflip sel
    6837 
    6838 Flipping the peptide bond for 1 residues 
    6839 
    6840 > select clear
    6841 
    6842 > isolde pepflip sel
    6843 
    6844 Flipping the peptide bond for 1 residues 
    6845 
    6846 > select clear
    6847 
    6848 > isolde pepflip sel
    6849 
    6850 Flipping the peptide bond for 1 residues 
    6851 
    6852 > isolde pepflip sel
    6853 
    6854 Flipping the peptide bond for 1 residues 
    6855 
    6856 > ui tool show "Ramachandran Plot"
    6857 
    6858 > select clear
    6859 
    6860 > isolde pepflip sel
    6861 
    6862 Flipping the peptide bond for 1 residues 
    6863 
    6864 > isolde pepflip sel
    6865 
    6866 Flipping the peptide bond for 1 residues 
    6867 
    6868 > ui tool show "Ramachandran Plot"
    6869 
    6870 [Repeated 1 time(s)]Traceback (most recent call last): 
    6871 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6872 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6873 func(*args, **kwargs) 
    6874 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6875 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6876 on_resize 
    6877 c.draw() 
    6878 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6879 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6880 self.figure.draw(self.renderer) 
    6881 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6882 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6883 result = draw(artist, renderer, *args, **kwargs) 
    6884 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6885 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6886 return draw(artist, renderer) 
    6887 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6888 packages/matplotlib/figure.py", line 2796, in draw 
    6889 artists = self._get_draw_artists(renderer) 
    6890 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6891 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6892 ax.apply_aspect() 
    6893 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6894 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6895 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6896 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6897 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6898 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6899 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6900 
    6901 > select clear
    6902 
    6903 > ui tool show "Ramachandran Plot"
    6904 
    6905 > isolde pepflip sel
    6906 
    6907 Flipping the peptide bond for 1 residues 
    6908 
    6909 > select clear
    6910 
    6911 > isolde pepflip sel
    6912 
    6913 Flipping the peptide bond for 1 residues 
    6914 
    6915 > isolde pepflip sel
    6916 
    6917 Flipping the peptide bond for 1 residues 
    6918 Unable to flip peptide bond after 50 rounds. Giving up. 
    6919 Traceback (most recent call last): 
    6920 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6921 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6922 func(*args, **kwargs) 
    6923 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6924 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6925 on_resize 
    6926 c.draw() 
    6927 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6928 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6929 self.figure.draw(self.renderer) 
    6930 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6931 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6932 result = draw(artist, renderer, *args, **kwargs) 
    6933 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6934 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6935 return draw(artist, renderer) 
    6936 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6937 packages/matplotlib/figure.py", line 2796, in draw 
    6938 artists = self._get_draw_artists(renderer) 
    6939 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6940 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6941 ax.apply_aspect() 
    6942 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6943 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6944 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6945 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6946 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6947 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6948 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6949 
    6950 > isolde pepflip sel
    6951 
    6952 Flipping the peptide bond for 1 residues 
    6953 
    6954 > select #1/h
    6955 
    6956 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6957 
    6958 > select clear
    6959 
    6960 [Repeated 1 time(s)]
    6961 
    6962 > ui tool show "Ramachandran Plot"
    6963 
    6964 Traceback (most recent call last): 
    6965 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6966 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6967 func(*args, **kwargs) 
    6968 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6969 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6970 on_resize 
    6971 c.draw() 
    6972 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6973 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6974 self.figure.draw(self.renderer) 
    6975 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6976 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6977 result = draw(artist, renderer, *args, **kwargs) 
    6978 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6979 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6980 return draw(artist, renderer) 
    6981 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6982 packages/matplotlib/figure.py", line 2796, in draw 
    6983 artists = self._get_draw_artists(renderer) 
    6984 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6985 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6986 ax.apply_aspect() 
    6987 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6988 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6989 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6990 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6991 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6992 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6993 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6994 Traceback (most recent call last): 
    6995 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6996 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6997 func(*args, **kwargs) 
    6998 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6999 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7000 on_resize 
    7001 c.draw() 
    7002 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7003 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7004 self.figure.draw(self.renderer) 
    7005 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7006 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7007 result = draw(artist, renderer, *args, **kwargs) 
    7008 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7009 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7010 return draw(artist, renderer) 
    7011 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7012 packages/matplotlib/figure.py", line 2796, in draw 
    7013 artists = self._get_draw_artists(renderer) 
    7014 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7015 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7016 ax.apply_aspect() 
    7017 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7018 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7019 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7020 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7021 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7022 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7023 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7024 
    7025 > isolde pepflip sel
    7026 
    7027 Flipping the peptide bond for 1 residues 
    7028 
    7029 > select clear
    7030 
    7031 > isolde pepflip sel
    7032 
    7033 Flipping the peptide bond for 1 residues 
    7034 
    7035 > select clear
    7036 
    7037 [Repeated 2 time(s)]
    7038 
    7039 > isolde pepflip sel
    7040 
    7041 Flipping the peptide bond for 1 residues 
    7042 
    7043 > ui tool show "Ramachandran Plot"
    7044 
    7045 [Repeated 1 time(s)]
    7046 
    7047 > select clear
    7048 
    7049 > isolde pepflip sel
    7050 
    7051 Flipping the peptide bond for 1 residues 
    7052 
    7053 > isolde pepflip sel
    7054 
    7055 Flipping the peptide bond for 1 residues 
    7056 
    7057 > ui tool show "Ramachandran Plot"
    7058 
    7059 > select clear
    7060 
    7061 [Repeated 1 time(s)]
    7062 
    7063 > isolde pepflip sel
    7064 
    7065 Flipping the peptide bond for 1 residues 
    7066 
    7067 > select clear
    7068 
    7069 > isolde pepflip sel
    7070 
    7071 Flipping the peptide bond for 1 residues 
    7072 
    7073 > isolde pepflip sel
    7074 
    7075 Flipping the peptide bond for 1 residues 
    7076 
    7077 > select clear
    7078 
    7079 > isolde pepflip sel
    7080 
    7081 Flipping the peptide bond for 1 residues 
    7082 
    7083 > select clear
    7084 
    7085 [Repeated 1 time(s)]
    7086 
    7087 > select #1/h
    7088 
    7089 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7090 
    7091 > select #1/h
    7092 
    7093 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7094 
    7095 > ui tool show "Ramachandran Plot"
    7096 
    7097 > select clear
    7098 
    7099 Traceback (most recent call last): 
    7100 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7101 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7102 func(*args, **kwargs) 
    7103 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7104 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7105 on_resize 
    7106 c.draw() 
    7107 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7108 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7109 self.figure.draw(self.renderer) 
    7110 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7111 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7112 result = draw(artist, renderer, *args, **kwargs) 
    7113 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7114 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7115 return draw(artist, renderer) 
    7116 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7117 packages/matplotlib/figure.py", line 2796, in draw 
    7118 artists = self._get_draw_artists(renderer) 
    7119 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7120 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7121 ax.apply_aspect() 
    7122 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7123 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7124 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7125 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7126 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7127 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7128 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7129 Traceback (most recent call last): 
    7130 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7131 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7132 func(*args, **kwargs) 
    7133 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7134 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7135 on_resize 
    7136 c.draw() 
    7137 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7138 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7139 self.figure.draw(self.renderer) 
    7140 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7141 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7142 result = draw(artist, renderer, *args, **kwargs) 
    7143 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7144 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7145 return draw(artist, renderer) 
    7146 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7147 packages/matplotlib/figure.py", line 2796, in draw 
    7148 artists = self._get_draw_artists(renderer) 
    7149 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7150 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7151 ax.apply_aspect() 
    7152 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7153 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7154 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7155 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7156 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7157 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7158 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7159 
    7160 > isolde pepflip sel
    7161 
    7162 Flipping the peptide bond for 1 residues 
    7163 
    7164 > isolde pepflip sel
    7165 
    7166 Flipping the peptide bond for 1 residues 
    7167 Traceback (most recent call last): 
    7168 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7169 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7170 func(*args, **kwargs) 
    7171 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7172 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7173 on_resize 
    7174 c.draw() 
    7175 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7176 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7177 self.figure.draw(self.renderer) 
    7178 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7179 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7180 result = draw(artist, renderer, *args, **kwargs) 
    7181 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7182 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7183 return draw(artist, renderer) 
    7184 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7185 packages/matplotlib/figure.py", line 2796, in draw 
    7186 artists = self._get_draw_artists(renderer) 
    7187 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7188 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7189 ax.apply_aspect() 
    7190 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7191 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7192 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7193 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7194 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7195 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7196 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7197 
    7198 > ui tool show "Ramachandran Plot"
    7199 
    7200 > select #1/h
    7201 
    7202 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7203 
    7204 > select clear
    7205 
    7206 > ui tool show "Ramachandran Plot"
    7207 
    7208 [Repeated 1 time(s)]
    7209 
    7210 > select clear
    7211 
    7212 > ui tool show "Ramachandran Plot"
    7213 
    7214 Traceback (most recent call last): 
    7215 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7216 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7217 func(*args, **kwargs) 
    7218 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7219 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7220 on_resize 
    7221 c.draw() 
    7222 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7223 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7224 self.figure.draw(self.renderer) 
    7225 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7226 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7227 result = draw(artist, renderer, *args, **kwargs) 
    7228 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7229 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7230 return draw(artist, renderer) 
    7231 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7232 packages/matplotlib/figure.py", line 2796, in draw 
    7233 artists = self._get_draw_artists(renderer) 
    7234 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7235 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7236 ax.apply_aspect() 
    7237 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7238 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7239 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7240 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7241 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7242 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7243 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7244 
    7245 > ui tool show "Ramachandran Plot"
    7246 
    7247 [Repeated 1 time(s)]
    7248 
    7249 > select clear
    7250 
    7251 > ui tool show "Ramachandran Plot"
    7252 
    7253 > isolde pepflip sel
    7254 
    7255 Flipping the peptide bond for 1 residues 
    7256 
    7257 > select clear
    7258 
    7259 [Repeated 1 time(s)]
    7260 
    7261 > ui tool show "Ramachandran Plot"
    7262 
    7263 > select #1/h
    7264 
    7265 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7266 
    7267 > select #1/h
    7268 
    7269 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7270 
    7271 > select clear
    7272 
    7273 [Repeated 1 time(s)]
    7274 
    7275 > ui tool show "Ramachandran Plot"
    7276 
    7277 > select clear
    7278 
    7279 > isolde pepflip sel
    7280 
    7281 Flipping the peptide bond for 1 residues 
    7282 
    7283 > isolde pepflip sel
    7284 
    7285 Flipping the peptide bond for 1 residues 
    7286 
    7287 > select clear
    7288 
    7289 > isolde pepflip sel
    7290 
    7291 Flipping the peptide bond for 1 residues 
    7292 
    7293 > select clear
    7294 
    7295 > isolde pepflip sel
    7296 
    7297 Flipping the peptide bond for 1 residues 
    7298 
    7299 > select clear
    7300 
    7301 Traceback (most recent call last): 
    7302 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7303 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7304 func(*args, **kwargs) 
    7305 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7306 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7307 on_resize 
    7308 c.draw() 
    7309 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7310 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7311 self.figure.draw(self.renderer) 
    7312 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7313 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7314 result = draw(artist, renderer, *args, **kwargs) 
    7315 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7316 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7317 return draw(artist, renderer) 
    7318 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7319 packages/matplotlib/figure.py", line 2796, in draw 
    7320 artists = self._get_draw_artists(renderer) 
    7321 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7322 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7323 ax.apply_aspect() 
    7324 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7325 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7326 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7327 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7328 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7329 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7330 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7331 
    7332 > isolde pepflip sel
    7333 
    7334 Flipping the peptide bond for 1 residues 
    7335 
    7336 > ui tool show "Ramachandran Plot"
    7337 
    7338 > select clear
    7339 
    7340 [Repeated 1 time(s)]
    7341 
    7342 > ui tool show "Ramachandran Plot"
    7343 
    7344 > isolde pepflip sel
    7345 
    7346 Flipping the peptide bond for 1 residues 
    7347 
    7348 > ui tool show "Ramachandran Plot"
    7349 
    7350 > isolde pepflip sel
    7351 
    7352 Flipping the peptide bond for 1 residues 
    7353 
    7354 > isolde pepflip sel
    7355 
    7356 Flipping the peptide bond for 1 residues 
    7357 
    7358 > select clear
    7359 
    7360 [Repeated 3 time(s)]
    7361 
    7362 > ui tool show "Ramachandran Plot"
    7363 
    7364 > isolde pepflip sel
    7365 
    7366 Flipping the peptide bond for 1 residues 
    7367 
    7368 > select clear
    7369 
    7370 > ui tool show "Ramachandran Plot"
    7371 
    7372 > select #1/h
    7373 
    7374 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7375 
    7376 > select clear
    7377 
    7378 Traceback (most recent call last): 
    7379 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7380 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7381 func(*args, **kwargs) 
    7382 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7383 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7384 on_resize 
    7385 c.draw() 
    7386 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7387 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7388 self.figure.draw(self.renderer) 
    7389 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7390 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7391 result = draw(artist, renderer, *args, **kwargs) 
    7392 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7393 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7394 return draw(artist, renderer) 
    7395 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7396 packages/matplotlib/figure.py", line 2796, in draw 
    7397 artists = self._get_draw_artists(renderer) 
    7398 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7399 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7400 ax.apply_aspect() 
    7401 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7402 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7403 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7404 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7405 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7406 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7407 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7408 
    7409 > select #1/h
    7410 
    7411 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7412 
    7413 > select #1/h
    7414 
    7415 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7416 
    7417 > ui tool show "Ramachandran Plot"
    7418 
    7419 > select clear
    7420 
    7421 [Repeated 1 time(s)]
    7422 
    7423 > ui tool show "Ramachandran Plot"
    7424 
    7425 Traceback (most recent call last): 
    7426 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7427 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7428 func(*args, **kwargs) 
    7429 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7430 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7431 on_resize 
    7432 c.draw() 
    7433 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7434 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7435 self.figure.draw(self.renderer) 
    7436 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7437 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7438 result = draw(artist, renderer, *args, **kwargs) 
    7439 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7440 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7441 return draw(artist, renderer) 
    7442 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7443 packages/matplotlib/figure.py", line 2796, in draw 
    7444 artists = self._get_draw_artists(renderer) 
    7445 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7446 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7447 ax.apply_aspect() 
    7448 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7449 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7450 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7451 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7452 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7453 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7454 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7455 
    7456 > isolde pepflip sel
    7457 
    7458 Flipping the peptide bond for 1 residues 
    7459 
    7460 > select clear
    7461 
    7462 > ui tool show "Ramachandran Plot"
    7463 
    7464 [Repeated 1 time(s)]
    7465 
    7466 > isolde pepflip sel
    7467 
    7468 Flipping the peptide bond for 1 residues 
    7469 
    7470 > ui tool show "Ramachandran Plot"
    7471 
    7472 > select clear
    7473 
    7474 > ui tool show "Ramachandran Plot"
    7475 
    7476 > select clear
    7477 
    7478 [Repeated 1 time(s)]
    7479 
    7480 > ui tool show "Ramachandran Plot"
    7481 
    7482 [Repeated 2 time(s)]Traceback (most recent call last): 
    7483 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7484 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7485 func(*args, **kwargs) 
    7486 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7487 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7488 on_resize 
    7489 c.draw() 
    7490 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7491 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7492 self.figure.draw(self.renderer) 
    7493 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7494 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7495 result = draw(artist, renderer, *args, **kwargs) 
    7496 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7497 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7498 return draw(artist, renderer) 
    7499 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7500 packages/matplotlib/figure.py", line 2796, in draw 
    7501 artists = self._get_draw_artists(renderer) 
    7502 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7503 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7504 ax.apply_aspect() 
    7505 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7506 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7507 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7508 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7509 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7510 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7511 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7512 
    7513 > isolde pepflip sel
    7514 
    7515 Flipping the peptide bond for 1 residues 
    7516 Traceback (most recent call last): 
    7517 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7518 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7519 func(*args, **kwargs) 
    7520 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7521 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7522 on_resize 
    7523 c.draw() 
    7524 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7525 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7526 self.figure.draw(self.renderer) 
    7527 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7528 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7529 result = draw(artist, renderer, *args, **kwargs) 
    7530 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7531 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7532 return draw(artist, renderer) 
    7533 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7534 packages/matplotlib/figure.py", line 2796, in draw 
    7535 artists = self._get_draw_artists(renderer) 
    7536 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7537 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7538 ax.apply_aspect() 
    7539 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7540 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7541 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7542 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7543 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7544 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7545 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7546 
    7547 > isolde pepflip sel
    7548 
    7549 Flipping the peptide bond for 1 residues 
    7550 
    7551 > isolde sim stop
    7552 
    7553 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7554 chains... 
    7555 ISOLDE: Corrected atom nomenclature of 13 residues in model #1.2 to IUPAC-IUB
    7556 standards. 
    7557 ISOLDE: stopped sim 
    7558 
    7559 > select #1/h
    7560 
    7561 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7562 
    7563 > isolde sim start sel
    7564 
    7565 ISOLDE: started sim 
    7566 
    7567 > ui tool show "Ramachandran Plot"
    7568 
    7569 [Repeated 1 time(s)]
    7570 
    7571 > isolde sim pause
    7572 
    7573 > isolde sim resume
    7574 
    7575 > ui tool show "Ramachandran Plot"
    7576 
    7577 > select clear
    7578 
    7579 > isolde pepflip sel
    7580 
    7581 Flipping the peptide bond for 1 residues 
    7582 
    7583 > isolde pepflip sel
    7584 
    7585 Flipping the peptide bond for 1 residues 
    7586 
    7587 > isolde pepflip sel
    7588 
    7589 Flipping the peptide bond for 1 residues 
    7590 
    7591 > isolde pepflip sel
    7592 
    7593 Flipping the peptide bond for 1 residues 
    7594 
    7595 > isolde pepflip sel
    7596 
    7597 Flipping the peptide bond for 1 residues 
    7598 
    7599 > isolde pepflip sel
    7600 
    7601 Flipping the peptide bond for 1 residues 
    7602 Unable to flip peptide bond after 50 rounds. Giving up. 
    7603 
    7604 > select clear
    7605 
    7606 [Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up. 
