Changes between Initial Version and Version 1 of Ticket #8875


Ignore:
Timestamp:
Apr 20, 2023, 1:17:40 PM (3 years ago)
Author:
Eric Pettersen
Comment:

Hi Alvin,

This problem has been reported to the XMAS developers along with a fix (​https://github.com/ScheltemaLab/ChimeraX_bundle/issues/2) but they have not issued a corrected version of the XMAS bundle yet.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #8875

    • Property Cc Eric Pettersen added
    • Property Component Unassigned → Third Party
    • Property Owner set to Richard Scheltema
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → XMAS: crash in ~QGridLayout()

  • Ticket #8875 – Description

    initial v1  
    907907> #4,0.95986,-0.22484,0.16768,73.526,0.27579,0.64758,-0.71034,90.606,0.051126,0.72807,0.68359,-47.104
    908908
    909 > view matrix models
    910 > #4,0.75847,0.64831,0.066474,-35.582,0.26049,-0.20809,-0.94278,276.59,-0.59738,0.73239,-0.32671,193.1
    911 
    912 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    913 (#1) using 3401 atoms 
    914 average map value = 0.09049, steps = 88 
    915 shifted from previous position = 2.42 
    916 rotated from previous position = 6.19 degrees 
    917 atoms outside contour = 1911, contour level = 0.072 
    918  
    919 Position of F562a.pdb (#4) relative to
    920 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    921 Matrix rotation and translation 
    922 0.72637414 0.68694818 -0.02197301 -24.03798979 
    923 0.18664733 -0.22792648 -0.95562142 294.38643021 
    924 -0.66147062 0.69003748 -0.29377694 209.53189487 
    925 Axis 0.89678670 0.34848835 -0.27263435 
    926 Axis point 0.00000000 72.78629578 205.81231454 
    927 Rotation angle (degrees) 113.43226483 
    928 Shift along axis 23.90769923 
    929  
    930 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    931 (#1) using 3401 atoms 
    932 average map value = 0.0905, steps = 44 
    933 shifted from previous position = 0.0137 
    934 rotated from previous position = 0.0204 degrees 
    935 atoms outside contour = 1906, contour level = 0.072 
    936  
    937 Position of F562a.pdb (#4) relative to
    938 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    939 Matrix rotation and translation 
    940 0.72623985 0.68709241 -0.02190190 -24.03578291 
    941 0.18654834 -0.22764140 -0.95570869 294.36480593 
    942 -0.66164597 0.68998798 -0.29349821 209.53312556 
    943 Axis 0.89671635 0.34858730 -0.27273923 
    944 Axis point 0.00000000 72.74870511 205.83733915 
    945 Rotation angle (degrees) 113.41885466 
    946 Shift along axis 23.91065009 
    947  
    948 
    949 > view matrix models
    950 > #4,0.4777,0.81916,-0.31746,33.473,0.28288,-0.48553,-0.82719,308.03,-0.83173,0.30535,-0.46366,331.51
    951 
    952 > view matrix models
    953 > #4,0.53443,0.7221,-0.43927,54.882,0.15416,-0.59427,-0.78935,347.48,-0.83104,0.35413,-0.42891,318.4
    954 
    955 > view matrix models
    956 > #4,0.55861,0.65321,-0.51116,71.372,0.070767,-0.65156,-0.75529,369.52,-0.82641,0.38574,-0.41019,309.57
    957 
    958 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    959 (#1) using 3401 atoms 
    960 average map value = 0.0972, steps = 104 
    961 shifted from previous position = 3.1 
    962 rotated from previous position = 2.07 degrees 
    963 atoms outside contour = 1844, contour level = 0.072 
    964  
    965 Position of F562a.pdb (#4) relative to
    966 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    967 Matrix rotation and translation 
    968 0.58731938 0.63730986 -0.49889086 69.51709433 
    969 0.06189895 -0.64996950 -0.75743526 371.85473470 
    970 -0.80698480 0.41397558 -0.42118849 304.38816914 
    971 Axis 0.87354940 0.22975311 -0.42909784 
    972 Axis point 0.00000000 108.25389938 250.40641939 
    973 Rotation angle (degrees) 137.89516888 
    974 Shift along axis 15.54909083 
    975  
    976 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    977 (#1) using 3401 atoms 
    978 average map value = 0.0972, steps = 100 
    979 shifted from previous position = 0.0102 
    980 rotated from previous position = 0.0178 degrees 
    981 atoms outside contour = 1844, contour level = 0.072 
    982  
    983 Position of F562a.pdb (#4) relative to
    984 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    985 Matrix rotation and translation 
    986 0.58732049 0.63712467 -0.49912604 69.58840441 