    7607 
    7608 > isolde pepflip sel
    7609 
    7610 Flipping the peptide bond for 1 residues 
    7611 
    7612 > select #1/h
    7613 
    7614 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7615 
    7616 > select clear
    7617 
    7618 > isolde sim pause
    7619 
    7620 > isolde sim resume
    7621 
    7622 > ui tool show "Ramachandran Plot"
    7623 
    7624 > isolde pepflip sel
    7625 
    7626 Flipping the peptide bond for 1 residues 
    7627 
    7628 > isolde pepflip sel
    7629 
    7630 Flipping the peptide bond for 1 residues 
    7631 
    7632 > isolde pepflip sel
    7633 
    7634 Flipping the peptide bond for 1 residues 
    7635 
    7636 > select clear
    7637 
    7638 Unable to flip peptide bond after 50 rounds. Giving up. 
    7639 
    7640 > isolde pepflip sel
    7641 
    7642 Flipping the peptide bond for 1 residues 
    7643 
    7644 > isolde pepflip sel
    7645 
    7646 Flipping the peptide bond for 1 residues 
    7647 
    7648 > isolde pepflip sel
    7649 
    7650 Flipping the peptide bond for 1 residues 
    7651 
    7652 > select clear
    7653 
    7654 > select #1/h
    7655 
    7656 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7657 
    7658 > ui tool show "Ramachandran Plot"
    7659 
    7660 > select clear
    7661 
    7662 > ui tool show "Ramachandran Plot"
    7663 
    7664 > select clear
    7665 
    7666 > ui tool show "Ramachandran Plot"
    7667 
    7668 > select clear
    7669 
    7670 > ui tool show "Ramachandran Plot"
    7671 
    7672 > isolde pepflip sel
    7673 
    7674 Flipping the peptide bond for 1 residues 
    7675 
    7676 > isolde pepflip sel
    7677 
    7678 Flipping the peptide bond for 1 residues 
    7679 
    7680 > isolde pepflip sel
    7681 
    7682 Flipping the peptide bond for 1 residues 
    7683 Unable to flip peptide bond after 50 rounds. Giving up. 
    7684 
    7685 > select clear
    7686 
    7687 > ui tool show "Ramachandran Plot"
    7688 
    7689 > isolde pepflip sel
    7690 
    7691 Flipping the peptide bond for 1 residues 
    7692 
    7693 > isolde pepflip sel
    7694 
    7695 Flipping the peptide bond for 1 residues 
    7696 
    7697 > select clear
    7698 
    7699 > ui tool show "Ramachandran Plot"
    7700 
    7701 > isolde pepflip sel
    7702 
    7703 Flipping the peptide bond for 1 residues 
    7704 
    7705 > isolde pepflip sel
    7706 
    7707 Flipping the peptide bond for 1 residues 
    7708 
    7709 > isolde pepflip sel
    7710 
    7711 Flipping the peptide bond for 1 residues 
    7712 
    7713 > isolde pepflip sel
    7714 
    7715 Flipping the peptide bond for 1 residues 
    7716 Unable to flip peptide bond after 50 rounds. Giving up. 
    7717 
    7718 > isolde pepflip sel
    7719 
    7720 Flipping the peptide bond for 1 residues 
    7721 Traceback (most recent call last): 
    7722 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7723 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7724 func(*args, **kwargs) 
    7725 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7726 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7727 on_resize 
    7728 c.draw() 
    7729 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7730 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7731 self.figure.draw(self.renderer) 
    7732 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7733 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7734 result = draw(artist, renderer, *args, **kwargs) 
    7735 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7736 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7737 return draw(artist, renderer) 
    7738 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7739 packages/matplotlib/figure.py", line 2796, in draw 
    7740 artists = self._get_draw_artists(renderer) 
    7741 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7742 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7743 ax.apply_aspect() 
    7744 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7745 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7746 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7747 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7748 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7749 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7750 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7751 Unable to flip peptide bond after 50 rounds. Giving up. 
    7752 
    7753 > isolde sim pause
    7754 
    7755 > isolde sim resume
    7756 
    7757 > ui tool show "Ramachandran Plot"
    7758 
    7759 Traceback (most recent call last): 
    7760 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7761 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7762 func(*args, **kwargs) 
    7763 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7764 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7765 on_resize 
    7766 c.draw() 
    7767 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7768 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7769 self.figure.draw(self.renderer) 
    7770 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7771 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7772 result = draw(artist, renderer, *args, **kwargs) 
    7773 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7774 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7775 return draw(artist, renderer) 
    7776 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7777 packages/matplotlib/figure.py", line 2796, in draw 
    7778 artists = self._get_draw_artists(renderer) 
    7779 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7780 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7781 ax.apply_aspect() 
    7782 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7783 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7784 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7785 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7786 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7787 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7788 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7789 
    7790 > select clear
    7791 
    7792 > ui tool show "Ramachandran Plot"
    7793 
    7794 > select clear
    7795 
    7796 > style #1/h:84|/h:125 sphere
    7797 
    7798 Changed 39 atom styles 
    7799 
    7800 > style #1/h:84|/h:125 stick
    7801 
    7802 Changed 39 atom styles 
    7803 
    7804 > ui tool show "Ramachandran Plot"
    7805 
    7806 [Repeated 1 time(s)]
    7807 
    7808 > isolde sim stop
    7809 
    7810 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7811 chains... 
    7812 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7813 standards. 
    7814 ISOLDE: stopped sim 
    7815 
    7816 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7817 > mut8-no-C-ter/18-KSRP-no-C-ter-Step1-SevententhSubsteps-POST-FIRST-SIM-ANN-
    7818 > KSRP.cxs
    7819 
    7820 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    7821 
    7822 ——— End of log from Fri Mar 24 14:43:56 2023 ———
    7823 
    7824 opened ChimeraX session 
    7825 
    7826 > isolde start
    7827 
    7828 > set selectionWidth 4
    7829 
    7830 > isolde restrain ligands #1
    7831 
    7832 > select clear
    7833 
    7834 > select #1/h
    7835 
    7836 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7837 
    7838 > isolde sim start sel
    7839 
    7840 Launching using CUDA failed with the below message. Falling back to using
    7841 OpenCL. 
    7842  
    7843 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    7844 (-arch) 
    7845  
    7846 
    7847 ISOLDE: started sim 
    7848 
    7849 > isolde sim stop discardTo start
    7850 
    7851 reverting to start 
    7852 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7853 chains... 
    7854 ISOLDE: stopped sim 
    7855 
    7856 > select #1/h
    7857 
    7858 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7859 
    7860 > isolde sim start sel
    7861 
    7862 ISOLDE: started sim 
    7863 
    7864 > isolde sim stop discardTo start
    7865 
    7866 reverting to start 
    7867 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7868 chains... 
    7869 ISOLDE: stopped sim 
    7870 
    7871 > select #1/h
    7872 
    7873 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7874 
    7875 > isolde sim start sel
    7876 
    7877 ISOLDE: started sim 
    7878 
    7879 > ui tool show "Ramachandran Plot"
    7880 
    7881 > select clear
    7882 
    7883 > ui tool show "Ramachandran Plot"
    7884 
    7885 [Repeated 2 time(s)]
    7886 
    7887 > isolde sim pause
    7888 
    7889 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7890 > mut8-no-C-ter/19a-Test-KSRP-Env-System-on-the-middle-of-
    7891 > overFittingTo-6Times-densityField.pdb
    7892 
    7893 > isolde sim resume
    7894 
    7895 > ui tool show "Ramachandran Plot"
    7896 
    7897 [Repeated 1 time(s)]
    7898 
    7899 > isolde sim pause
    7900 
    7901 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7902 > mut8-no-C-ter/19b-Test-KSRP-Env-System-on-the-overFittingTo-6Times-
    7903 > densityFieldSmoth-NoSmoth.pdb
    7904 
    7905 > isolde sim resume
    7906 
    7907 > ui tool show "Ramachandran Plot"
    7908 
    7909 [Repeated 4 time(s)]
    7910 
    7911 > isolde sim pause
    7912 
    7913 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7914 > mut8-no-C-ter/19c-Test-KSRP-Env-System-After-the-overFittingTo-6Times-And-
    7915 > ComeBack-to-Default.pdb
    7916 
    7917 > isolde sim resume
    7918 
    7919 > ui tool show "Ramachandran Plot"
    7920 
    7921 [Repeated 3 time(s)]
    7922 
    7923 > select clear
    7924 
    7925 [Repeated 3 time(s)]
    7926 
    7927 > ui tool show "Ramachandran Plot"
    7928 
    7929 > isolde pepflip sel
    7930 
    7931 Flipping the peptide bond for 1 residues 
    7932 
    7933 > ui tool show "Ramachandran Plot"
    7934 
    7935 > select clear
    7936 
    7937 > isolde pepflip sel
    7938 
    7939 Flipping the peptide bond for 1 residues 
    7940 
    7941 > ui tool show "Ramachandran Plot"
    7942 
    7943 > select clear
    7944 
    7945 > isolde pepflip sel
    7946 
    7947 Flipping the peptide bond for 1 residues 
    7948 
    7949 > ui tool show "Ramachandran Plot"
    7950 
    7951 > select clear
    7952 
    7953 > isolde pepflip sel
    7954 
    7955 Flipping the peptide bond for 1 residues 
    7956 
    7957 > isolde pepflip sel
    7958 
    7959 Flipping the peptide bond for 1 residues 
    7960 
    7961 > select clear
    7962 
    7963 > ui tool show "Ramachandran Plot"
    7964 
    7965 [Repeated 3 time(s)]
    7966 
    7967 > isolde pepflip sel
    7968 
    7969 Flipping the peptide bond for 1 residues 
    7970 
    7971 > ui tool show "Ramachandran Plot"
    7972 
    7973 > select clear
    7974 
    7975 > ui tool show "Ramachandran Plot"
    7976 
    7977 > select clear
    7978 
    7979 > isolde pepflip sel
    7980 
    7981 Flipping the peptide bond for 1 residues 
    7982 
    7983 > select clear
    7984 
    7985 > isolde pepflip sel
    7986 
    7987 Flipping the peptide bond for 1 residues 
    7988 
    7989 > ui tool show "Ramachandran Plot"
    7990 
    7991 > select clear
    7992 
    7993 [Repeated 1 time(s)]
    7994 
    7995 > ui tool show "Ramachandran Plot"
    7996 
    7997 > isolde pepflip sel
    7998 
    7999 Flipping the peptide bond for 1 residues 
    8000 
    8001 > isolde pepflip sel
    8002 
    8003 Flipping the peptide bond for 1 residues 
    8004 
    8005 > select clear
    8006 
    8007 > ui tool show "Ramachandran Plot"
    8008 
    8009 [Repeated 1 time(s)]
    8010 
    8011 > select clear
    8012 
    8013 > ui tool show "Ramachandran Plot"
    8014 
    8015 > select clear
    8016 
    8017 > isolde pepflip sel
    8018 
    8019 Flipping the peptide bond for 1 residues 
    8020 
    8021 > select clear
    8022 
    8023 > ui tool show "Ramachandran Plot"
    8024 
    8025 [Repeated 1 time(s)]
    8026 
    8027 > isolde pepflip sel
    8028 
    8029 Flipping the peptide bond for 1 residues 
    8030 
    8031 > select clear
    8032 
    8033 > ui tool show "Ramachandran Plot"
    8034 
    8035 > select clear
    8036 
    8037 [Repeated 3 time(s)]
    8038 
    8039 > isolde pepflip sel
    8040 
    8041 Flipping the peptide bond for 1 residues 
    8042 
    8043 > isolde pepflip sel
    8044 
    8045 Flipping the peptide bond for 1 residues 
    8046 
    8047 > ui tool show "Ramachandran Plot"
    8048 
    8049 [Repeated 1 time(s)]
    8050 
    8051 > isolde pepflip sel
    8052 
    8053 Flipping the peptide bond for 1 residues 
    8054 
    8055 > select clear
    8056 
    8057 > ui tool show "Ramachandran Plot"
    8058 
    8059 [Repeated 2 time(s)]
    8060 
    8061 > select clear
    8062 
    8063 > ui tool show "Ramachandran Plot"
    8064 
    8065 [Repeated 1 time(s)]
    8066 
    8067 > isolde pepflip sel
    8068 
    8069 Flipping the peptide bond for 1 residues 
    8070 
    8071 > select clear
    8072 
    8073 [Repeated 1 time(s)]
    8074 
    8075 > isolde pepflip sel
    8076 
    8077 Flipping the peptide bond for 1 residues 
    8078 
    8079 > select clear
    8080 
    8081 > isolde pepflip sel
    8082 
    8083 Flipping the peptide bond for 1 residues 
    8084 
    8085 > ui tool show "Ramachandran Plot"
    8086 
    8087 [Repeated 1 time(s)]Traceback (most recent call last): 
    8088 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8089 packages/matplotlib/cbook/__init__.py", line 287, in process 
    8090 func(*args, **kwargs) 
    8091 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    8092 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    8093 on_resize 
    8094 c.draw() 
    8095 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8096 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    8097 self.figure.draw(self.renderer) 
    8098 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8099 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    8100 result = draw(artist, renderer, *args, **kwargs) 
    8101 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8102 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    8103 return draw(artist, renderer) 
    8104 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8105 packages/matplotlib/figure.py", line 2796, in draw 
    8106 artists = self._get_draw_artists(renderer) 
    8107 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8108 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    8109 ax.apply_aspect() 
    8110 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8111 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    8112 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    8113 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8114 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    8115 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    8116 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    8117 
    8118 > select clear
    8119 
    8120 [Repeated 2 time(s)]
    8121 
    8122 > ui tool show "Ramachandran Plot"
    8123 
    8124 [Repeated 2 time(s)]
    8125 
    8126 > select clear
    8127 
    8128 > ui tool show "Ramachandran Plot"
    8129 
    8130 > select clear
    8131 
    8132 [Repeated 1 time(s)]
    8133 
    8134 > ui tool show "Ramachandran Plot"
    8135 
    8136 > select clear
    8137 
    8138 > ui tool show "Ramachandran Plot"
    8139 
    8140 > isolde sim stop
    8141 
    8142 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8143 chains... 
    8144 ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
    8145 standards. 
    8146 ISOLDE: stopped sim 
    8147 
    8148 > ui tool show "Ramachandran Plot"
    8149 
    8150 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8151 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8152 > KSRP.pdb
    8153 
    8154 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8155 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8156 > KSRP.cxs
    8157 
    8158 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8159 
    8160 ——— End of log from Mon Mar 27 09:38:45 2023 ———
    8161 
    8162 opened ChimeraX session 
    8163 
    8164 > isolde start
    8165 
    8166 > ui tool show "Ramachandran Plot"
    8167 
    8168 > view #1/P:240-249
    8169 
    8170 > select #1/P:240-249
    8171 
    8172 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8173 
    8174 > isolde sim start sel
    8175 
    8176 ISOLDE: started sim 
    8177 
    8178 > isolde sim stop discardTo start
    8179 
    8180 reverting to start 
    8181 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8182 chains... 
    8183 ISOLDE: stopped sim 
    8184 
    8185 > select #1/P:240-249
    8186 
    8187 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8188 
    8189 > isolde sim start sel
    8190 
    8191 ISOLDE: started sim 
    8192 
    8193 > isolde sim stop discardTo start
    8194 
    8195 reverting to start 
    8196 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8197 chains... 
    8198 ISOLDE: stopped sim 
    8199 
    8200 > select #1/P:240-249
    8201 
    8202 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8203 
    8204 > isolde sim start sel
    8205 
    8206 ISOLDE: started sim 
    8207 
    8208 > isolde sim stop discardTo start
    8209 
    8210 reverting to start 
    8211 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8212 chains... 
    8213 ISOLDE: stopped sim 
    8214 
    8215 > ui tool show "Ramachandran Plot"
    8216 
    8217 > select clear
    8218 
    8219 > isolde sim start sel
    8220 
    8221 ISOLDE: started sim 
    8222 
    8223 > isolde sim stop discardTo start
    8224 
    8225 reverting to start 
    8226 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8227 chains... 
    8228 ISOLDE: stopped sim 
    8229 
    8230 > select #1/V:92
    8231 
    8232 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8233 
    8234 > isolde sim start sel
    8235 
    8236 ISOLDE: started sim 
    8237 
    8238 > isolde pepflip sel
    8239 
    8240 Flipping the peptide bond for 1 residues 
    8241 
    8242 > select clear
    8243 
    8244 > isolde pepflip sel
    8245 
    8246 Flipping the peptide bond for 1 residues 
    8247 
    8248 > select clear
    8249 
    8250 > ui tool show "Ramachandran Plot"
    8251 
    8252 [Repeated 1 time(s)]
    8253 
    8254 > isolde sim stop
    8255 
    8256 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8257 chains... 
    8258 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8259 standards. 
    8260 ISOLDE: stopped sim 
    8261 
    8262 > isolde sim start sel
    8263 
    8264 ISOLDE: started sim 
    8265 
    8266 > ui tool show "Ramachandran Plot"
    8267 
    8268 > isolde pepflip sel
    8269 
    8270 Flipping the peptide bond for 1 residues 
    8271 
    8272 > select clear
    8273 
    8274 > ui tool show "Ramachandran Plot"
    8275 
    8276 > isolde sim stop
    8277 
    8278 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8279 chains... 
    8280 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8281 standards. 
    8282 ISOLDE: stopped sim 
    8283 
    8284 > isolde sim start sel
    8285 
    8286 ISOLDE: started sim 
    8287 
    8288 > select clear
    8289 
    8290 > isolde pepflip sel
    8291 
    8292 Flipping the peptide bond for 1 residues 
    8293 
    8294 > ui tool show "Ramachandran Plot"
    8295 
    8296 [Repeated 1 time(s)]
    8297 
    8298 > isolde sim stop
    8299 
    8300 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8301 chains... 
    8302 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8303 standards. 
    8304 ISOLDE: stopped sim 
    8305 
    8306 > view #1/V:92
    8307 
    8308 > select #1/V:92
    8309 
    8310 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8311 
    8312 > isolde sim start sel
    8313 
    8314 ISOLDE: started sim 
    8315 
    8316 > ui tool show "Ramachandran Plot"
    8317 
    8318 > isolde pepflip sel
    8319 
    8320 Flipping the peptide bond for 1 residues 
    8321 
    8322 > isolde pepflip sel
    8323 
    8324 Flipping the peptide bond for 1 residues 
    8325 
    8326 > select clear
    8327 
    8328 > isolde pepflip sel
    8329 
    8330 Flipping the peptide bond for 1 residues 
    8331 
    8332 > select clear
    8333 
    8334 > ui tool show "Ramachandran Plot"
    8335 
    8336 > isolde sim stop
    8337 
    8338 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8339 chains... 
    8340 ISOLDE: stopped sim 
    8341 
    8342 > ui tool show "Ramachandran Plot"
    8343 
    8344 > isolde sim start sel
    8345 
    8346 ISOLDE: started sim 
    8347 
    8348 > ui tool show "Ramachandran Plot"
    8349 
    8350 > select clear
    8351 
    8352 > ui tool show "Ramachandran Plot"
    8353 
    8354 > isolde pepflip sel
    8355 
    8356 Flipping the peptide bond for 1 residues 
    8357 
    8358 > select clear
    8359 
    8360 > isolde pepflip sel
    8361 
    8362 Flipping the peptide bond for 1 residues 
    8363 
    8364 > isolde pepflip sel
    8365 
    8366 Flipping the peptide bond for 1 residues 
    8367 
    8368 > ui tool show "Ramachandran Plot"
    8369 
    8370 > select clear
    8371 
    8372 [Repeated 1 time(s)]
    8373 
    8374 > isolde pepflip sel
    8375 
    8376 Flipping the peptide bond for 1 residues 
    8377 
    8378 > isolde pepflip sel
    8379 
    8380 Flipping the peptide bond for 1 residues 
    8381 
    8382 > select clear
    8383 
    8384 > ui tool show "Ramachandran Plot"
    8385 
    8386 > isolde pepflip sel
    8387 
    8388 Flipping the peptide bond for 1 residues 
    8389 
    8390 > select clear
    8391 
    8392 [Repeated 1 time(s)]
    8393 
    8394 > ui tool show "Ramachandran Plot"
    8395 
    8396 > style #1/i:72|/i:75 sphere
    8397 
    8398 Changed 37 atom styles 
    8399 
    8400 > style #1/i:72|/i:75 stick
    8401 
    8402 Changed 37 atom styles 
    8403 
    8404 > select clear
    8405 
    8406 [Repeated 1 time(s)]
    8407 
    8408 > ui tool show "Ramachandran Plot"
    8409 
    8410 > isolde sim stop
    8411 
    8412 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8413 chains... 
    8414 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    8415 standards. 
    8416 ISOLDE: stopped sim 
    8417 
    8418 > ui tool show "Ramachandran Plot"
    8419 
    8420 > isolde sim start sel
    8421 
    8422 ISOLDE: started sim 
    8423 
    8424 > isolde pepflip sel
    8425 
    8426 Flipping the peptide bond for 1 residues 
    8427 
    8428 > select clear
    8429 
    8430 [Repeated 3 time(s)]
    8431 
    8432 > isolde pepflip sel
    8433 
    8434 Flipping the peptide bond for 1 residues 
    8435 
    8436 > isolde pepflip sel
    8437 
    8438 Flipping the peptide bond for 1 residues 
    8439 
    8440 > isolde pepflip sel
    8441 
    8442 Flipping the peptide bond for 1 residues 
    8443 
    8444 > select clear
    8445 
    8446 [Repeated 1 time(s)]
    8447 
    8448 > isolde pepflip sel
    8449 
    8450 Flipping the peptide bond for 1 residues 
    8451 
    8452 > isolde pepflip sel
    8453 
    8454 Flipping the peptide bond for 1 residues 
    8455 
    8456 > isolde pepflip sel
    8457 
    8458 Flipping the peptide bond for 1 residues 
    8459 
    8460 > isolde pepflip sel
    8461 
    8462 Flipping the peptide bond for 1 residues 
    8463 
    8464 > isolde pepflip sel
    8465 
    8466 Flipping the peptide bond for 1 residues 
    8467 
    8468 > isolde pepflip sel
    8469 
    8470 Flipping the peptide bond for 1 residues 
    8471 
    8472 > select clear
    8473 
    8474 [Repeated 1 time(s)]
    8475 
    8476 > ui tool show "Ramachandran Plot"
    8477 
    8478 > select clear
    8479 
    8480 [Repeated 1 time(s)]
    8481 
    8482 > ui tool show "Ramachandran Plot"
    8483 
    8484 [Repeated 1 time(s)]
    8485 
    8486 > isolde sim stop
    8487 
    8488 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8489 chains... 
    8490 ISOLDE: stopped sim 
    8491 
    8492 > ui tool show "Ramachandran Plot"
    8493 
    8494 > isolde sim start sel
    8495 
    8496 ISOLDE: started sim 
    8497 
    8498 > isolde pepflip sel
    8499 
    8500 Flipping the peptide bond for 1 residues 
    8501 
    8502 > isolde pepflip sel
    8503 
    8504 Flipping the peptide bond for 1 residues 
    8505 
    8506 > isolde pepflip sel
    8507 
    8508 Flipping the peptide bond for 1 residues 
    8509 
    8510 > select clear
    8511 
    8512 > ui tool show "Ramachandran Plot"
    8513 
    8514 > isolde pepflip sel
    8515 
    8516 Flipping the peptide bond for 1 residues 
    8517 
    8518 > select clear
    8519 
    8520 > ui tool show "Ramachandran Plot"
    8521 
    8522 [Repeated 1 time(s)]
    8523 
    8524 > isolde sim stop
    8525 
    8526 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8527 chains... 
    8528 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8529 standards. 
    8530 ISOLDE: stopped sim 
    8531 
    8532 > ui tool show "Ramachandran Plot"
    8533 
    8534 [Repeated 1 time(s)]
    8535 
    8536 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8537 > mut8-no-C-ter/20-continuingNew-FirstSteps-RefiningBEFORE-Annealing.cxs
    8538 
    8539 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8540 
    8541 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8542 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8543 > KSRP.pdb
    8544 
    8545 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8546 > mut8-no-C-ter/20-continuingNew-FirstSteps-RefiningBEFORE-Annealing.pdb
    8547 
    8548 > isolde sim start sel
    8549 
    8550 ISOLDE: started sim 
    8551 
    8552 > isolde sim stop discardTo start
    8553 
    8554 reverting to start 
    8555 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8556 chains... 
    8557 ISOLDE: stopped sim 
    8558 
    8559 > isolde sim start sel
    8560 
    8561 ISOLDE: started sim 
    8562 
    8563 > isolde pepflip sel
    8564 
    8565 Flipping the peptide bond for 1 residues 
    8566 
    8567 > isolde pepflip sel
    8568 
    8569 Flipping the peptide bond for 1 residues 
    8570 
    8571 > select clear
    8572 
    8573 > ui tool show "Ramachandran Plot"
    8574 
    8575 [Repeated 1 time(s)]
    8576 
    8577 > isolde sim pause
    8578 
    8579 > ui tool show "Ramachandran Plot"
    8580 
    8581 > isolde sim resume
    8582 
    8583 > ui tool show "Ramachandran Plot"
    8584 
    8585 > isolde pepflip sel
    8586 
    8587 Flipping the peptide bond for 1 residues 
    8588 
    8589 > isolde pepflip sel
    8590 
    8591 Flipping the peptide bond for 1 residues 
    8592 
    8593 > select clear
    8594 
    8595 > isolde pepflip sel
    8596 
    8597 Flipping the peptide bond for 1 residues 
    8598 
    8599 > isolde pepflip sel
    8600 
    8601 Flipping the peptide bond for 1 residues 
    8602 
    8603 > isolde sim stop
    8604 
    8605 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8606 chains... 
    8607 ISOLDE: stopped sim 
    8608 
    8609 > isolde sim start sel
    8610 
    8611 ISOLDE: started sim 
    8612 
    8613 > select clear
    8614 
    8615 > ui tool show "Ramachandran Plot"
    8616 
    8617 [Repeated 2 time(s)]
    8618 
    8619 > isolde pepflip sel
    8620 
    8621 Flipping the peptide bond for 1 residues 
    8622 
    8623 > ui tool show "Ramachandran Plot"
    8624 
    8625 [Repeated 1 time(s)]
    8626 
    8627 > select clear
    8628 
    8629 > ui tool show "Ramachandran Plot"
    8630 
    8631 > isolde sim stop
    8632 
    8633 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8634 chains... 
    8635 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8636 standards. 
    8637 ISOLDE: stopped sim 
    8638 
    8639 > isolde sim start sel
    8640 
    8641 ISOLDE: started sim 
    8642 
    8643 > ui tool show "Ramachandran Plot"
    8644 
    8645 > select clear
    8646 
    8647 > ui tool show "Ramachandran Plot"
    8648 
    8649 > select clear
    8650 
    8651 > ui tool show "Ramachandran Plot"
    8652 
    8653 > select clear
    8654 
    8655 > ui tool show "Ramachandran Plot"
    8656 
    8657 [Repeated 1 time(s)]
    8658 
    8659 > isolde sim stop
    8660 
    8661 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8662 chains... 
    8663 ISOLDE: stopped sim 
    8664 
    8665 > ui tool show "Ramachandran Plot"
    8666 
    8667 > isolde sim start sel
    8668 
    8669 ISOLDE: started sim 
    8670 
    8671 > ui tool show "Ramachandran Plot"
    8672 
    8673 > select clear
    8674 
    8675 [Repeated 1 time(s)]
    8676 
    8677 > isolde pepflip sel
    8678 
    8679 Flipping the peptide bond for 1 residues 
    8680 
    8681 > select clear
    8682 
    8683 > ui tool show "Ramachandran Plot"
    8684 
    8685 > isolde sim stop
    8686 
    8687 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8688 chains... 
    8689 ISOLDE: stopped sim 
    8690 
    8691 > ui tool show "Ramachandran Plot"
    8692 
    8693 > isolde sim start sel
    8694 
    8695 ISOLDE: started sim 
    8696 
    8697 > ui tool show "Ramachandran Plot"
    8698 
    8699 [Repeated 1 time(s)]
    8700 
    8701 > isolde sim stop
    8702 
    8703 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8704 chains... 
    8705 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8706 standards. 
    8707 ISOLDE: stopped sim 
    8708 
    8709 > isolde sim start sel
    8710 
    8711 ISOLDE: started sim 
    8712 
    8713 > select clear
    8714 
    8715 [Repeated 2 time(s)]
    8716 
    8717 > isolde pepflip sel
    8718 
    8719 Flipping the peptide bond for 1 residues 
    8720 
    8721 > isolde pepflip sel
    8722 
    8723 Flipping the peptide bond for 1 residues 
    8724 
    8725 > isolde pepflip sel
    8726 
    8727 Flipping the peptide bond for 1 residues 
    8728 
    8729 > isolde pepflip sel
    8730 
    8731 Flipping the peptide bond for 1 residues 
    8732 
    8733 > ui tool show "Ramachandran Plot"
    8734 
    8735 > isolde pepflip sel
    8736 
    8737 Flipping the peptide bond for 1 residues 
    8738 
    8739 > select clear
    8740 
    8741 > isolde pepflip sel
    8742 
    8743 Flipping the peptide bond for 1 residues 
    8744 
    8745 > isolde pepflip sel
    8746 
    8747 Flipping the peptide bond for 1 residues 
    8748 
    8749 > select clear
    8750 
    8751 [Repeated 1 time(s)]
    8752 
    8753 > isolde pepflip sel
    8754 
    8755 Flipping the peptide bond for 1 residues 
    8756 
    8757 > ui tool show "Ramachandran Plot"
    8758 
    8759 > select clear
    8760 
    8761 > ui tool show "Ramachandran Plot"
    8762 
    8763 [Repeated 1 time(s)]
    8764 
    8765 > isolde sim stop
    8766 
    8767 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8768 chains... 
    8769 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8770 standards. 
    8771 ISOLDE: stopped sim 
    8772 
    8773 > ui tool show "Ramachandran Plot"
    8774 
    8775 > isolde sim start sel
    8776 
    8777 ISOLDE: started sim 
    8778 
    8779 > ui tool show "Ramachandran Plot"
    8780 
    8781 > select clear
    8782 
    8783 > isolde sim stop
    8784 
    8785 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8786 chains... 
    8787 ISOLDE: stopped sim 
    8788 
    8789 > ui tool show "Ramachandran Plot"
    8790 
    8791 > isolde sim start sel
    8792 
    8793 ISOLDE: started sim 
    8794 
    8795 > isolde pepflip sel
    8796 
    8797 Flipping the peptide bond for 1 residues 
    8798 
    8799 > select clear
    8800 
    8801 > isolde pepflip sel
    8802 
    8803 Flipping the peptide bond for 1 residues 
    8804 
    8805 > select clear
    8806 
    8807 > isolde pepflip sel
    8808 
    8809 Flipping the peptide bond for 1 residues 
    8810 
    8811 > isolde pepflip sel
    8812 
    8813 Flipping the peptide bond for 1 residues 
    8814 
    8815 > select clear
    8816 
    8817 > ui tool show "Ramachandran Plot"
    8818 
    8819 > select clear
    8820 
    8821 [Repeated 2 time(s)]
    8822 
    8823 > ui tool show "Ramachandran Plot"
    8824 
    8825 > isolde pepflip sel
    8826 
    8827 Flipping the peptide bond for 1 residues 
    8828 
    8829 > isolde pepflip sel
    8830 
    8831 Flipping the peptide bond for 1 residues 
    8832 
    8833 > ui tool show "Ramachandran Plot"
    8834 
    8835 > select clear
    8836 
    8837 > isolde sim stop
    8838 
    8839 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8840 chains... 
    8841 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8842 standards. 
    8843 ISOLDE: stopped sim 
    8844 
    8845 > ui tool show "Ramachandran Plot"
    8846 
    8847 [Repeated 1 time(s)]
    8848 
    8849 > isolde sim start sel
    8850 
    8851 ISOLDE: started sim 
    8852 
    8853 > select clear
    8854 
    8855 > ui tool show "Ramachandran Plot"
    8856 
    8857 [Repeated 1 time(s)]
    8858 
    8859 > view #1/d:155
    8860 
    8861 > select clear
    8862 
    8863 > isolde sim stop
    8864 
    8865 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8866 chains... 
    8867 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8868 standards. 
    8869 ISOLDE: stopped sim 
    8870 
    8871 > ui tool show "Ramachandran Plot"
    8872 
    8873 > isolde sim start sel
    8874 
    8875 ISOLDE: started sim 
    8876 
    8877 > isolde pepflip sel
    8878 
    8879 Flipping the peptide bond for 1 residues 
    8880 
    8881 > ui tool show "Ramachandran Plot"
    8882 
    8883 > select clear
    8884 
    8885 > isolde sim pause
    8886 
    8887 > isolde sim resume
    8888 
    8889 > ui tool show "Ramachandran Plot"
    8890 
    8891 > isolde sim stop
    8892 
    8893 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8894 chains... 
    8895 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    8896 standards. 
    8897 ISOLDE: stopped sim 
    8898 
    8899 > ui tool show "Ramachandran Plot"
    8900 
    8901 > isolde sim start sel
    8902 
    8903 ISOLDE: started sim 
    8904 
    8905 > isolde pepflip sel
    8906 
    8907 Flipping the peptide bond for 1 residues 
    8908 
    8909 > isolde pepflip sel
    8910 
    8911 Flipping the peptide bond for 1 residues 
    8912 
    8913 > isolde pepflip sel
    8914 
    8915 Flipping the peptide bond for 1 residues 
    8916 
    8917 > isolde pepflip sel
    8918 
    8919 Flipping the peptide bond for 1 residues 
    8920 
    8921 > isolde pepflip sel
    8922 
    8923 Flipping the peptide bond for 1 residues 
    8924 
    8925 > select clear
    8926 
    8927 > isolde pepflip sel
    8928 
    8929 Flipping the peptide bond for 1 residues 
    8930 
    8931 > isolde pepflip sel
    8932 
    8933 Flipping the peptide bond for 1 residues 
    8934 
    8935 > isolde pepflip sel
    8936 
    8937 Flipping the peptide bond for 1 residues 
    8938 
    8939 > isolde pepflip sel
    8940 
    8941 Flipping the peptide bond for 1 residues 
    8942 
    8943 > select clear
    8944 
    8945 > ui tool show "Ramachandran Plot"
    8946 
    8947 > isolde sim pause
    8948 
    8949 > isolde sim resume
    8950 
    8951 > ui tool show "Ramachandran Plot"
    8952 
    8953 > isolde sim stop
    8954 
    8955 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8956 chains... 
    8957 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    8958 standards. 
    8959 ISOLDE: stopped sim 
    8960 
    8961 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8962 > mut8-no-C-ter/20-1-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    8963 > step20-1.cxs
    8964 
    8965 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8966 
    8967 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8968 > mut8-no-C-ter/20-1-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    8969 > step20-1.pdb
    8970 
    8971 > ui tool show "Ramachandran Plot"
    8972 
    8973 > isolde sim start sel
    8974 
    8975 ISOLDE: started sim 
    8976 
    8977 > select clear
    8978 
    8979 > ui tool show "Ramachandran Plot"
    8980 
    8981 > select clear
    8982 
    8983 > isolde sim stop
    8984 
    8985 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8986 chains... 
    8987 ISOLDE: stopped sim 
    8988 
    8989 > ui tool show "Ramachandran Plot"
    8990 
    8991 > isolde sim start sel
    8992 
    8993 ISOLDE: started sim 
    8994 
    8995 > ui tool show "Ramachandran Plot"
    8996 
    8997 > select clear
    8998 
    8999 > ui tool show "Ramachandran Plot"
    9000 
    9001 > isolde pepflip sel
    9002 
    9003 Flipping the peptide bond for 1 residues 
    9004 
    9005 > select clear
    9006 
    9007 > isolde pepflip sel
    9008 
    9009 Flipping the peptide bond for 1 residues 
    9010 
    9011 > select clear
    9012 
    9013 > ui tool show "Ramachandran Plot"
    9014 
    9015 > select clear
    9016 
    9017 [Repeated 1 time(s)]
    9018 
    9019 > view #1/q:29
    9020 
    9021 > isolde sim pause
    9022 
    9023 > ui tool show "Ramachandran Plot"
    9024 
    9025 Traceback (most recent call last): 
    9026 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9027 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9028 func(*args, **kwargs) 
    9029 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9030 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9031 on_resize 
    9032 c.draw() 
    9033 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9034 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9035 self.figure.draw(self.renderer) 
    9036 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9037 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9038 result = draw(artist, renderer, *args, **kwargs) 
    9039 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9040 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9041 return draw(artist, renderer) 
    9042 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9043 packages/matplotlib/figure.py", line 2796, in draw 
    9044 artists = self._get_draw_artists(renderer) 
    9045 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9046 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9047 ax.apply_aspect() 
    9048 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9049 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9050 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9051 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9052 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9053 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9054 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9055 
    9056 > ui tool show "Ramachandran Plot"
    9057 
    9058 [Repeated 1 time(s)]Traceback (most recent call last): 
    9059 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9060 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9061 func(*args, **kwargs) 
    9062 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9063 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9064 on_resize 
    9065 c.draw() 
    9066 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9067 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9068 self.figure.draw(self.renderer) 
    9069 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9070 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9071 result = draw(artist, renderer, *args, **kwargs) 
    9072 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9073 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9074 return draw(artist, renderer) 
    9075 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9076 packages/matplotlib/figure.py", line 2796, in draw 
    9077 artists = self._get_draw_artists(renderer) 
    9078 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9079 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9080 ax.apply_aspect() 
    9081 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9082 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9083 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9084 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9085 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9086 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9087 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9088 
    9089 > isolde sim resume
    9090 
    9091 > isolde sim pause
    9092 
    9093 > isolde sim resume
    9094 
    9095 > select clear
    9096 
    9097 > isolde pepflip sel
    9098 
    9099 Flipping the peptide bond for 1 residues 
    9100 
    9101 > select clear
    9102 
    9103 > isolde sim pause
    9104 
    9105 > isolde sim resume
    9106 
    9107 > select clear
    9108 
    9109 > isolde pepflip sel
    9110 
    9111 Flipping the peptide bond for 1 residues 
    9112 
    9113 > isolde pepflip sel
    9114 
    9115 Flipping the peptide bond for 1 residues 
    9116 
    9117 > select clear
    9118 
    9119 > ui tool show "Ramachandran Plot"
    9120 
    9121 > select clear
    9122 
    9123 > isolde sim pause
    9124 
    9125 > ui tool show "Ramachandran Plot"
    9126 
    9127 > isolde sim resume
    9128 
    9129 > select clear
    9130 
    9131 > isolde pepflip sel
    9132 
    9133 Flipping the peptide bond for 1 residues 
    9134 
    9135 > isolde pepflip sel
    9136 
    9137 Flipping the peptide bond for 1 residues 
    9138 
    9139 > isolde pepflip sel
    9140 
    9141 Flipping the peptide bond for 1 residues 
    9142 
    9143 > isolde pepflip sel
    9144 
    9145 Flipping the peptide bond for 1 residues 
    9146 
    9147 > isolde pepflip sel
    9148 
    9149 Flipping the peptide bond for 1 residues 
    9150 
    9151 > isolde pepflip sel
    9152 
    9153 Flipping the peptide bond for 1 residues 
    9154 
    9155 > ui tool show "Ramachandran Plot"
    9156 
    9157 > select clear
    9158 
    9159 > isolde sim pause
    9160 
    9161 > ui tool show "Ramachandran Plot"
    9162 
    9163 > select clear
    9164 
    9165 > isolde sim resume
    9166 
    9167 > isolde pepflip sel
    9168 
    9169 Flipping the peptide bond for 1 residues 
    9170 
    9171 > select clear
    9172 
    9173 > isolde pepflip sel
    9174 
    9175 Flipping the peptide bond for 1 residues 
    9176 
    9177 > ui tool show "Ramachandran Plot"
    9178 
    9179 > select clear
    9180 
    9181 > isolde sim pause
    9182 
    9183 > isolde sim resume
    9184 
    9185 > ui tool show "Ramachandran Plot"
    9186 
    9187 [Repeated 2 time(s)]
    9188 
    9189 > select clear
    9190 
    9191 > isolde pepflip sel
    9192 
    9193 Flipping the peptide bond for 1 residues 
    9194 
    9195 > ui tool show "Ramachandran Plot"
    9196 
    9197 > select clear
    9198 
    9199 [Repeated 2 time(s)]
    9200 
    9201 > ui tool show "Ramachandran Plot"
    9202 
    9203 > select clear
    9204 
    9205 > ui tool show "Ramachandran Plot"
    9206 
    9207 Traceback (most recent call last): 
    9208 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9209 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9210 func(*args, **kwargs) 
    9211 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9212 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9213 on_resize 
    9214 c.draw() 
    9215 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9216 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9217 self.figure.draw(self.renderer) 
    9218 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9219 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9220 result = draw(artist, renderer, *args, **kwargs) 
    9221 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9222 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9223 return draw(artist, renderer) 
    9224 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9225 packages/matplotlib/figure.py", line 2796, in draw 
    9226 artists = self._get_draw_artists(renderer) 
    9227 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9228 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9229 ax.apply_aspect() 
    9230 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9231 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9232 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9233 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9234 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9235 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9236 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9237 
    9238 > select clear
    9239 
    9240 > ui tool show "Ramachandran Plot"
    9241 
    9242 > select clear
    9243 
    9244 > ui tool show "Ramachandran Plot"
    9245 
    9246 > style #1/q:34|/q:39 sphere
    9247 
    9248 Changed 38 atom styles 
    9249 
    9250 > style #1/q:34|/q:39 stick
    9251 
    9252 Changed 38 atom styles 
    9253 
    9254 > ui tool show "Ramachandran Plot"
    9255 
    9256 > select clear
    9257 
    9258 > isolde sim pause
    9259 
    9260 > style #1/q:34|/q:39|/q:32 sphere
    9261 
    9262 Changed 57 atom styles 
    9263 
    9264 > style #1/q:34|/q:39|/q:32 stick
    9265 
    9266 Changed 57 atom styles 
    9267 
    9268 > ui tool show "Ramachandran Plot"
    9269 
    9270 > isolde sim resume
    9271 
    9272 > isolde sim stop
    9273 
    9274 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9275 chains... 