    987 0.06165901 -0.65012663 -0.75731997 371.91413492 
    988 -0.80700236 0.41401391 -0.42111716 304.37603978 
    989 Axis 0.87355306 0.22960687 -0.42916866 
    990 Axis point 0.00000000 108.28874120 250.42594564 
    991 Rotation angle (degrees) 137.89878759 
    992 Shift along axis 15.55454641 
    993  
    994 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    995 (#1) using 3401 atoms 
    996 average map value = 0.0972, steps = 84 
    997 shifted from previous position = 0.011 
    998 rotated from previous position = 0.0172 degrees 
    999 atoms outside contour = 1844, contour level = 0.072 
    1000  
    1001 Position of F562a.pdb (#4) relative to
    1002 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1003 Matrix rotation and translation 
    1004 0.58733885 0.63729229 -0.49889038 69.51578518 
    1005 0.06188954 -0.64997620 -0.75743028 371.85701767 
    1006 -0.80697135 0.41399213 -0.42119800 304.38350057 
    1007 Axis 0.87355567 0.22974281 -0.42909059 
    1008 Axis point 0.00000000 108.25696578 250.40359329 
    1009 Rotation angle (degrees) 137.89502914 
    1010 Shift along axis 15.54928904 
    1011  
    1012 
    1013 > view matrix models
    1014 > #4,0.65819,-0.32045,-0.68124,252,0.74547,0.15105,0.6492,-68.256,-0.10513,-0.93515,0.3383,328.44
    1015 
    1016 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1017 (#1) using 3401 atoms 
    1018 average map value = 0.102, steps = 172 
    1019 shifted from previous position = 4.22 
    1020 rotated from previous position = 10.1 degrees 
    1021 atoms outside contour = 1745, contour level = 0.072 
    1022  
    1023 Position of F562a.pdb (#4) relative to
    1024 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1025 Matrix rotation and translation 
    1026 0.62980729 -0.32213914 -0.70680207 259.21419516 
    1027 0.77615676 0.29659722 0.55642680 -86.34491343 
    1028 0.03038868 -0.89903085 0.43682956 282.25072430 
    1029 Axis -0.74003611 -0.37482903 0.55843509 
    1030 Axis point 0.00000000 121.16366768 309.58820660 
    1031 Rotation angle (degrees) 79.53603811 
    1032 Shift along axis -1.84457671 
    1033  
    1034 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1035 (#1) using 3401 atoms 
    1036 average map value = 0.1019, steps = 48 
    1037 shifted from previous position = 0.0802 
    1038 rotated from previous position = 0.389 degrees 
    1039 atoms outside contour = 1748, contour level = 0.072 
    1040  
    1041 Position of F562a.pdb (#4) relative to
    1042 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1043 Matrix rotation and translation 
    1044 0.62493642 -0.32416938 -0.71018919 260.92042942 
    1045 0.78000765 0.29690303 0.55085085 -86.37873091 
    1046 0.03228835 -0.89819976 0.43840012 281.55642716 
    1047 Axis -0.73657217 -0.37741145 0.56126823 
    1048 Axis point 0.00000000 119.97837519 311.01534570 
    1049 Rotation angle (degrees) 79.62326298 
    1050 Shift along axis -1.55772605 
    1051  
    1052 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1053 (#1) using 3401 atoms 
    1054 average map value = 0.1019, steps = 44 
    1055 shifted from previous position = 0.00561 
    1056 rotated from previous position = 0.0322 degrees 
    1057 atoms outside contour = 1746, contour level = 0.072 
    1058  
    1059 Position of F562a.pdb (#4) relative to
    1060 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1061 Matrix rotation and translation 
    1062 0.62451536 -0.32441238 -0.71044858 261.07250560 
    1063 0.78034368 0.29682398 0.55041736 -86.36985039 
    1064 0.03231597 -0.89813815 0.43852428 281.52393140 
    1065 Axis -0.73629476 -0.37754414 0.56154292 
    1066 Axis point 0.00000000 119.89834457 311.14057931 
    1067 Rotation angle (degrees) 79.63421202 
    1068 Shift along axis -1.53011648 
    1069  
    1070 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1071 (#1) using 3401 atoms 
    1072 average map value = 0.1019, steps = 80 
    1073 shifted from previous position = 0.189 
    1074 rotated from previous position = 1.07 degrees 
    1075 atoms outside contour = 1750, contour level = 0.072 
    1076  
    1077 Position of F562a.pdb (#4) relative to
    1078 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1079 Matrix rotation and translation 
    1080 0.61106207 -0.33151468 -0.71881930 265.86650256 
    1081 0.79073980 0.29753498 0.53497991 -86.41685086 