    9276 ISOLDE: stopped sim 
    9277 
    9278 > isolde sim start sel
    9279 
    9280 ISOLDE: started sim 
    9281 
    9282 > select clear
    9283 
    9284 > isolde pepflip sel
    9285 
    9286 Flipping the peptide bond for 1 residues 
    9287 
    9288 > isolde pepflip sel
    9289 
    9290 Flipping the peptide bond for 1 residues 
    9291 
    9292 > isolde pepflip sel
    9293 
    9294 Flipping the peptide bond for 1 residues 
    9295 
    9296 > isolde pepflip sel
    9297 
    9298 Flipping the peptide bond for 1 residues 
    9299 
    9300 > isolde pepflip sel
    9301 
    9302 Flipping the peptide bond for 1 residues 
    9303 
    9304 > isolde pepflip sel
    9305 
    9306 Flipping the peptide bond for 1 residues 
    9307 
    9308 > isolde pepflip sel
    9309 
    9310 Flipping the peptide bond for 1 residues 
    9311 
    9312 > isolde sim pause
    9313 
    9314 > isolde sim resume
    9315 
    9316 > ui tool show "Ramachandran Plot"
    9317 
    9318 [Repeated 1 time(s)]
    9319 
    9320 > select clear
    9321 
    9322 [Repeated 2 time(s)]
    9323 
    9324 > ui tool show "Ramachandran Plot"
    9325 
    9326 [Repeated 2 time(s)]
    9327 
    9328 > isolde pepflip sel
    9329 
    9330 Flipping the peptide bond for 1 residues 
    9331 
    9332 > select clear
    9333 
    9334 > isolde pepflip sel
    9335 
    9336 Flipping the peptide bond for 1 residues 
    9337 
    9338 > isolde pepflip sel
    9339 
    9340 Flipping the peptide bond for 1 residues 
    9341 
    9342 > select clear
    9343 
    9344 [Repeated 2 time(s)]
    9345 
    9346 > style #1/q:23-24 sphere
    9347 
    9348 Changed 35 atom styles 
    9349 
    9350 > style #1/q:23-24 stick
    9351 
    9352 Changed 35 atom styles 
    9353 
    9354 > ui tool show "Ramachandran Plot"
    9355 
    9356 > select clear
    9357 
    9358 > ui tool show "Ramachandran Plot"
    9359 
    9360 > select clear
    9361 
    9362 [Repeated 2 time(s)]
    9363 
    9364 > isolde sim pause
    9365 
    9366 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    9367 > mut8-no-C-ter/20-2-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    9368 > step20-2.pdb
    9369 
    9370 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    9371 > mut8-no-C-ter/20-2-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    9372 > step20-2.cxs
    9373 
    9374 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    9375 
    9376 > isolde sim resume
    9377 
    9378 > ui tool show "Ramachandran Plot"
    9379 
    9380 Traceback (most recent call last): 
    9381 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9382 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9383 func(*args, **kwargs) 
    9384 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9385 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9386 on_resize 
    9387 c.draw() 
    9388 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9389 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9390 self.figure.draw(self.renderer) 
    9391 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9392 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9393 result = draw(artist, renderer, *args, **kwargs) 
    9394 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9395 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9396 return draw(artist, renderer) 
    9397 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9398 packages/matplotlib/figure.py", line 2796, in draw 
    9399 artists = self._get_draw_artists(renderer) 
    9400 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9401 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9402 ax.apply_aspect() 
    9403 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9404 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9405 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9406 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9407 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9408 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9409 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9410 
    9411 > isolde sim pause
    9412 
    9413 > view #1/q:24
    9414 
    9415 > isolde sim resume
    9416 
    9417 > select clear
    9418 
    9419 [Repeated 2 time(s)]
    9420 
    9421 > isolde pepflip sel
    9422 
    9423 Flipping the peptide bond for 1 residues 
    9424 
    9425 > select clear
    9426 
    9427 [Repeated 4 time(s)]
    9428 
    9429 > ui tool show "Ramachandran Plot"
    9430 
    9431 > style #1/i:23-24|/n:68 sphere
    9432 
    9433 Changed 53 atom styles 
    9434 
    9435 > style #1/i:23-24|/n:68 stick]
    9436 
    9437 Expected a keyword 
    9438 
    9439 > style #1/i:23-24|/n:68 stick
    9440 
    9441 Changed 53 atom styles 
    9442 
    9443 > style #1/q:23-24|/n:68 sphere
    9444 
    9445 Changed 59 atom styles 
    9446 
    9447 > style #1/q:23-24|/n:68 stick
    9448 
    9449 Changed 59 atom styles 
    9450 
    9451 > ui tool show "Ramachandran Plot"
    9452 
    9453 > isolde sim stop
    9454 
    9455 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9456 chains... 
    9457 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    9458 standards. 
    9459 ISOLDE: stopped sim 
    9460 
    9461 > view #1/q:41
    9462 
    9463 > select #1/q:41
    9464 
    9465 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9466 
    9467 > isolde sim start sel
    9468 
    9469 ISOLDE: started sim 
    9470 
    9471 > ui tool show "Ramachandran Plot"
    9472 
    9473 > select clear
    9474 
    9475 > isolde sim stop
    9476 
    9477 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9478 chains... 
    9479 ISOLDE: stopped sim 
    9480 
    9481 > isolde sim start sel
    9482 
    9483 ISOLDE: started sim 
    9484 
    9485 > ui tool show "Ramachandran Plot"
    9486 
    9487 > select clear
    9488 
    9489 [Repeated 1 time(s)]
    9490 
    9491 > isolde pepflip sel
    9492 
    9493 Flipping the peptide bond for 1 residues 
    9494 
    9495 > isolde pepflip sel
    9496 
    9497 Flipping the peptide bond for 1 residues 
    9498 
    9499 > isolde pepflip sel
    9500 
    9501 Flipping the peptide bond for 1 residues 
    9502 
    9503 > isolde sim stop discardTo start
    9504 
    9505 reverting to start 
    9506 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9507 chains... 
    9508 ISOLDE: stopped sim 
    9509 
    9510 > isolde sim start sel
    9511 
    9512 ISOLDE: started sim 
    9513 
    9514 > ui tool show "Ramachandran Plot"
    9515 
    9516 > select clear
    9517 
    9518 > isolde pepflip sel
    9519 
    9520 Flipping the peptide bond for 1 residues 
    9521 
    9522 > select clear
    9523 
    9524 > isolde pepflip sel
    9525 
    9526 Flipping the peptide bond for 1 residues 
    9527 
    9528 > isolde pepflip sel
    9529 
    9530 Flipping the peptide bond for 1 residues 
    9531 
    9532 > select clear
    9533 
    9534 > isolde pepflip sel
    9535 
    9536 Flipping the peptide bond for 1 residues 
    9537 
    9538 > isolde pepflip sel
    9539 
    9540 Flipping the peptide bond for 1 residues 
    9541 
    9542 > isolde pepflip sel
    9543 
    9544 Flipping the peptide bond for 1 residues 
    9545 
    9546 > isolde pepflip sel
    9547 
    9548 Flipping the peptide bond for 1 residues 
    9549 
    9550 > isolde pepflip sel
    9551 
    9552 Flipping the peptide bond for 1 residues 
    9553 
    9554 > select clear
    9555 
    9556 > ui tool show "Ramachandran Plot"
    9557 
    9558 [Repeated 1 time(s)]
    9559 
    9560 > isolde sim stop
    9561 
    9562 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9563 chains... 
    9564 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    9565 standards. 
    9566 ISOLDE: stopped sim 
    9567 
    9568 > view #1/q:41
    9569 
    9570 > select #1/q:41
    9571 
    9572 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9573 
    9574 > isolde sim start sel
    9575 
    9576 ISOLDE: started sim 
    9577 
    9578 > ui tool show "Ramachandran Plot"
    9579 
    9580 > select clear
    9581 
    9582 > isolde sim stop
    9583 
    9584 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9585 chains... 
    9586 ISOLDE: stopped sim 
    9587 
    9588 > ui tool show "Ramachandran Plot"
    9589 
    9590 > isolde sim start sel
    9591 
    9592 ISOLDE: started sim 
    9593 
    9594 > isolde pepflip sel
    9595 
    9596 Flipping the peptide bond for 1 residues 
    9597 
    9598 > isolde pepflip sel
    9599 
    9600 Flipping the peptide bond for 1 residues 
    9601 
    9602 > select clear
    9603 
    9604 > ui tool show "Ramachandran Plot"
    9605 
    9606 > isolde pepflip sel
    9607 
    9608 Flipping the peptide bond for 1 residues 
    9609 
    9610 > select clear
    9611 
    9612 > ui tool show "Ramachandran Plot"
    9613 
    9614 > select clear
    9615 
    9616 [Repeated 1 time(s)]
    9617 
    9618 > isolde sim stop
    9619 
    9620 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9621 chains... 
    9622 ISOLDE: stopped sim 
    9623 
    9624 > ui tool show "Ramachandran Plot"
    9625 
    9626 > isolde sim start sel
    9627 
    9628 ISOLDE: started sim 
    9629 
    9630 > ui tool show "Ramachandran Plot"
    9631 
    9632 > select clear
    9633 
    9634 > isolde sim stop
    9635 
    9636 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9637 chains... 
    9638 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9639 standards. 
    9640 ISOLDE: stopped sim 
    9641 
    9642 > ui tool show "Ramachandran Plot"
    9643 
    9644 > isolde sim start sel
    9645 
    9646 ISOLDE: started sim 
    9647 
    9648 > ui tool show "Ramachandran Plot"
    9649 
    9650 > select clear
    9651 
    9652 > ui tool show "Ramachandran Plot"
    9653 
    9654 > isolde sim stop
    9655 
    9656 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9657 chains... 
    9658 ISOLDE: stopped sim 
    9659 
    9660 > ui tool show "Ramachandran Plot"
    9661 
    9662 > isolde sim start sel
    9663 
    9664 ISOLDE: started sim 
    9665 
    9666 > ui tool show "Ramachandran Plot"
    9667 
    9668 > isolde pepflip sel
    9669 
    9670 Flipping the peptide bond for 1 residues 
    9671 
    9672 > isolde pepflip sel
    9673 
    9674 Flipping the peptide bond for 1 residues 
    9675 
    9676 > isolde pepflip sel
    9677 
    9678 Flipping the peptide bond for 1 residues 
    9679 
    9680 > isolde pepflip sel
    9681 
    9682 Flipping the peptide bond for 1 residues 
    9683 
    9684 > select clear
    9685 
    9686 [Repeated 1 time(s)]
    9687 
    9688 > isolde pepflip sel
    9689 
    9690 Flipping the peptide bond for 1 residues 
    9691 
    9692 > select clear
    9693 
    9694 [Repeated 1 time(s)]
    9695 
    9696 > ui tool show "Ramachandran Plot"
    9697 
    9698 > select clear
    9699 
    9700 > ui tool show "Ramachandran Plot"
    9701 
    9702 > select clear
    9703 
    9704 > isolde pepflip sel
    9705 
    9706 Flipping the peptide bond for 1 residues 
    9707 
    9708 > select clear
    9709 
    9710 [Repeated 2 time(s)]
    9711 
    9712 > ui tool show "Ramachandran Plot"
    9713 
    9714 > select clear
    9715 
    9716 > isolde sim stop
    9717 
    9718 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9719 chains... 
    9720 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    9721 standards. 
    9722 ISOLDE: stopped sim 
    9723 
    9724 > ui tool show "Ramachandran Plot"
    9725 
    9726 > isolde sim start sel
    9727 
    9728 ISOLDE: started sim 
    9729 
    9730 > isolde pepflip sel
    9731 
    9732 Flipping the peptide bond for 1 residues 
    9733 
    9734 > isolde pepflip sel
    9735 
    9736 Flipping the peptide bond for 1 residues 
    9737 
    9738 > isolde pepflip sel
    9739 
    9740 Flipping the peptide bond for 1 residues 
    9741 
    9742 > select clear
    9743 
    9744 > isolde pepflip sel
    9745 
    9746 Flipping the peptide bond for 1 residues 
    9747 
    9748 > isolde pepflip sel
    9749 
    9750 Flipping the peptide bond for 1 residues 
    9751 
    9752 > select clear
    9753 
    9754 > isolde pepflip sel
    9755 
    9756 Flipping the peptide bond for 1 residues 
    9757 
    9758 > isolde pepflip sel
    9759 
    9760 Flipping the peptide bond for 1 residues 
    9761 
    9762 > select clear
    9763 
    9764 [Repeated 1 time(s)]
    9765 
    9766 > ui tool show "Ramachandran Plot"
    9767 
    9768 > select clear
    9769 
    9770 > isolde pepflip sel
    9771 
    9772 Flipping the peptide bond for 1 residues 
    9773 
    9774 > select clear
    9775 
    9776 [Repeated 2 time(s)]
    9777 
    9778 > ui tool show "Ramachandran Plot"
    9779 
    9780 > select clear
    9781 
    9782 [Repeated 2 time(s)]
    9783 
    9784 > isolde pepflip sel
    9785 
    9786 Flipping the peptide bond for 1 residues 
    9787 
    9788 > select clear
    9789 
    9790 [Repeated 1 time(s)]
    9791 
    9792 > isolde pepflip sel
    9793 
    9794 Flipping the peptide bond for 1 residues 
    9795 
    9796 > isolde pepflip sel
    9797 
    9798 Flipping the peptide bond for 1 residues 
    9799 
    9800 > isolde pepflip sel
    9801 
    9802 Flipping the peptide bond for 1 residues 
    9803 
    9804 > select clear
    9805 
    9806 > isolde sim pause
    9807 
    9808 > isolde sim resume
    9809 
    9810 > isolde sim stop
    9811 
    9812 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9813 chains... 
    9814 ISOLDE: stopped sim 
    9815 
    9816 > select #1/o:74-81|/o:12
    9817 
    9818 140 atoms, 138 bonds, 9 residues, 1 model selected 
    9819 
    9820 > isolde sim start sel
    9821 
    9822 ISOLDE: started sim 
    9823 
    9824 > isolde pepflip sel
    9825 
    9826 Flipping the peptide bond for 1 residues 
    9827 
    9828 Multiple residues selected! Going to the first... 
    9829 
    9830 > view #1/o:74
    9831 
    9832 > select clear
    9833 
    9834 [Repeated 3 time(s)]
    9835 
    9836 > ui tool show "Ramachandran Plot"
    9837 
    9838 > isolde pepflip sel
    9839 
    9840 Flipping the peptide bond for 1 residues 
    9841 
    9842 > isolde pepflip sel
    9843 
    9844 Flipping the peptide bond for 1 residues 
    9845 
    9846 > select clear
    9847 
    9848 > isolde pepflip sel
    9849 
    9850 Flipping the peptide bond for 1 residues 
    9851 
    9852 > select clear
    9853 
    9854 > ui tool show "Ramachandran Plot"
    9855 
    9856 > view #1/o:74
    9857 
    9858 > select clear
    9859 
    9860 > ui tool show "Ramachandran Plot"
    9861 
    9862 > select clear
    9863 
    9864 [Repeated 1 time(s)]Traceback (most recent call last): 
    9865 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9866 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9867 func(*args, **kwargs) 
    9868 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9869 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9870 on_resize 
    9871 c.draw() 
    9872 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9873 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9874 self.figure.draw(self.renderer) 
    9875 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9876 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9877 result = draw(artist, renderer, *args, **kwargs) 
    9878 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9879 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9880 return draw(artist, renderer) 
    9881 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9882 packages/matplotlib/figure.py", line 2796, in draw 
    9883 artists = self._get_draw_artists(renderer) 
    9884 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9885 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9886 ax.apply_aspect() 
    9887 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9888 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9889 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9890 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9891 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9892 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9893 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9894 
    9895 > select clear
    9896 
    9897 > isolde pepflip sel
    9898 
    9899 Flipping the peptide bond for 1 residues 
    9900 
    9901 > isolde pepflip sel
    9902 
    9903 Flipping the peptide bond for 1 residues 
    9904 
    9905 > select clear
    9906 
    9907 [Repeated 1 time(s)]
    9908 
    9909 > view #1/o:74
    9910 
    9911 > isolde sim pause
    9912 
    9913 > ui tool show "Ramachandran Plot"
    9914 
    9915 > isolde sim resume
    9916 
    9917 > ui tool show "Ramachandran Plot"
    9918 
    9919 > select clear
    9920 
    9921 > ui tool show "Ramachandran Plot"
    9922 
    9923 > isolde sim pause
    9924 
    9925 > ui tool show "Ramachandran Plot"
    9926 
    9927 > view #1/o:74
    9928 
    9929 > isolde sim resume
    9930 
    9931 > ui tool show "Ramachandran Plot"
    9932 
    9933 > isolde sim pause
    9934 
    9935 > isolde sim stop
    9936 
    9937 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9938 chains... 
    9939 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9940 standards. 
    9941 ISOLDE: stopped sim 
    9942 
    9943 > isolde sim start sel
    9944 
    9945 ISOLDE: started sim 
    9946 
    9947 > ui tool show "Ramachandran Plot"
    9948 
    9949 > select clear
    9950 
    9951 > isolde sim stop
    9952 
    9953 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9954 chains... 
    9955 ISOLDE: stopped sim 
    9956 
    9957 > view #1/o:74
    9958 
    9959 > view #1/o:74-81|/o:12
    9960 
    9961 > select #1/o:74-81|/o:12
    9962 
    9963 140 atoms, 138 bonds, 9 residues, 1 model selected 
    9964 
    9965 > isolde sim start sel
    9966 
    9967 ISOLDE: started sim 
    9968 
    9969 > ui tool show "Ramachandran Plot"
    9970 
    9971 > select clear
    9972 
    9973 > isolde sim stop
    9974 
    9975 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9976 chains... 