    1082 0.03652019 -0.89530496 0.44395419 279.51480621 
    1083 Axis -0.72651910 -0.38367781 0.57005380 
    1084 Axis point 0.00000000 116.77430340 315.34054751 
    1085 Rotation angle (degrees) 79.84710044 
    1086 Shift along axis -0.66238880 
    1087  
    1088 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1089 (#1) using 3401 atoms 
    1090 average map value = 0.1019, steps = 60 
    1091 shifted from previous position = 0.014 
    1092 rotated from previous position = 0.0403 degrees 
    1093 atoms outside contour = 1749, contour level = 0.072 
    1094  
    1095 Position of F562a.pdb (#4) relative to
    1096 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1097 Matrix rotation and translation 
    1098 0.61056528 -0.33194773 -0.71904155 266.05161554 
    1099 0.79112724 0.29741686 0.53447255 -86.39981112 
    1100 0.03643813 -0.89518374 0.44420530 279.47442312 
    1101 Axis -0.72617579 -0.38373633 0.57045170 
    1102 Axis point 0.00000000 116.70216550 315.50779421 
    1103 Rotation angle (degrees) 79.85768786 
    1104 Shift along axis -0.61883651 
    1105  
    1106 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1107 (#1) using 3401 atoms 
    1108 average map value = 0.1019, steps = 56 
    1109 shifted from previous position = 0.00922 
    1110 rotated from previous position = 0.0302 degrees 
    1111 atoms outside contour = 1747, contour level = 0.072 
    1112  
    1113 Position of F562a.pdb (#4) relative to
    1114 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1115 Matrix rotation and translation 
    1116 0.61096453 -0.33178461 -0.71877766 265.91505542 
    1117 0.79082389 0.29745317 0.53490111 -86.40973158 
    1118 0.03633074 -0.89523215 0.44411653 279.51627475 
    1119 Axis -0.72644097 -0.38355984 0.57023274 
    1120 Axis point -0.00000000 116.79213793 315.39803173 
    1121 Rotation angle (degrees) 79.84759520 
    1122 Shift along axis -0.63895706 
    1123  
    1124 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1125 (#1) using 3401 atoms 
    1126 average map value = 0.1019, steps = 60 
    1127 shifted from previous position = 0.0112 
    1128 rotated from previous position = 0.0392 degrees 
    1129 atoms outside contour = 1755, contour level = 0.072 
    1130  
    1131 Position of F562a.pdb (#4) relative to
    1132 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1133 Matrix rotation and translation 
    1134 0.61092141 -0.33119723 -0.71908514 265.86201413 
    1135 0.79084444 0.29729954 0.53495614 -86.39268360 
    1136 0.03660768 -0.89550063 0.44355214 279.58799940 
    1137 Axis -0.72655505 -0.38383015 0.56990540 
    1138 Axis point 0.00000000 116.72048670 315.29183470 
    1139 Rotation angle (degrees) 79.86974659 
    1140 Shift along axis -0.66456157 
    1141  
    1142 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1143 (#1) using 3401 atoms 
    1144 average map value = 0.1019, steps = 48 
    1145 shifted from previous position = 0.0123 
    1146 rotated from previous position = 0.0779 degrees 
    1147 atoms outside contour = 1747, contour level = 0.072 
    1148  
    1149 Position of F562a.pdb (#4) relative to
    1150 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1151 Matrix rotation and translation 
    1152 0.61046660 -0.33218219 -0.71901706 266.11491018 
    1153 0.79119095 0.29782655 0.53415002 -86.45092816 
    1154 0.03670725 -0.89496053 0.44463270 279.33262127 
    1155 Axis -0.72594735 -0.38388637 0.57064148 
    1156 Axis point 0.00000000 116.64464322 315.61501173 
    1157 Rotation angle (degrees) 79.83619740 
    1158 Shift along axis -0.59930216 
    1159  
    1160 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1161 (#1) using 3401 atoms 
    1162 average map value = 0.1019, steps = 36 
    1163 shifted from previous position = 0.00553 
    1164 rotated from previous position = 0.0185 degrees 
    1165 atoms outside contour = 1746, contour level = 0.072 
    1166  
    1167 Position of F562a.pdb (#4) relative to
    1168 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1169 Matrix rotation and translation 
    1170 0.61052405 -0.33197184 -0.71906543 266.07628678 
    1171 0.79114928 0.29764543 0.53431266 -86.42628442 
    1172 0.03664978 -0.89509882 0.44435898 279.40085187 
    1173 Axis -0.72607396 -0.38386786 0.57049283 
    1174 Axis point 0.00000000 116.66062451 315.54721201 
    1175 Rotation angle (degrees) 79.84776315 