    9977 ISOLDE: stopped sim 
    9978 
    9979 > select #1/o:74
    9980 
    9981 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9982 
    9983 > view #1/o:74
    9984 
    9985 > isolde sim start sel
    9986 
    9987 ISOLDE: started sim 
    9988 
    9989 > ui tool show "Ramachandran Plot"
    9990 
    9991 [Repeated 1 time(s)]
    9992 
    9993 > select clear
    9994 
    9995 > ui tool show "Ramachandran Plot"
    9996 
    9997 > isolde sim stop
    9998 
    9999 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10000 chains... 
    10001 ISOLDE: stopped sim 
    10002 
    10003 > ui tool show "Ramachandran Plot"
    10004 
    10005 > isolde sim start sel
    10006 
    10007 ISOLDE: started sim 
    10008 
    10009 > ui tool show "Ramachandran Plot"
    10010 
    10011 > select clear
    10012 
    10013 > ui tool show "Ramachandran Plot"
    10014 
    10015 [Repeated 1 time(s)]
    10016 
    10017 > isolde sim stop
    10018 
    10019 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10020 chains... 
    10021 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10022 standards. 
    10023 ISOLDE: stopped sim 
    10024 
    10025 > ui tool show "Ramachandran Plot"
    10026 
    10027 > isolde sim start sel
    10028 
    10029 ISOLDE: started sim 
    10030 
    10031 > select clear
    10032 
    10033 > ui tool show "Ramachandran Plot"
    10034 
    10035 > isolde sim pause
    10036 
    10037 > isolde sim resume
    10038 
    10039 > isolde pepflip sel
    10040 
    10041 Flipping the peptide bond for 1 residues 
    10042 
    10043 > isolde pepflip sel
    10044 
    10045 Flipping the peptide bond for 1 residues 
    10046 
    10047 > isolde pepflip sel
    10048 
    10049 Flipping the peptide bond for 1 residues 
    10050 
    10051 > isolde pepflip sel
    10052 
    10053 Flipping the peptide bond for 1 residues 
    10054 
    10055 > select clear
    10056 
    10057 > isolde pepflip sel
    10058 
    10059 Flipping the peptide bond for 1 residues 
    10060 
    10061 > isolde pepflip sel
    10062 
    10063 Flipping the peptide bond for 1 residues 
    10064 
    10065 > select clear
    10066 
    10067 [Repeated 2 time(s)]
    10068 
    10069 > ui tool show "Ramachandran Plot"
    10070 
    10071 > select clear
    10072 
    10073 [Repeated 1 time(s)]
    10074 
    10075 > view #1/l:33
    10076 
    10077 > select clear
    10078 
    10079 [Repeated 1 time(s)]
    10080 
    10081 > isolde pepflip sel
    10082 
    10083 Flipping the peptide bond for 1 residues 
    10084 
    10085 > select clear
    10086 
    10087 > ui tool show "Ramachandran Plot"
    10088 
    10089 > select clear
    10090 
    10091 > isolde sim pause
    10092 
    10093 > isolde sim resume
    10094 
    10095 > ui tool show "Ramachandran Plot"
    10096 
    10097 > isolde sim pause
    10098 
    10099 > isolde sim stop
    10100 
    10101 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10102 chains... 
    10103 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    10104 standards. 
    10105 ISOLDE: stopped sim 
    10106 
    10107 > isolde sim start sel
    10108 
    10109 ISOLDE: started sim 
    10110 
    10111 > ui tool show "Ramachandran Plot"
    10112 
    10113 > select clear
    10114 
    10115 > isolde sim pause
    10116 
    10117 > isolde sim resume
    10118 
    10119 > ui tool show "Ramachandran Plot"
    10120 
    10121 > select clear
    10122 
    10123 > isolde pepflip sel
    10124 
    10125 Flipping the peptide bond for 1 residues 
    10126 
    10127 > isolde pepflip sel
    10128 
    10129 Flipping the peptide bond for 1 residues 
    10130 
    10131 > isolde pepflip sel
    10132 
    10133 Flipping the peptide bond for 1 residues 
    10134 
    10135 > ui tool show "Ramachandran Plot"
    10136 
    10137 > select clear
    10138 
    10139 > ui tool show "Ramachandran Plot"
    10140 
    10141 > select clear
    10142 
    10143 > isolde pepflip sel
    10144 
    10145 Flipping the peptide bond for 1 residues 
    10146 
    10147 > isolde pepflip sel
    10148 
    10149 Flipping the peptide bond for 1 residues 
    10150 
    10151 > ui tool show "Ramachandran Plot"
    10152 
    10153 > select clear
    10154 
    10155 [Repeated 1 time(s)]
    10156 
    10157 > isolde sim stop
    10158 
    10159 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10160 chains... 
    10161 ISOLDE: stopped sim 
    10162 
    10163 > view #1/l:33
    10164 
    10165 > select #1/l:33
    10166 
    10167 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10168 
    10169 > isolde sim start sel
    10170 
    10171 ISOLDE: started sim 
    10172 
    10173 > ui tool show "Ramachandran Plot"
    10174 
    10175 > select clear
    10176 
    10177 > ui tool show "Ramachandran Plot"
    10178 
    10179 > isolde sim stop
    10180 
    10181 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10182 chains... 
    10183 ISOLDE: stopped sim 
    10184 
    10185 > isolde sim start sel
    10186 
    10187 ISOLDE: started sim 
    10188 
    10189 > select clear
    10190 
    10191 > ui tool show "Ramachandran Plot"
    10192 
    10193 > isolde pepflip sel
    10194 
    10195 Flipping the peptide bond for 1 residues 
    10196 
    10197 > select clear
    10198 
    10199 [Repeated 2 time(s)]
    10200 
    10201 > ui tool show "Ramachandran Plot"
    10202 
    10203 [Repeated 2 time(s)]
    10204 
    10205 > select clear
    10206 
    10207 > ui tool show "Ramachandran Plot"
    10208 
    10209 > isolde sim pause
    10210 
    10211 > isolde sim resume
    10212 
    10213 > ui tool show "Ramachandran Plot"
    10214 
    10215 > isolde sim stop
    10216 
    10217 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10218 chains... 
    10219 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10220 standards. 
    10221 ISOLDE: stopped sim 
    10222 
    10223 > view #1/l:33
    10224 
    10225 > select #1/l:33
    10226 
    10227 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10228 
    10229 > isolde sim start sel
    10230 
    10231 ISOLDE: started sim 
    10232 
    10233 > ui tool show "Ramachandran Plot"
    10234 
    10235 > select clear
    10236 
    10237 > ui tool show "Ramachandran Plot"
    10238 
    10239 > isolde sim stop
    10240 
    10241 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10242 chains... 
    10243 ISOLDE: stopped sim 
    10244 
    10245 > ui tool show "Ramachandran Plot"
    10246 
    10247 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    10248 > mut8-no-C-ter/20-3-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    10249 > step20-3-afterStep1d2.cxs
    10250 
    10251 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    10252 
    10253 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    10254 > mut8-no-C-ter/20-3-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    10255 > step20-3-afterStep1d2.pdb
    10256 
    10257 > ui tool show "Ramachandran Plot"
    10258 
    10259 > isolde sim start sel
    10260 
    10261 ISOLDE: started sim 
    10262 
    10263 > select clear
    10264 
    10265 > isolde sim pause
    10266 
    10267 > select clear
    10268 
    10269 > isolde sim resume
    10270 
    10271 > select clear
    10272 
    10273 > ui tool show "Ramachandran Plot"
    10274 
    10275 > select clear
    10276 
    10277 > isolde sim pause
    10278 
    10279 > isolde sim resume
    10280 
    10281 > ui tool show "Ramachandran Plot"
    10282 
    10283 > isolde sim stop
    10284 
    10285 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10286 chains... 
    10287 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    10288 standards. 
    10289 ISOLDE: stopped sim 
    10290 
    10291 > select #1/u:100-109
    10292 
    10293 161 atoms, 160 bonds, 10 residues, 1 model selected 
    10294 
    10295 > isolde sim start sel
    10296 
    10297 ISOLDE: started sim 
    10298 
    10299 > ui tool show "Ramachandran Plot"
    10300 
    10301 > isolde sim pause
    10302 
    10303 > ui tool show "Ramachandran Plot"
    10304 
    10305 > isolde sim resume
    10306 
    10307 > ui tool show "Ramachandran Plot"
    10308 
    10309 > isolde sim pause
    10310 
    10311 > isolde sim resume
    10312 
    10313 > isolde sim stop
    10314 
    10315 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10316 chains... 
    10317 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    10318 standards. 
    10319 ISOLDE: stopped sim 
    10320 
    10321 > select #1/u:115-116
    10322 
    10323 43 atoms, 42 bonds, 2 residues, 1 model selected 
    10324 
    10325 > isolde sim start sel
    10326 
    10327 ISOLDE: started sim 
    10328 
    10329 > select clear
    10330 
    10331 > isolde pepflip sel
    10332 
    10333 Flipping the peptide bond for 1 residues 
    10334 
    10335 > ui tool show "Ramachandran Plot"
    10336 
    10337 > view #1/u:115-116
    10338 
    10339 > isolde sim pause
    10340 
    10341 > ui tool show "Ramachandran Plot"
    10342 
    10343 > isolde sim resume
    10344 
    10345 > isolde sim stop
    10346 
    10347 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10348 chains... 
    10349 ISOLDE: stopped sim 
    10350 
    10351 > isolde sim start sel
    10352 
    10353 ISOLDE: started sim 
    10354 
    10355 > isolde sim pause
    10356 
    10357 > isolde sim resume
    10358 
    10359 > isolde sim pause
    10360 
    10361 > isolde sim resume
    10362 
    10363 > ui tool show "Ramachandran Plot"
    10364 
    10365 > isolde sim stop
    10366 
    10367 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10368 chains... 
    10369 ISOLDE: stopped sim 
    10370 
    10371 > select #1/t:127-131
    10372 
    10373 85 atoms, 85 bonds, 5 residues, 1 model selected 
    10374 
    10375 > isolde sim start sel
    10376 
    10377 ISOLDE: started sim 
    10378 
    10379 > isolde pepflip sel
    10380 
    10381 Flipping the peptide bond for 1 residues 
    10382 
    10383 > isolde pepflip sel
    10384 
    10385 Flipping the peptide bond for 1 residues 
    10386 
    10387 > ui tool show "Ramachandran Plot"
    10388 
    10389 > select clear
    10390 
    10391 > isolde sim pause
    10392 
    10393 > ui tool show "Ramachandran Plot"
    10394 
    10395 > isolde sim resume
    10396 
    10397 > isolde pepflip sel
    10398 
    10399 Flipping the peptide bond for 1 residues 
    10400 
    10401 > isolde pepflip sel
    10402 
    10403 Flipping the peptide bond for 1 residues 
    10404 
    10405 > isolde sim stop
    10406 
    10407 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10408 chains... 
    10409 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10410 standards. 
    10411 ISOLDE: stopped sim 
    10412 
    10413 > select #1/t:107-111
    10414 
    10415 85 atoms, 85 bonds, 5 residues, 1 model selected 
    10416 
    10417 > isolde sim start sel
    10418 
    10419 ISOLDE: started sim 
    10420 
    10421 > select clear
    10422 
    10423 > isolde pepflip sel
    10424 
    10425 Flipping the peptide bond for 1 residues 
    10426 
    10427 > isolde pepflip sel
    10428 
    10429 Flipping the peptide bond for 1 residues 
    10430 
    10431 > isolde pepflip sel
    10432 
    10433 Flipping the peptide bond for 1 residues 
    10434 
    10435 > isolde pepflip sel
    10436 
    10437 Flipping the peptide bond for 1 residues 
    10438 
    10439 > ui tool show "Ramachandran Plot"
    10440 
    10441 > select clear
    10442 
    10443 > isolde sim pause
    10444 
    10445 3 models selected 
    10446 
    10447 > select clear
    10448 
    10449 > isolde sim resume
    10450 
    10451 > select clear
    10452 
    10453 > ui tool show "Ramachandran Plot"
    10454 
    10455 > select clear
    10456 
    10457 > isolde sim stop
    10458 
    10459 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10460 chains... 
    10461 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10462 standards. 
    10463 ISOLDE: stopped sim 
    10464 
    10465 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    10466 > mut8-no-C-ter/20-4-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    10467 > step20-4.pdb
    10468 
    10469 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    10470 > mut8-no-C-ter/20-4-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    10471 > step20-4.cxs
    10472 
    10473 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    10474 
    10475 > ui tool show "Ramachandran Plot"
    10476 
    10477 > isolde sim start sel
    10478 
    10479 ISOLDE: started sim 
    10480 
    10481 > ui tool show "Ramachandran Plot"
    10482 
    10483 > isolde sim stop
    10484 
    10485 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10486 chains... 
    10487 ISOLDE: stopped sim 
    10488 
    10489 > view #1/t:86
    10490 
    10491 > select #1/t:86
    10492 
    10493 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10494 
    10495 > isolde sim start sel
    10496 
    10497 ISOLDE: started sim 
    10498 
    10499 > ui tool show "Ramachandran Plot"
    10500 
    10501 > isolde sim pause
    10502 
    10503 > isolde sim resume
    10504 
    10505 > ui tool show "Ramachandran Plot"
    10506 
    10507 > isolde sim pause
    10508 
    10509 > isolde sim stop
    10510 
    10511 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10512 chains... 
    10513 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10514 standards. 
    10515 ISOLDE: stopped sim 
    10516 
    10517 > isolde sim start sel
    10518 
    10519 ISOLDE: started sim 
    10520 
    10521 > ui tool show "Ramachandran Plot"
    10522 
    10523 > select clear
    10524 
    10525 > isolde sim pause
    10526 
    10527 > ui tool show "Ramachandran Plot"
    10528 
    10529 > isolde sim stop
    10530 
    10531 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10532 chains... 
    10533 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10534 standards. 
    10535 ISOLDE: stopped sim 
    10536 
    10537 > isolde sim start sel
    10538 
    10539 ISOLDE: started sim 
    10540 
    10541 > ui tool show "Ramachandran Plot"
    10542 
    10543 [Repeated 1 time(s)]
    10544 
    10545 > isolde sim stop
    10546 
    10547 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10548 chains... 
    10549 ISOLDE: stopped sim 
    10550 
    10551 > view #1/t:125
    10552 
    10553 > select #1/t:125
    10554 
    10555 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10556 
    10557 > isolde sim start sel
    10558 
    10559 ISOLDE: started sim 
    10560 
    10561 > select clear
    10562 
    10563 > isolde sim pause
    10564 
    10565 > isolde sim stop
    10566 
    10567 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10568 chains... 
    10569 ISOLDE: stopped sim 
    10570 
    10571 > isolde sim start sel
    10572 
    10573 ISOLDE: started sim 
    10574 
    10575 > ui tool show "Ramachandran Plot"
    10576 
    10577 > isolde sim pause
    10578 
    10579 > ui tool show "Ramachandran Plot"
    10580 
    10581 > isolde sim stop
    10582 
    10583 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10584 chains... 
    10585 ISOLDE: stopped sim 
    10586 
    10587 > isolde sim start sel
    10588 
    10589 ISOLDE: started sim 
    10590 
    10591 > ui tool show "Ramachandran Plot"
    10592 
    10593 > isolde sim pause
    10594 
    10595 > isolde sim resume
    10596 
    10597 > isolde sim pause
    10598 
    10599 > isolde sim resume
    10600 
    10601 > ui tool show "Ramachandran Plot"
    10602 
    10603 [Repeated 1 time(s)]
    10604 
    10605 > isolde sim pause
    10606 
    10607 > isolde sim stop
    10608 
    10609 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10610 chains... 
    10611 ISOLDE: stopped sim 
    10612 
    10613 > select #1/t:60-61
    10614 
    10615 24 atoms, 24 bonds, 2 residues, 1 model selected 
    10616 
    10617 > isolde sim start sel
    10618 
    10619 ISOLDE: started sim 
    10620 
    10621 > isolde sim pause
    10622 
    10623 > isolde sim resume
    10624 
    10625 > ui tool show "Ramachandran Plot"
    10626 
    10627 > select clear
    10628 
    10629 > isolde pepflip sel
    10630 
    10631 Flipping the peptide bond for 1 residues 
    10632 
    10633 > isolde pepflip sel
    10634 
    10635 Flipping the peptide bond for 1 residues 
    10636 
    10637 > isolde pepflip sel
    10638 
    10639 Flipping the peptide bond for 1 residues 
    10640 
    10641 > select clear
    10642 
    10643 [Repeated 1 time(s)]
    10644 
    10645 > isolde pepflip sel
    10646 
    10647 Flipping the peptide bond for 1 residues 
    10648 
    10649 > isolde pepflip sel
    10650 
    10651 Flipping the peptide bond for 1 residues 
    10652 
    10653 > isolde pepflip sel
    10654 
    10655 Flipping the peptide bond for 1 residues 
    10656 Unable to flip peptide bond after 50 rounds. Giving up. 
    10657 
    10658 > isolde pepflip sel
    10659 
    10660 Flipping the peptide bond for 1 residues 
    10661 
    10662 > isolde pepflip sel
    10663 
    10664 Flipping the peptide bond for 1 residues 
    10665 
    10666 > isolde pepflip sel
    10667 
    10668 Flipping the peptide bond for 1 residues 
    10669 
    10670 > select clear
    10671 
    10672 > ui tool show "Ramachandran Plot"
    10673 
    10674 [Repeated 2 time(s)]
    10675 
    10676 > select clear
    10677 
    10678 > ui tool show "Ramachandran Plot"
    10679 
    10680 > isolde sim stop
    10681 
    10682 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10683 chains... 
    10684 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10685 standards. 
    10686 ISOLDE: stopped sim 
    10687 
    10688 > ui tool show "Ramachandran Plot"
    10689 
    10690 > view #1/t:55
    10691 
    10692 > select #1/t:55
    10693 
    10694 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10695 
    10696 > isolde sim start sel
    10697 
    10698 ISOLDE: started sim 
    10699 
    10700 > ui tool show "Ramachandran Plot"
    10701 
    10702 > isolde sim stop
    10703 
    10704 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10705 chains... 
    10706 ISOLDE: stopped sim 
    10707 
    10708 > view #1/t:47]
    10709 
    10710 No objects specified. 
    10711 
    10712 > view #1/t:47
    10713 
    10714 > select #1/t:47
    10715 
    10716 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10717 
    10718 > isolde sim start sel
    10719 
    10720 ISOLDE: started sim 
    10721 
    10722 > ui tool show "Ramachandran Plot"
    10723 
    10724 [Repeated 1 time(s)]
    10725 
    10726 > isolde sim stop
    10727 
    10728 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10729 chains... 
    10730 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10731 standards. 
    10732 ISOLDE: stopped sim 
    10733 
    10734 > view #1/t:125
    10735 
    10736 > select #1/t:125
    10737 
    10738 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10739 
    10740 > isolde sim start sel
    10741 
    10742 ISOLDE: started sim 
    10743 
    10744 > ui tool show "Ramachandran Plot"
    10745 
    10746 > isolde sim stop
    10747 
    10748 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10749 chains... 
    10750 ISOLDE: stopped sim 
    10751 
    10752 > select #1/t:125
    10753 
    10754 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10755 
    10756 > isolde sim start sel
    10757 
    10758 ISOLDE: started sim 
    10759 
    10760 > select clear
    10761 
    10762 [Repeated 2 time(s)]
    10763 
    10764 > ui tool show "Ramachandran Plot"
    10765 
    10766 > isolde sim stop
    10767 
    10768 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10769 chains... 
    10770 ISOLDE: stopped sim 
    10771 
    10772 > select #1/t:86
    10773 
    10774 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10775 
    10776 > view #1/t:86
    10777 
    10778 > isolde sim start sel
    10779 
    10780 ISOLDE: started sim 
    10781 
    10782 > ui tool show "Ramachandran Plot"
    10783 
    10784 > select clear
    10785 
    10786 > isolde sim stop
    10787 
    10788 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10789 chains... 
    10790 ISOLDE: stopped sim 
    10791 
    10792 > view #1/u:87
    10793 
    10794 > select #1/u:87
    10795 
    10796 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10797 
    10798 > isolde sim start sel
    10799 
    10800 ISOLDE: started sim 
    10801 
    10802 > ui tool show "Ramachandran Plot"
    10803 
    10804 > select clear
    10805 
    10806 > isolde sim stop
    10807 
    10808 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10809 chains... 
    10810 ISOLDE: stopped sim 
    10811 
    10812 > view #1/t:107-111
    10813 
    10814 > select #1/t:107-111
    10815 
    10816 85 atoms, 85 bonds, 5 residues, 1 model selected 
    10817 
    10818 > isolde sim start sel
    10819 
    10820 ISOLDE: started sim 
    10821 
    10822 > ui tool show "Ramachandran Plot"
    10823 
    10824 > select clear
    10825 
    10826 > isolde pepflip sel
    10827 
    10828 Flipping the peptide bond for 1 residues 
    10829 
    10830 > ui tool show "Ramachandran Plot"
    10831 
    10832 [Repeated 1 time(s)]
    10833 
    10834 > isolde pepflip sel
    10835 
    10836 Flipping the peptide bond for 1 residues 
    10837 
    10838 > ui tool show "Ramachandran Plot"
    10839 
    10840 > isolde sim pause
    10841 
    10842 > view #1/t:100
    10843 
    10844 > select #1/t:100
    10845 
    10846 16 atoms, 15 bonds, 1 residue, 1 model selected 
    10847 
    10848 > isolde sim start sel
    10849 
    10850 Simulation already running! 
    10851 
    10852 > isolde sim stop
    10853 
    10854 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10855 chains... 
    10856 ISOLDE: stopped sim 
    10857 
    10858 > select #1/t:100
    10859 
    10860 16 atoms, 15 bonds, 1 residue, 1 model selected 
    10861 
    10862 > isolde sim start sel
    10863 
    10864 ISOLDE: started sim 
    10865 
    10866 > ui tool show "Ramachandran Plot"
    10867 
    10868 > isolde sim pause
    10869 
    10870 > isolde sim stop
    10871 
    10872 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10873 chains... 
    10874 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    10875 standards. 
    10876 ISOLDE: stopped sim 
    10877 
    10878 > isolde sim start sel
    10879 
    10880 ISOLDE: started sim 
    10881 
    10882 > select clear
    10883 
    10884 [Repeated 1 time(s)]
    10885 
    10886 > isolde pepflip sel
    10887 
    10888 Flipping the peptide bond for 1 residues 
    10889 
    10890 > isolde pepflip sel
    10891 
    10892 Flipping the peptide bond for 1 residues 
    10893 
    10894 > isolde pepflip sel
    10895 
    10896 Flipping the peptide bond for 1 residues 
    10897 
    10898 > isolde pepflip sel
    10899 
    10900 Flipping the peptide bond for 1 residues 
    10901 
    10902 > select clear
    10903 
    10904 [Repeated 1 time(s)]
    10905 
    10906 > ui tool show "Ramachandran Plot"
    10907 
    10908 > isolde pepflip sel
    10909 
    10910 Flipping the peptide bond for 1 residues 
    10911 
    10912 > ui tool show "Ramachandran Plot"
    10913 
    10914 > isolde sim pause
    10915 
    10916 > isolde sim resume
    10917 
    10918 > isolde pepflip sel
    10919 
    10920 Flipping the peptide bond for 1 residues 
    10921 
    10922 > ui tool show "Ramachandran Plot"
    10923 
    10924 > isolde sim stop
    10925 
    10926 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10927 chains... 
    10928 ISOLDE: stopped sim 
    10929 
    10930 > select #1/t:100
    10931 
    10932 16 atoms, 15 bonds, 1 residue, 1 model selected 
    10933 
    10934 > isolde sim start sel
    10935 
    10936 ISOLDE: started sim 
    10937 
    10938 > ui tool show "Ramachandran Plot"
    10939 
    10940 > isolde sim pause
    10941 
    10942 > ui tool show "Ramachandran Plot"
    10943 
    10944 > isolde sim resume
    10945 
    10946 > isolde pepflip sel
    10947 
    10948 Flipping the peptide bond for 1 residues 
    10949 
    10950 > isolde sim pause
    10951 
    10952 > ui tool show "Ramachandran Plot"
    10953 
    10954 [Repeated 1 time(s)]
    10955 
    10956 > isolde sim resume
    10957 
    10958 > isolde pepflip sel
    10959 
    10960 Flipping the peptide bond for 1 residues 
    10961 
    10962 > isolde pepflip sel
    10963 
    10964 Flipping the peptide bond for 1 residues 
    10965 
    10966 > isolde pepflip sel
    10967 
    10968 Flipping the peptide bond for 1 residues 
    10969 
    10970 > isolde sim pause
    10971 
    10972 > isolde sim stop
    10973 
    10974 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10975 chains... 
    10976 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    10977 standards. 
    10978 ISOLDE: stopped sim 
    10979 
    10980 > isolde sim start sel
    10981 
    10982 ISOLDE: started sim 
    10983 
    10984 > isolde sim stop
    10985 
    10986 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10987 chains... 
    10988 ISOLDE: stopped sim 
    10989 
    10990 > select #1/t:80|t:75
    10991 
    10992 Expected an objects specifier or a keyword 
    10993 
    10994 > select #1/t:80|/t:75
    10995 
    10996 36 atoms, 35 bonds, 2 residues, 1 model selected 
    10997 
    10998 > isolde sim start sel
    10999 
    11000 ISOLDE: started sim 
    11001 
    11002 > select clear
    11003 
    11004 > isolde sim pause
    11005 
    11006 > isolde sim resume
    11007 
    11008 > isolde pepflip sel
    11009 
    11010 Flipping the peptide bond for 1 residues 
    11011 
    11012 > select clear
    11013 
    11014 > isolde pepflip sel
    11015 
    11016 Flipping the peptide bond for 1 residues 
    11017 
    11018 > select clear
    11019 
    11020 > ui tool show "Ramachandran Plot"
    11021 
    11022 > isolde sim pause
    11023 
    11024 > isolde sim resume
    11025 
    11026 > select clear
    11027 
    11028 [Repeated 1 time(s)]
    11029 
    11030 > ui tool show "Ramachandran Plot"
    11031 
    11032 > isolde sim stop
    11033 
    11034 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11035 chains... 
    11036 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    11037 standards. 
    11038 ISOLDE: stopped sim 
    11039 
    11040 > view #1/t:80
    11041 
    11042 > select #1/t:80
    11043 
    11044 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11045 
    11046 > isolde sim start sel
    11047 
    11048 ISOLDE: started sim 
    11049 
    11050 > ui tool show "Ramachandran Plot"
    11051 
    11052 > isolde sim stop
    11053 
    11054 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11055 chains... 
    11056 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11057 standards. 
    11058 ISOLDE: stopped sim 
    11059 
    11060 > view #1/t:100
    11061 
    11062 > select #1/t:100
    11063 
    11064 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11065 
    11066 > isolde sim start sel
    11067 
    11068 ISOLDE: started sim 
    11069 
    11070 > ui tool show "Ramachandran Plot"
    11071 
    11072 > isolde sim stop
    11073 
    11074 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11075 chains... 
    11076 ISOLDE: stopped sim 
    11077 
    11078 > view #1/t:107-111
    11079 
    11080 > select #1/t:107-111
    11081 
    11082 85 atoms, 85 bonds, 5 residues, 1 model selected 
    11083 
    11084 > isolde sim start sel
    11085 
    11086 ISOLDE: started sim 
    11087 
    11088 > ui tool show "Ramachandran Plot"
    11089 
    11090 > isolde sim stop
    11091 
    11092 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11093 chains... 
    11094 ISOLDE: stopped sim 
    11095 
    11096 > view #1/t:127-131
    11097 
    11098 > select #1/t:127-131
    11099 
    11100 85 atoms, 85 bonds, 5 residues, 1 model selected 
    11101 
    11102 > isolde sim start sel
    11103 
    11104 ISOLDE: started sim 
    11105 
    11106 > ui tool show "Ramachandran Plot"
    11107 
    11108 > isolde sim stop
    11109 
    11110 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11111 chains... 
    11112 ISOLDE: stopped sim 
    11113 
    11114 > view #1/u:115-116
    11115 
    11116 > select #1/u:115-116
    11117 
    11118 43 atoms, 42 bonds, 2 residues, 1 model selected 
    11119 
    11120 > isolde sim start sel
    11121 
    11122 ISOLDE: started sim 
    11123 
    11124 > ui tool show "Ramachandran Plot"
    11125 
    11126 > isolde sim pause
    11127 
    11128 > isolde sim resume
    11129 
    11130 > ui tool show "Ramachandran Plot"
    11131 
    11132 > isolde sim stop
    11133 
    11134 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11135 chains... 
    11136 ISOLDE: stopped sim 
    11137 
    11138 > view #1/u:100-109
    11139 
    11140 > select #1/u:100-109
    11141 
    11142 161 atoms, 160 bonds, 10 residues, 1 model selected 
    11143 
    11144 > isolde sim start sel
    11145 
    11146 ISOLDE: started sim 
    11147 
    11148 > ui tool show "Ramachandran Plot"
    11149 
    11150 [Repeated 1 time(s)]
    11151 
    11152 > isolde sim stop
    11153 
    11154 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11155 chains... 
    11156 ISOLDE: stopped sim 
    11157 
    11158 > select clear
    11159 
    11160 > view #1/u:101
    11161 
    11162 [Repeated 1 time(s)]
    11163 
    11164 > select #1/u:101
    11165 
    11166 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11167 
    11168 > isolde sim start sel
    11169 
    11170 ISOLDE: started sim 
    11171 
    11172 > ui tool show "Ramachandran Plot"
    11173 
    11174 > isolde sim stop
    11175 
    11176 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11177 chains... 
    11178 ISOLDE: stopped sim 
    11179 
    11180 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    11181 > mut8-no-C-ter/20-5-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    11182 > step20-5.cxs
    11183 
    11184 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    11185 
    11186 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    11187 > mut8-no-C-ter/20-5-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    11188 > step20-5.pdb
    11189 
    11190 > isolde sim start sel
    11191 
    11192 ISOLDE: started sim 
    11193 
    11194 > ui tool show "Ramachandran Plot"
    11195 
    11196 > isolde sim stop
    11197 
    11198 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11199 chains... 
    11200 ISOLDE: stopped sim 
    11201 
    11202 > isolde sim start sel
    11203 
    11204 ISOLDE: started sim 
    11205 
    11206 > ui tool show "Ramachandran Plot"
    11207 
    11208 > isolde sim stop
    11209 
    11210 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11211 chains... 
    11212 ISOLDE: stopped sim 
    11213 
    11214 > isolde sim start sel
    11215 
    11216 ISOLDE: started sim 
    11217 
    11218 > ui tool show "Ramachandran Plot"
    11219 
    11220 > isolde sim stop
    11221 
    11222 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11223 chains... 
    11224 ISOLDE: stopped sim 
    11225 
    11226 > isolde sim start sel
    11227 
    11228 ISOLDE: started sim 
    11229 
    11230 > ui tool show "Ramachandran Plot"
    11231 
    11232 > select clear
    11233 
    11234 > isolde sim stop
    11235 
    11236 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11237 chains... 
    11238 ISOLDE: stopped sim 
    11239 
    11240 > isolde sim start sel
    11241 
    11242 ISOLDE: started sim 
    11243 
    11244 > ui tool show "Ramachandran Plot"
    11245 
    11246 > isolde sim stop
    11247 
    11248 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11249 chains... 
    11250 ISOLDE: stopped sim 
    11251 
    11252 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    11253 > mut8-no-C-ter/20-6-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    11254 > step20-6-fixedNewTwistedBonds.pdb
    11255 
    11256 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    11257 > mut8-no-C-ter/20-6-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    11258 > step20-6-fixedNewTwistedBonds.cxs
    11259 
    11260 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    11261 
    11262 > ui tool show "Ramachandran Plot"
    11263 
    11264 [Repeated 1 time(s)]
    11265 
    11266 > isolde sim start sel
    11267 
    11268 ISOLDE: started sim 
    11269 
    11270 > isolde pepflip sel
    11271 
    11272 Flipping the peptide bond for 1 residues 
    11273 
    11274 > isolde pepflip sel
    11275 
    11276 Flipping the peptide bond for 1 residues 
    11277 
    11278 > ui tool show "Ramachandran Plot"
    11279 
    11280 [Repeated 1 time(s)]
    11281 
    11282 > isolde sim stop
    11283 
    11284 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11285 chains... 
    11286 ISOLDE: stopped sim 
    11287 
    11288 > ui tool show "Ramachandran Plot"
    11289 
    11290 > isolde sim start sel
    11291 
    11292 ISOLDE: started sim 
    11293 
    11294 > ui tool show "Ramachandran Plot"
    11295 
    11296 > select clear
    11297 
    11298 > isolde pepflip sel
    11299 
    11300 Flipping the peptide bond for 1 residues 
    11301 
    11302 > ui tool show "Ramachandran Plot"
    11303 
    11304 > isolde sim stop
    11305 
    11306 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11307 chains... 
    11308 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11309 standards. 
    11310 ISOLDE: stopped sim 
    11311 
    11312 > ui tool show "Ramachandran Plot"
    11313 
    11314 > isolde sim start sel
    11315 
    11316 ISOLDE: started sim 
    11317 
    11318 > isolde pepflip sel
    11319 
    11320 Flipping the peptide bond for 1 residues 
    11321 
    11322 > ui tool show "Ramachandran Plot"
    11323 
    11324 > view #1/f:43
    11325 
    11326 > ui tool show "Ramachandran Plot"
    11327 
    11328 > isolde sim stop
    11329 
    11330 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11331 chains... 
    11332 ISOLDE: stopped sim 
    11333 
    11334 > ui tool show "Ramachandran Plot"
    11335 
    11336 > isolde sim start sel
    11337 
    11338 ISOLDE: started sim 
    11339 
    11340 > isolde pepflip sel
    11341 
    11342 Flipping the peptide bond for 1 residues 
    11343 
    11344 > ui tool show "Ramachandran Plot"
    11345 
    11346 > select clear
    11347 
    11348 > ui tool show "Ramachandran Plot"
    11349 
    11350 > isolde sim stop
    11351 
    11352 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11353 chains... 
    11354 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11355 standards. 
    11356 ISOLDE: stopped sim 
    11357 
    11358 > ui tool show "Ramachandran Plot"
    11359 
    11360 > hide #!1.2 models
    11361 
    11362 > show #!1.2 models
    11363 
    11364 > hide #!1.2 models
    11365 
    11366 > show #!1.2 models
    11367 
    11368 > hide #!1.2 models
    11369 
    11370 > show #!1.2 models
    11371 
    11372 > hide #!1.1 models
    11373 
    11374 > show #!1.1 models
    11375 
    11376 > hide #!1.2 models
    11377 
    11378 > show #!1.2 models
    11379 
    11380 > hide #!1.2 models
    11381 
    11382 > show #!1.2 models
    11383 
    11384 > ui tool show "Ramachandran Plot"
    11385 
    11386 > isolde sim start sel
    11387 
    11388 ISOLDE: started sim 
    11389 
    11390 > ui tool show "Ramachandran Plot"
    11391 
    11392 > isolde pepflip sel
    11393 
    11394 Flipping the peptide bond for 1 residues 
    11395 
    11396 > select clear
    11397 
    11398 > ui tool show "Ramachandran Plot"
    11399 
    11400 > isolde sim stop
    11401 
    11402 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11403 chains... 
    11404 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11405 standards. 
    11406 ISOLDE: stopped sim 
    11407 
    11408 > ui tool show "Ramachandran Plot"
    11409 
    11410 > isolde sim start sel
    11411 
    11412 ISOLDE: started sim 
    11413 
    11414 > isolde pepflip sel
    11415 
    11416 Flipping the peptide bond for 1 residues 
    11417 
    11418 > ui tool show "Ramachandran Plot"
    11419 
    11420 > isolde sim pause
    11421 
    11422 > isolde sim resume
    11423 
    11424 > isolde sim stop
    11425 
    11426 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11427 chains... 
    11428 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11429 standards. 
    11430 ISOLDE: stopped sim 
    11431 
    11432 > ui tool show "Ramachandran Plot"
    11433 
    11434 > isolde sim start sel
    11435 
    11436 ISOLDE: started sim 
    11437 
    11438 > isolde pepflip sel
    11439 
    11440 Flipping the peptide bond for 1 residues 
    11441 
    11442 > ui tool show "Ramachandran Plot"
    11443 
    11444 > isolde sim pause
    11445 
    11446 > ui tool show "Ramachandran Plot"
    11447 
    11448 > isolde sim stop
    11449 
    11450 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11451 chains... 
    11452 ISOLDE: stopped sim 
    11453 
    11454 > isolde sim start sel
    11455 
    11456 ISOLDE: started sim 
    11457 
    11458 > isolde pepflip sel
    11459 
    11460 Flipping the peptide bond for 1 residues 
    11461 
    11462 > isolde pepflip sel
    11463 
    11464 Flipping the peptide bond for 1 residues 
    11465 
    11466 > isolde pepflip sel
    11467 
    11468 Flipping the peptide bond for 1 residues 
    11469 
    11470 > ui tool show "Ramachandran Plot"
    11471 
    11472 > select clear
    11473 
    11474 > ui tool show "Ramachandran Plot"
    11475 
    11476 > isolde sim pause
    11477 
    11478 > ui tool show "Ramachandran Plot"
    11479 
    11480 > isolde sim resume
    11481 
    11482 > isolde sim stop
    11483 
    11484 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11485 chains... 
    11486 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11487 standards. 
    11488 ISOLDE: stopped sim 
    11489 
    11490 > isolde sim start sel
    11491 
    11492 ISOLDE: started sim 
    11493 
    11494 > select clear
    11495 
    11496 [Repeated 2 time(s)]
    11497 
    11498 > ui tool show "Ramachandran Plot"
    11499 
    11500 > isolde sim pause
    11501 
    11502 > select clear
    11503 
    11504 > ui tool show "Ramachandran Plot"
    11505 
    11506 > isolde sim stop
    11507 
    11508 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11509 chains... 
    11510 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    11511 standards. 
    11512 ISOLDE: stopped sim 
    11513 
    11514 > isolde sim start sel
    11515 
    11516 ISOLDE: started sim 
    11517 
    11518 > ui tool show "Ramachandran Plot"
    11519 
    11520 > isolde sim pause
    11521 
    11522 > isolde sim resume
    11523 
    11524 > select clear
    11525 
    11526 > ui tool show "Ramachandran Plot"
    11527 
    11528 > isolde sim stop
    11529 
    11530 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11531 chains... 
    11532 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    11533 standards. 
    11534 ISOLDE: stopped sim 
    11535 
    11536 > view #1/k:137
    11537 
    11538 > select #1/k:137
    11539 
    11540 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11541 
    11542 > isolde sim start sel
    11543 
    11544 ISOLDE: started sim 
    11545 
    11546 > ui tool show "Ramachandran Plot"
    11547 
    11548 > isolde sim stop
    11549 
    11550 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11551 chains... 
    11552 ISOLDE: stopped sim 
    11553 
    11554 > view #1/k:142
    11555 
    11556 > select #1/k:142
    11557 
    11558 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11559 
    11560 > isolde sim start sel
    11561 
    11562 ISOLDE: started sim 
    11563 
    11564 > ui tool show "Ramachandran Plot"
    11565 
    11566 > isolde sim stop
    11567 
    11568 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11569 chains... 
    11570 ISOLDE: stopped sim 
    11571 
    11572 > view #1/k:149
    11573 
    11574 > select #1/k:149
    11575 
    11576 10 atoms, 9 bonds, 1 residue, 1 model selected 
    11577 
    11578 > isolde sim start sel
    11579 
    11580 ISOLDE: started sim 
    11581 
    11582 > ui tool show "Ramachandran Plot"
    11583 
    11584 > isolde sim stop
    11585 
    11586 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11587 chains... 
    11588 ISOLDE: stopped sim 
    11589 
    11590 > ui tool show "Ramachandran Plot"
    11591 
    11592 > isolde sim start sel
    11593 
    11594 ISOLDE: started sim 
    11595 
    11596 > ui tool show "Ramachandran Plot"
    11597 
    11598 > isolde pepflip sel
    11599 
    11600 Flipping the peptide bond for 1 residues 
    11601 
    11602 > isolde pepflip sel
    11603 
    11604 Flipping the peptide bond for 1 residues 
    11605 
    11606 > isolde pepflip sel
    11607 
    11608 Flipping the peptide bond for 1 residues 
    11609 
    11610 > isolde pepflip sel
    11611 
    11612 Flipping the peptide bond for 1 residues 
    11613 
    11614 > ui tool show "Ramachandran Plot"
    11615 
    11616 > isolde sim pause
    11617 
    11618 > isolde sim resume
    11619 
    11620 > isolde pepflip sel
    11621 
    11622 Flipping the peptide bond for 1 residues 
    11623 
    11624 > isolde pepflip sel
    11625 
    11626 Flipping the peptide bond for 1 residues 
    11627 
    11628 > isolde pepflip sel
    11629 
    11630 Flipping the peptide bond for 1 residues 
    11631 
    11632 > select clear
    11633 
    11634 [Repeated 2 time(s)]
    11635 
    11636 > isolde sim pause
    11637 
    11638 > isolde sim resume
    11639 
    11640 > select clear
    11641 
    11642 [Repeated 1 time(s)]
    11643 
    11644 > isolde sim pause
    11645 
    11646 > isolde sim resume
    11647 
    11648 > ui tool show "Ramachandran Plot"
    11649 
    11650 > isolde sim stop
    11651 
    11652 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11653 chains... 
    11654 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    11655 standards. 
    11656 ISOLDE: stopped sim 
    11657 
    11658 > isolde sim start sel
    11659 
    11660 ISOLDE: started sim 
    11661 
    11662 > ui tool show "Ramachandran Plot"
    11663 
    11664 > isolde sim pause
    11665 
    11666 > ui tool show "Ramachandran Plot"
    11667 
    11668 > isolde sim stop
    11669 
    11670 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11671 chains... 
    11672 ISOLDE: stopped sim 
    11673 
    11674 > isolde sim start sel
    11675 
    11676 ISOLDE: started sim 
    11677 
    11678 > ui tool show "Ramachandran Plot"
    11679 
    11680 > isolde pepflip sel
    11681 
    11682 Flipping the peptide bond for 1 residues 
    11683 
    11684 > ui tool show "Ramachandran Plot"
    11685 
    11686 > isolde pepflip sel
    11687 
    11688 Flipping the peptide bond for 1 residues 
    11689 
    11690 > select clear
    11691 
    11692 > ui tool show "Ramachandran Plot"
    11693 
    11694 > isolde sim stop
    11695 
    11696 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11697 chains... 
    11698 ISOLDE: stopped sim 
    11699 
    11700 > view #1/Z:116
    11701 
    11702 > select #1/Z:116
    11703 
    11704 17 atoms, 17 bonds, 1 residue, 1 model selected 
    11705 
    11706 > isolde sim start sel
    11707 
    11708 ISOLDE: started sim 
    11709 
    11710 > ui tool show "Ramachandran Plot"
    11711 
    11712 > isolde sim stop
    11713 
    11714 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11715 chains... 
    11716 ISOLDE: stopped sim 
    11717 
    11718 > view #1/Z:69
    11719 
    11720 > select #1/Z:69
    11721 
    11722 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11723 
    11724 > isolde sim start sel
    11725 
    11726 ISOLDE: started sim 
    11727 
    11728 > ui tool show "Ramachandran Plot"
    11729 
    11730 > isolde sim stop
    11731 
    11732 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11733 chains... 
    11734 ISOLDE: stopped sim 
    11735 
    11736 > ui tool show "Ramachandran Plot"
    11737 
    11738 > isolde sim start sel
    11739 
    11740 ISOLDE: started sim 
    11741 
    11742 > ui tool show "Ramachandran Plot"
    11743 
    11744 [Repeated 1 time(s)]
    11745 
    11746 > isolde sim stop
    11747 
    11748 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11749 chains... 
    11750 ISOLDE: stopped sim 
    11751 
    11752 > ui tool show "Ramachandran Plot"
    11753 
    11754 > isolde sim start sel
    11755 
    11756 ISOLDE: started sim 
    11757 
    11758 > ui tool show "Ramachandran Plot"
    11759 
    11760 > isolde sim pause
    11761 
    11762 > ui tool show "Ramachandran Plot"
    11763 
    11764 [Repeated 1 time(s)]
    11765 
    11766 > isolde sim resume
    11767 
    11768 > isolde pepflip sel
    11769 
    11770 Flipping the peptide bond for 1 residues 
    11771 
    11772 > isolde pepflip sel
    11773 
    11774 Flipping the peptide bond for 1 residues 
    11775 
    11776 > isolde pepflip sel
    11777 
    11778 Flipping the peptide bond for 1 residues 
    11779 
    11780 > isolde pepflip sel
    11781 
    11782 Flipping the peptide bond for 1 residues 
    11783 Unable to flip peptide bond after 50 rounds. Giving up. 
    11784 [Repeated 1 time(s)]
    11785 
    11786 > isolde pepflip sel
    11787 
    11788 Flipping the peptide bond for 1 residues 
    11789 
    11790 > isolde pepflip sel
    11791 
    11792 Flipping the peptide bond for 1 residues 
    11793 
    11794 > isolde sim stop
    11795 
    11796 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11797 chains... 
    11798 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    11799 standards. 
    11800 ISOLDE: stopped sim 
    11801 
    11802 > select #1/W:111-113
    11803 
    11804 61 atoms, 61 bonds, 3 residues, 1 model selected 
    11805 
    11806 > isolde sim start sel
    11807 
    11808 ISOLDE: started sim 
    11809 
    11810 > isolde pepflip sel
    11811 
    11812 Flipping the peptide bond for 1 residues 
    11813 
    11814 > select clear
    11815 
    11816 > ui tool show "Ramachandran Plot"
    11817 
    11818 > isolde sim stop
    11819 
    11820 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11821 chains... 
    11822 ISOLDE: stopped sim 
    11823 
    11824 > select #1/W:119
    11825 
    11826 24 atoms, 25 bonds, 1 residue, 1 model selected 
    11827 
    11828 > view #1/W:119
    11829 
    11830 > isolde sim start sel
    11831 
    11832 ISOLDE: started sim 
    11833 
    11834 > ui tool show "Ramachandran Plot"
    11835 
    11836 [Repeated 1 time(s)]
    11837 
    11838 > isolde sim pause
    11839 
    11840 > isolde sim stop
    11841 
    11842 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11843 chains... 
    11844 ISOLDE: stopped sim 
    11845 
    11846 > isolde sim start sel
    11847 
    11848 ISOLDE: started sim 
    11849 
    11850 > ui tool show "Ramachandran Plot"
    11851 
    11852 > isolde sim stop
    11853 
    11854 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11855 chains... 
    11856 ISOLDE: stopped sim 
    11857 
    11858 > view #1/W:119
    11859 
    11860 > select #1/W:119
    11861 
    11862 24 atoms, 25 bonds, 1 residue, 1 model selected 
    11863 
    11864 > isolde sim start sel
    11865 
    11866 ISOLDE: started sim 
    11867 
    11868 > ui tool show "Ramachandran Plot"
    11869 
    11870 > isolde sim stop
    11871 
    11872 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11873 chains... 
    11874 ISOLDE: stopped sim 
    11875 
    11876 > ui tool show "Ramachandran Plot"
    11877 
    11878 > isolde sim start sel
    11879 
    11880 ISOLDE: started sim 
    11881 
    11882 > isolde pepflip sel
    11883 
    11884 Flipping the peptide bond for 1 residues 
    11885 
    11886 > isolde pepflip sel
    11887 
    11888 Flipping the peptide bond for 1 residues 
    11889 
    11890 > isolde sim pause
    11891 
    11892 > isolde sim resume
    11893 
    11894 > isolde sim pause
    11895 
    11896 > isolde sim resume
    11897 
    11898 > isolde sim pause
    11899 
    11900 > ui tool show "Ramachandran Plot"
    11901 
    11902 > ui tool show "Build Structure"
    11903 
    11904 > isolde sim resume
    11905 
    11906 > ui tool show "Ramachandran Plot"
    11907 
    11908 > isolde sim stop
    11909 
    11910 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11911 chains... 
    11912 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11913 standards. 
    11914 ISOLDE: stopped sim 
    11915 
    11916 > isolde sim start sel
    11917 
    11918 ISOLDE: started sim 
    11919 
    11920 > ui tool show "Ramachandran Plot"
    11921 
    11922 > isolde sim stop
    11923 
    11924 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11925 chains... 
    11926 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11927 standards. 
    11928 ISOLDE: stopped sim 
    11929 
    11930 > select #1/f:9
    11931 
    11932 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11933 
    11934 > view #1/f:9
    11935 
    11936 > isolde sim start sel
    11937 
    11938 ISOLDE: started sim 
    11939 
    11940 > isolde sim stop
    11941 
    11942 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11943 chains... 
    11944 ISOLDE: stopped sim 
    11945 
    11946 > view #1/f:9
    11947 
    11948 > select #1/f:9
    11949 
    11950 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11951 
    11952 > isolde sim start sel
    11953 
    11954 ISOLDE: started sim 
    11955 
    11956 > ui tool show "Ramachandran Plot"
    11957 
    11958 > select clear
    11959 
    11960 > isolde sim stop
    11961 
    11962 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11963 chains... 
    11964 ISOLDE: stopped sim 
    11965 
    11966 > isolde sim start sel
    11967 
    11968 ISOLDE: started sim 
    11969 
    11970 > ui tool show "Ramachandran Plot"
    11971 
    11972 > isolde pepflip sel
    11973 
    11974 Flipping the peptide bond for 1 residues 
    11975 
    11976 > ui tool show "Ramachandran Plot"
    11977 
    11978 > isolde pepflip sel
    11979 
    11980 Flipping the peptide bond for 1 residues 
    11981 
    11982 > ui tool show "Ramachandran Plot"
    11983 
    11984 > isolde pepflip sel
    11985 
    11986 Flipping the peptide bond for 1 residues 
    11987 
    11988 > select clear
    11989 
    11990 [Repeated 1 time(s)]
    11991 
    11992 > isolde pepflip sel
    11993 
    11994 Flipping the peptide bond for 1 residues 
    11995 
    11996 > isolde pepflip sel
    11997 
    11998 Flipping the peptide bond for 1 residues 
    11999 
    12000 > isolde pepflip sel
    12001 
    12002 Flipping the peptide bond for 1 residues 
    12003 
    12004 > select clear
    12005 
    12006 > isolde pepflip sel
    12007 
    12008 Flipping the peptide bond for 1 residues 
    12009 
    12010 > isolde pepflip sel
    12011 
    12012 Flipping the peptide bond for 1 residues 
    12013 
    12014 > isolde pepflip sel
    12015 
    12016 Flipping the peptide bond for 1 residues 
    12017 
    12018 > ui tool show "Ramachandran Plot"
    12019 
    12020 > select clear
    12021 
    12022 > ui tool show "Ramachandran Plot"
    12023 
    12024 > isolde sim pause
    12025 
    12026 > view #1/O:69
    12027 
    12028 > ui tool show "Ramachandran Plot"
    12029 
    12030 > isolde sim stop
    12031 
    12032 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12033 chains... 
    12034 ISOLDE: stopped sim 
    12035 
    12036 > view #1/f:9
    12037 
    12038 > select #1/f:9
    12039 
    12040 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12041 
    12042 > isolde sim start sel
    12043 
    12044 ISOLDE: started sim 
    12045 
    12046 > ui tool show "Ramachandran Plot"
    12047 
    12048 > isolde sim stop
    12049 
    12050 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12051 chains... 
    12052 ISOLDE: stopped sim 
    12053 
    12054 > ui tool show "Ramachandran Plot"
    12055 
    12056 > isolde sim start sel
    12057 
    12058 ISOLDE: started sim 
    12059 
    12060 > ui tool show "Ramachandran Plot"
    12061 
    12062 > isolde sim pause
    12063 
    12064 > isolde sim stop
    12065 
    12066 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12067 chains... 
    12068 ISOLDE: stopped sim 
    12069 
    12070 > isolde sim start sel
    12071 
    12072 ISOLDE: started sim 
    12073 
    12074 > select clear
    12075 
    12076 > ui tool show "Ramachandran Plot"
    12077 
    12078 > isolde sim stop
    12079 
    12080 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12081 chains... 
    12082 ISOLDE: stopped sim 
    12083 
    12084 > view #1/W:159
    12085 
    12086 > select #1/W:159
    12087 
    12088 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12089 
    12090 > isolde sim start sel
    12091 
    12092 ISOLDE: started sim 
    12093 
    12094 > ui tool show "Ramachandran Plot"
    12095 
    12096 > isolde sim stop
    12097 
    12098 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12099 chains... 
    12100 ISOLDE: stopped sim 
    12101 
    12102 > ui tool show "Ramachandran Plot"
    12103 
    12104 > isolde sim start sel
    12105 
    12106 ISOLDE: started sim 
    12107 
    12108 > ui tool show "Ramachandran Plot"
    12109 
    12110 > isolde sim pause
    12111 
    12112 > ui tool show "Ramachandran Plot"
    12113 
    12114 [Repeated 1 time(s)]
    12115 
    12116 > isolde sim resume
    12117 
    12118 > select clear
    12119 
    12120 > isolde sim pause
    12121 
    12122 > isolde sim resume
    12123 
    12124 > ui tool show "Ramachandran Plot"
    12125 
    12126 Traceback (most recent call last): 
    12127 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12128 packages/matplotlib/cbook/__init__.py", line 287, in process 
    12129 func(*args, **kwargs) 
    12130 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    12131 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    12132 on_resize 
    12133 c.draw() 
    12134 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12135 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    12136 self.figure.draw(self.renderer) 
    12137 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12138 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    12139 result = draw(artist, renderer, *args, **kwargs) 
    12140 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12141 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    12142 return draw(artist, renderer) 
    12143 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12144 packages/matplotlib/figure.py", line 2796, in draw 
    12145 artists = self._get_draw_artists(renderer) 
    12146 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12147 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    12148 ax.apply_aspect() 
    12149 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12150 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    12151 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    12152 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12153 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    12154 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    12155 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    12156 
    12157 > select clear
    12158 
    12159 > isolde sim pause
    12160 
    12161 > select #1/n:91-94
    12162 
    12163 55 atoms, 55 bonds, 4 residues, 1 model selected 
    12164 
    12165 > isolde sim start sel
    12166 
    12167 Simulation already running! 
    12168 
    12169 > isolde sim stop
    12170 
    12171 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12172 chains... 
    12173 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    12174 standards. 
    12175 ISOLDE: stopped sim 
    12176 
    12177 > select #1/n:91-94
    12178 
    12179 55 atoms, 55 bonds, 4 residues, 1 model selected 
    12180 
    12181 > isolde sim start sel
    12182 
    12183 ISOLDE: started sim 
    12184 
    12185 > select clear
    12186 
    12187 [Repeated 2 time(s)]
    12188 
    12189 > ui tool show "Ramachandran Plot"
    12190 
    12191 > isolde pepflip sel
    12192 
    12193 Flipping the peptide bond for 1 residues 
    12194 
    12195 > ui tool show "Ramachandran Plot"
    12196 
    12197 > isolde pepflip sel
    12198 
    12199 Flipping the peptide bond for 1 residues 
    12200 
    12201 > select clear
    12202 
    12203 > isolde pepflip sel
    12204 
    12205 Flipping the peptide bond for 1 residues 
    12206 
    12207 > isolde pepflip sel
    12208 
    12209 Flipping the peptide bond for 1 residues 
    12210 
    12211 > isolde pepflip sel
    12212 
    12213 Flipping the peptide bond for 1 residues 
    12214 
    12215 > select clear
    12216 
    12217 > ui tool show "Ramachandran Plot"
    12218 
    12219 Traceback (most recent call last): 
    12220 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12221 packages/matplotlib/cbook/__init__.py", line 287, in process 
    12222 func(*args, **kwargs) 
    12223 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    12224 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    12225 on_resize 
    12226 c.draw() 
    12227 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12228 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    12229 self.figure.draw(self.renderer) 
    12230 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12231 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    12232 result = draw(artist, renderer, *args, **kwargs) 
    12233 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12234 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    12235 return draw(artist, renderer) 
    12236 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12237 packages/matplotlib/figure.py", line 2796, in draw 
    12238 artists = self._get_draw_artists(renderer) 
    12239 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12240 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    12241 ax.apply_aspect() 
    12242 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12243 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    12244 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    12245 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12246 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    12247 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    12248 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    12249 
    12250 > select clear
    12251 
    12252 > ui tool show "Ramachandran Plot"
    12253 
    12254 > select clear
    12255 
    12256 > ui tool show "Ramachandran Plot"
    12257 
    12258 Traceback (most recent call last): 
    12259 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12260 packages/matplotlib/cbook/__init__.py", line 287, in process 
    12261 func(*args, **kwargs) 
    12262 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    12263 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    12264 on_resize 
    12265 c.draw() 
    12266 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12267 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    12268 self.figure.draw(self.renderer) 
    12269 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12270 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    12271 result = draw(artist, renderer, *args, **kwargs) 
    12272 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12273 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    12274 return draw(artist, renderer) 
    12275 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12276 packages/matplotlib/figure.py", line 2796, in draw 
    12277 artists = self._get_draw_artists(renderer) 
    12278 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12279 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    12280 ax.apply_aspect() 
    12281 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12282 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    12283 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    12284 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12285 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    12286 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    12287 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    12288 
    12289 > select clear
    12290 
    12291 > ui tool show "Ramachandran Plot"
    12292 
    12293 [Repeated 1 time(s)]
    12294 
    12295 > isolde sim stop
    12296 
    12297 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12298 chains... 
    12299 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12300 standards. 
    12301 ISOLDE: stopped sim 
    12302 
    12303 > select #1/n:88
    12304 
    12305 20 atoms, 20 bonds, 1 residue, 1 model selected 
    12306 
    12307 > view #1/n:88
    12308 
    12309 > isolde sim start sel
    12310 
    12311 ISOLDE: started sim 
    12312 
    12313 > ui tool show "Ramachandran Plot"
    12314 
    12315 > isolde sim stop
    12316 
    12317 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12318 chains... 
    12319 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    12320 standards. 
    12321 ISOLDE: stopped sim 
    12322 
    12323 > select clear
    12324 
    12325 > select #1/n:88|/i:40
    12326 
    12327 36 atoms, 35 bonds, 2 residues, 1 model selected 
    12328 
    12329 > isolde sim start sel
    12330 
    12331 ISOLDE: started sim 
    12332 
    12333 > select clear
    12334 
    12335 [Repeated 2 time(s)]
    12336 
    12337 > isolde pepflip sel
    12338 
    12339 Flipping the peptide bond for 1 residues 
    12340 
    12341 > select clear
    12342 
    12343 > style #1/i:38-39|/n:86 sphere
    12344 
    12345 Changed 60 atom styles 
    12346 
    12347 > style #1/i:38-39|/n:86|/i:36-40 sphere
    12348 
    12349 Changed 109 atom styles 
    12350 
    12351 > style #1/i:38-39|/n:86|/i:36-40|n:88-90 sphere
    12352 
    12353 Expected a keyword 
    12354 
    12355 > style #1/i:38-39|/n:86|/i:36-40|/n:88-90 sphere
    12356 
    12357 Changed 162 atom styles 
    12358 
    12359 > style #1/i:38-39|/n:86|/i:36-40|/n:88-90 stick
    12360 
    12361 Changed 162 atom styles 
    12362 
    12363 > ui tool show "Ramachandran Plot"
    12364 
    12365 > isolde sim stop
    12366 
    12367 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12368 chains... 
    12369 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    12370 standards. 
    12371 ISOLDE: stopped sim 
    12372 
    12373 > select #1/n:88
    12374 
    12375 20 atoms, 20 bonds, 1 residue, 1 model selected 
    12376 
    12377 > isolde sim start sel
    12378 
    12379 ISOLDE: started sim 
    12380 
    12381 > ui tool show "Ramachandran Plot"
    12382 
    12383 > isolde sim stop
    12384 
    12385 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12386 chains... 
    12387 ISOLDE: stopped sim 
    12388 
    12389 > ui tool show "Ramachandran Plot"
    12390 
    12391 > isolde sim start sel
    12392 
    12393 ISOLDE: started sim 
    12394 
    12395 > ui tool show "Ramachandran Plot"
    12396 
    12397 > isolde sim pause
    12398 
    12399 > isolde sim resume
    12400 
    12401 > ui tool show "Ramachandran Plot"
    12402 
    12403 > select clear
    12404 
    12405 > isolde sim stop
    12406 
    12407 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12408 chains... 
    12409 ISOLDE: stopped sim 
    12410 
    12411 > isolde sim start sel
    12412 
    12413 ISOLDE: started sim 
    12414 
    12415 > ui tool show "Ramachandran Plot"
    12416 
    12417 > isolde sim pause
    12418 
    12419 > isolde sim stop
    12420 
    12421 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12422 chains... 
    12423 ISOLDE: stopped sim 
    12424 
    12425 > isolde sim start sel
    12426 
    12427 ISOLDE: started sim 
    12428 
    12429 > ui tool show "Ramachandran Plot"
    12430 
    12431 > isolde sim stop
    12432 
    12433 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12434 chains... 
    12435 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12436 standards. 
    12437 ISOLDE: stopped sim 
    12438 
    12439 > isolde sim start sel
    12440 
    12441 ISOLDE: started sim 
    12442 
    12443 > ui tool show "Ramachandran Plot"
    12444 
    12445 > isolde pepflip sel
    12446 
    12447 Flipping the peptide bond for 1 residues 
    12448 
    12449 > ui tool show "Ramachandran Plot"
    12450 
    12451 > isolde sim stop
    12452 
    12453 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12454 chains... 
    12455 ISOLDE: stopped sim 
    12456 
    12457 > view #1/m:140
    12458 
    12459 > select #1/m:140
    12460 
    12461 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12462 
    12463 > isolde sim start sel
    12464 
    12465 ISOLDE: started sim 
    12466 
    12467 > ui tool show "Ramachandran Plot"
    12468 
    12469 > select clear
    12470 
    12471 > isolde sim stop
    12472 
    12473 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12474 chains... 
    12475 ISOLDE: stopped sim 
    12476 
    12477 > select #1/m:178
    12478 
    12479 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12480 
    12481 > view #1/m:178
    12482 
    12483 > isolde sim start sel
    12484 
    12485 ISOLDE: started sim 
    12486 
    12487 > ui tool show "Ramachandran Plot"
    12488 
    12489 > isolde sim stop
    12490 
    12491 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12492 chains... 
    12493 ISOLDE: stopped sim 
    12494 
    12495 > ui tool show "Ramachandran Plot"
    12496 
    12497 > isolde sim start sel
    12498 
    12499 ISOLDE: started sim 
    12500 
    12501 > ui tool show "Ramachandran Plot"
    12502 
    12503 > isolde sim pause
    12504 
    12505 > isolde sim resume
    12506 
    12507 > isolde sim pause
    12508 
    12509 > select #1/L:13|/L:16
    12510 
    12511 39 atoms, 37 bonds, 2 residues, 1 model selected 
    12512 
    12513 > isolde sim start sel
    12514 
    12515 Simulation already running! 
    12516 
    12517 > isolde sim stop
    12518 
    12519 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12520 chains... 
    12521 ISOLDE: stopped sim 
    12522 
    12523 > select #1/L:13|/L:16
    12524 
    12525 39 atoms, 37 bonds, 2 residues, 1 model selected 
    12526 
    12527 > isolde sim start sel
    12528 
    12529 ISOLDE: started sim 
    12530 
    12531 > isolde sim pause
    12532 
    12533 > isolde sim resume
    12534 
    12535 > ui tool show "Ramachandran Plot"
    12536 
    12537 > isolde sim stop
    12538 
    12539 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12540 chains... 
    12541 ISOLDE: stopped sim 
    12542 
    12543 > isolde sim start sel
    12544 
    12545 ISOLDE: started sim 
    12546 
    12547 > ui tool show "Ramachandran Plot"
    12548 
    12549 > isolde sim stop
    12550 
    12551 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12552 chains... 
    12553 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12554 standards. 
    12555 ISOLDE: stopped sim 
    12556 
    12557 > view #1/L:13|/L:16
    12558 
    12559 > select #1/L:13|/L:16
    12560 
    12561 39 atoms, 37 bonds, 2 residues, 1 model selected 
    12562 
    12563 > isolde sim start sel
    12564 
    12565 ISOLDE: started sim 
    12566 
    12567 > ui tool show "Ramachandran Plot"
    12568 
    12569 > isolde sim stop
    12570 
    12571 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12572 chains... 
    12573 ISOLDE: stopped sim 
    12574 
    12575 > view #1/L:21
    12576 
    12577 > select #1/L:21
    12578 
    12579 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12580 
    12581 > isolde sim start sel
    12582 
    12583 ISOLDE: started sim 
    12584 
    12585 > ui tool show "Ramachandran Plot"
    12586 
    12587 [Repeated 1 time(s)]
    12588 
    12589 > isolde sim stop
    12590 
    12591 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12592 chains... 
    12593 ISOLDE: stopped sim 
    12594 
    12595 > ui tool show "Ramachandran Plot"
    12596 
    12597 > isolde sim start sel
    12598 
    12599 ISOLDE: started sim 
    12600 
    12601 > isolde pepflip sel
    12602 
    12603 Flipping the peptide bond for 1 residues 
    12604 
    12605 > ui tool show "Ramachandran Plot"
    12606 
    12607 > select clear
    12608 
    12609 > isolde pepflip sel
    12610 
    12611 Flipping the peptide bond for 1 residues 
    12612 
    12613 > select clear
    12614 
    12615 > isolde sim pause
    12616 
    12617 > isolde sim stop
    12618 
    12619 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12620 chains... 
    12621 ISOLDE: stopped sim 
    12622 
    12623 > isolde sim start sel
    12624 
    12625 ISOLDE: started sim 
    12626 
    12627 > ui tool show "Ramachandran Plot"
    12628 
    12629 [Repeated 1 time(s)]
    12630 
    12631 > isolde sim pause
    12632 
    12633 > isolde sim resume
    12634 
    12635 > isolde pepflip sel
    12636 
    12637 Flipping the peptide bond for 1 residues 
    12638 
    12639 > isolde sim pause
    12640 
    12641 > ui tool show "Ramachandran Plot"
    12642 
    12643 > isolde sim resume
    12644 
    12645 > ui tool show "Ramachandran Plot"
    12646 
    12647 > select clear
    12648 
    12649 > isolde sim pause
    12650 
    12651 > select #1/l:103|/l:107
    12652 
    12653 35 atoms, 33 bonds, 2 residues, 1 model selected 
    12654 
    12655 > isolde sim start sel
    12656 
    12657 Simulation already running! 
    12658 
    12659 > isolde sim stop
    12660 
    12661 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12662 chains... 
    12663 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12664 standards. 
    12665 ISOLDE: stopped sim 
    12666 
    12667 > select #1/l:103|/l:107
    12668 
    12669 35 atoms, 33 bonds, 2 residues, 1 model selected 
    12670 
    12671 > isolde sim start sel
    12672 
    12673 ISOLDE: started sim 
    12674 
    12675 > ui tool show "Ramachandran Plot"
    12676 
    12677 > isolde sim pause
    12678 
    12679 > isolde sim resume
    12680 
    12681 > isolde pepflip sel
    12682 
    12683 Flipping the peptide bond for 1 residues 
    12684 
    12685 > select clear
    12686 
    12687 > isolde pepflip sel
    12688 
    12689 Flipping the peptide bond for 1 residues 
    12690 
    12691 > select clear
    12692 
    12693 > isolde pepflip sel
    12694 
    12695 Flipping the peptide bond for 1 residues 
    12696 
    12697 > isolde pepflip sel
    12698 
    12699 Flipping the peptide bond for 1 residues 
    12700 
    12701 > select clear
    12702 
    12703 > isolde pepflip sel
    12704 
    12705 Flipping the peptide bond for 1 residues 
    12706 
    12707 > select clear
    12708 
    12709 [Repeated 1 time(s)]
    12710 
    12711 > isolde pepflip sel
    12712 
    12713 Flipping the peptide bond for 1 residues 
    12714 
    12715 > isolde pepflip sel
    12716 
    12717 Flipping the peptide bond for 1 residues 
    12718 
    12719 > select clear
    12720 
    12721 > ui tool show "Ramachandran Plot"
    12722 
    12723 > isolde sim pause
    12724 
    12725 > isolde sim stop
    12726 
    12727 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12728 chains... 
    12729 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12730 standards. 
    12731 ISOLDE: stopped sim 
    12732 
    12733 > select #1/l:103|/l:107|/l:97|/l:95|/m:41
    12734 
    12735 87 atoms, 82 bonds, 5 residues, 1 model selected 
    12736 
    12737 > isolde sim start sel
    12738 
    12739 ISOLDE: started sim 
    12740 
    12741 > ui tool show "Ramachandran Plot"
    12742 
    12743 > isolde sim pause
    12744 
    12745 > isolde sim resume
    12746 
    12747 > ui tool show "Ramachandran Plot"
    12748 
    12749 > isolde sim stop
    12750 
    12751 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12752 chains... 
    12753 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    12754 standards. 
    12755 ISOLDE: stopped sim 
    12756 
    12757 > select #1/l:91|/l:93
    12758 
    12759 29 atoms, 28 bonds, 2 residues, 1 model selected 
    12760 
    12761 > isolde sim start sel
    12762 
    12763 ISOLDE: started sim 
    12764 
    12765 > select clear
    12766 
    12767 > isolde pepflip sel
    12768 
    12769 Flipping the peptide bond for 1 residues 
    12770 
    12771 > isolde pepflip sel
    12772 
    12773 Flipping the peptide bond for 1 residues 
    12774 
    12775 > isolde pepflip sel
    12776 
    12777 Flipping the peptide bond for 1 residues 
    12778 
    12779 > isolde pepflip sel
    12780 
    12781 Flipping the peptide bond for 1 residues 
    12782 
    12783 > isolde pepflip sel
    12784 
    12785 Flipping the peptide bond for 1 residues 
    12786 
    12787 > select clear
    12788 
    12789 > isolde pepflip sel
    12790 
    12791 Flipping the peptide bond for 1 residues 
    12792 
    12793 > isolde pepflip sel
    12794 
    12795 Flipping the peptide bond for 1 residues 
    12796 
    12797 > isolde sim stop
    12798 
    12799 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12800 chains... 
    12801 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12802 standards. 
    12803 ISOLDE: stopped sim 
    12804 
    12805 > select #1/l:91|/l:93
    12806 
    12807 29 atoms, 28 bonds, 2 residues, 1 model selected 
    12808 
    12809 > isolde sim start sel
    12810 
    12811 ISOLDE: started sim 
    12812 
    12813 > select clear
    12814 
    12815 [Repeated 2 time(s)]
    12816 
    12817 > isolde pepflip sel
    12818 
    12819 Flipping the peptide bond for 1 residues 
    12820 
    12821 > select clear
    12822 
    12823 > isolde sim pause
    12824 
    12825 > select #1
    12826 
    12827 144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    12828 
    12829 > select #1/R89
    12830 
    12831 Nothing selected 
    12832 
    12833 > select #1/R:89
    12834 
    12835 21 atoms, 21 bonds, 1 residue, 1 model selected 
    12836 
    12837 > select #1
    12838 
    12839 144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    12840 
    12841 > select #1/l:89
    12842 
    12843 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12844 
    12845 > isolde sim resume
    12846 
    12847 > select clear
    12848 
    12849 > select #1/l:88-87
    12850 
    12851 Nothing selected 
    12852 
    12853 > isolde sim pause
    12854 
    12855 > select #1/l:88-87
    12856 
    12857 Nothing selected 
    12858 
    12859 > select #1/l:88-90
    12860 
    12861 53 atoms, 52 bonds, 3 residues, 1 model selected 
    12862 
    12863 > isolde sim resume
    12864 
    12865 > select #1
    12866 
    12867 144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    12868 
    12869 > select clear
    12870 
    12871 > ui tool show "Ramachandran Plot"
    12872 
    12873 > isolde sim stop
    12874 
    12875 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12876 chains... 
    12877 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    12878 standards. 
    12879 ISOLDE: stopped sim 
    12880 
    12881 > view #1/l:103|/l:107|/l:97|/l:95|/m:41
    12882 
    12883 > select #1/l:103|/l:107|/l:97|/l:95|/m:41
    12884 
    12885 87 atoms, 82 bonds, 5 residues, 1 model selected 
    12886 
    12887 > isolde sim start sel
    12888 
    12889 ISOLDE: started sim 
    12890 
    12891 > ui tool show "Ramachandran Plot"
    12892 
    12893 > isolde sim stop
    12894 
    12895 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12896 chains... 
    12897 ISOLDE: stopped sim 
    12898 
    12899 > select #1/l:103|/l:107
    12900 
    12901 35 atoms, 33 bonds, 2 residues, 1 model selected 
    12902 
    12903 > isolde sim start sel
    12904 
    12905 ISOLDE: started sim 
    12906 
    12907 > ui tool show "Ramachandran Plot"
    12908 
    12909 > isolde sim stop
    12910 
    12911 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12912 chains... 
    12913 ISOLDE: stopped sim 
    12914 
    12915 > select #1/m:39
    12916 
    12917 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12918 
    12919 > view #1/m:39
    12920 
    12921 > view #1/m:38
    12922 
    12923 > select #1/m:38
    12924 
    12925 17 atoms, 17 bonds, 1 residue, 1 model selected 
    12926 
    12927 > isolde sim start sel
    12928 
    12929 ISOLDE: started sim 
    12930 
    12931 > ui tool show "Ramachandran Plot"
    12932 
    12933 > isolde sim stop
    12934 
    12935 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12936 chains... 
    12937 ISOLDE: stopped sim 
    12938 
    12939 > select #1/m:42
    12940 
    12941 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12942 
    12943 > view #1/m:42
    12944 
    12945 > isolde sim start sel
    12946 
    12947 ISOLDE: started sim 
    12948 
    12949 > ui tool show "Ramachandran Plot"
    12950 
    12951 > isolde sim stop
    12952 
    12953 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12954 chains... 
    12955 ISOLDE: stopped sim 
    12956 
    12957 > ui tool show "Ramachandran Plot"
    12958 
    12959 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    12960 > mut8-no-C-ter/20-7-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    12961 > step20-7-FinishedStep1d2dC.cxs
    12962 
    12963 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    12964 
    12965 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    12966 > mut8-no-C-ter/20-7-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    12967 > step20-7-FinishedStep1d2dC.pdb
    12968 
    12969 > ui tool show "Ramachandran Plot"
    12970 
    12971 > isolde sim start sel
    12972 
    12973 ISOLDE: started sim 
    12974 
    12975 > ui tool show "Ramachandran Plot"
    12976 
    12977 > isolde sim stop
    12978 
    12979 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12980 chains... 
    12981 ISOLDE: stopped sim 
    12982 
    12983 > ui tool show "Ramachandran Plot"
    12984 
    12985 > isolde sim start sel
    12986 
    12987 ISOLDE: started sim 
    12988 
    12989 > ui tool show "Ramachandran Plot"
    12990 
    12991 [Repeated 1 time(s)]
    12992 
    12993 > select clear
    12994 
    12995 > isolde sim stop
    12996 
    12997 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12998 chains... 
    12999 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    13000 standards. 
    13001 ISOLDE: stopped sim 
    13002 
    13003 > ui tool show "Ramachandran Plot"
    13004 
    13005 > isolde sim start sel
    13006 
    13007 ISOLDE: started sim 
    13008 
    13009 > ui tool show "Ramachandran Plot"
    13010 
    13011 > isolde sim pause
    13012 
    13013 > isolde sim resume
    13014 
    13015 > ui tool show "Ramachandran Plot"
    13016 
    13017 > isolde sim pause
    13018 
    13019 > isolde sim stop
    13020 
    13021 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13022 chains... 
    13023 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    13024 standards. 
    13025 ISOLDE: stopped sim 
    13026 
    13027 > select #1/S:59-64
    13028 
    13029 83 atoms, 82 bonds, 6 residues, 1 model selected 
    13030 
    13031 > isolde sim start sel
    13032 
    13033 ISOLDE: started sim 
    13034 
    13035 > ui tool show "Ramachandran Plot"
    13036 
    13037 > isolde sim pause
    13038 
    13039 > isolde sim resume
    13040 
    13041 > select clear
    13042 
    13043 > isolde pepflip sel
    13044 
    13045 Flipping the peptide bond for 1 residues 
    13046 
    13047 > isolde pepflip sel
    13048 
    13049 Flipping the peptide bond for 1 residues 
    13050 
    13051 > select clear
    13052 
    13053 > ui tool show "Ramachandran Plot"
    13054 
    13055 [Repeated 1 time(s)]
    13056 
    13057 > isolde sim stop
    13058 
    13059 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13060 chains... 
    13061 ISOLDE: stopped sim 
    13062 
    13063 > view #1/S:59-64
    13064 
    13065 > view #1/S:53
    13066 
    13067 > select #1/S:53
    13068 
    13069 11 atoms, 10 bonds, 1 residue, 1 model selected 
    13070 
    13071 > isolde sim start sel
    13072 
    13073 ISOLDE: started sim 
    13074 
    13075 > ui tool show "Ramachandran Plot"
     1592[deleted to fit within ticket limits]
    130761593
    130771594> isolde sim pause