    1176 Shift along axis -0.61860883 
    1177  
    1178 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1179 (#1) using 3401 atoms 
    1180 average map value = 0.1019, steps = 48 
    1181 shifted from previous position = 0.0181 
    1182 rotated from previous position = 0.0284 degrees 
    1183 atoms outside contour = 1749, contour level = 0.072 
    1184  
    1185 Position of F562a.pdb (#4) relative to
    1186 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1187 Matrix rotation and translation 
    1188 0.61082613 -0.33169276 -0.71893766 265.95113585 
    1189 0.79091989 0.29755592 0.53470198 -86.43037190 
    1190 0.03656738 -0.89523203 0.44409733 279.47798684 
    1191 Axis -0.72633614 -0.38375939 0.57023200 
    1192 Axis point -0.00000000 116.71858763 315.43181746 
    1193 Rotation angle (degrees) 79.84919126 
    1194 Shift along axis -0.63416214 
    1195  
    1196 
    1197 > view matrix models
    1198 > #4,0.4439,-0.28201,-0.85054,303.77,0.88884,0.018251,0.45784,-44.907,-0.11359,-0.95924,0.25876,341.18
    1199 
    1200 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1201 (#1) using 3401 atoms 
    1202 average map value = 0.1055, steps = 424 
    1203 shifted from previous position = 2.2 
    1204 rotated from previous position = 6.39 degrees 
    1205 atoms outside contour = 1635, contour level = 0.072 
    1206  
    1207 Position of F562a.pdb (#4) relative to
    1208 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1209 Matrix rotation and translation 
    1210 0.47014986 -0.27680804 -0.83805515 296.29282889 
    1211 0.88242695 0.12936746 0.45231266 -60.98673857 
    1212 -0.01678672 -0.95217718 0.30508496 317.15529629 
    1213 Axis -0.70304515 -0.41110215 0.58027799 
    1214 Axis point 0.00000000 97.60706796 321.98215187 
    1215 Rotation angle (degrees) 92.73398070 
    1216 Shift along axis 0.80277942 
    1217  
    1218 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1219 (#1) using 3401 atoms 
    1220 average map value = 0.1055, steps = 44 
    1221 shifted from previous position = 0.0281 
    1222 rotated from previous position = 0.296 degrees 
    1223 atoms outside contour = 1634, contour level = 0.072 
    1224  
    1225 Position of F562a.pdb (#4) relative to
    1226 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1227 Matrix rotation and translation 
    1228 0.47131282 -0.27849458 -0.83684228 296.21168106 
    1229 0.88186020 0.13410185 0.45203904 -61.71403302 
    1230 -0.01366832 -0.95102969 0.30879721 315.93242787 
    1231 Axis -0.70218063 -0.41196614 0.58071186 
    1232 Axis point 0.00000000 97.40904882 322.29816415 
    1233 Rotation angle (degrees) 92.45840264 
    1234 Shift along axis 0.89569574 
    1235  
    1236 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1237 (#1) using 3401 atoms 
    1238 average map value = 0.1055, steps = 40 
    1239 shifted from previous position = 0.0165 
    1240 rotated from previous position = 0.16 degrees 
    1241 atoms outside contour = 1637, contour level = 0.072 
    1242  
    1243 Position of F562a.pdb (#4) relative to
    1244 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1245 Matrix rotation and translation 
    1246 0.47202347 -0.27915399 -0.83622180 296.12646474 
    1247 0.88150690 0.13674791 0.45193539 -62.12511633 
    1248 -0.01180798 -0.95045940 0.31062439 315.27843547 
    1249 Axis -0.70176755 -0.41254208 0.58080232 
    1250 Axis point 0.00000000 97.28028496 322.43137386 
    1251 Rotation angle (degrees) 92.30976635 
    1252 Shift along axis 0.93172962 
    1253  
    1254 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1255 (#1) using 3401 atoms 
    1256 average map value = 0.1055, steps = 40 
    1257 shifted from previous position = 0.0221 
    1258 rotated from previous position = 0.193 degrees 
    1259 atoms outside contour = 1638, contour level = 0.072 
    1260  
    1261 Position of F562a.pdb (#4) relative to
    1262 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1263 Matrix rotation and translation 
    1264 0.47308077 -0.28050864 -0.83517034 296.03384583 
    1265 0.88096007 0.13964438 0.45211592 -62.58112928 
    1266 -0.01019558 -0.94963907 0.31317998 314.52160203 
    1267 Axis -0.70135897 -0.41277074 0.58113330 
    1268 Axis point 0.00000000 97.26838533 322.61659552 
    1269 Rotation angle (degrees) 92.12314752 
    1270 Shift along axis 0.98464198 
    1271  
    1272 
    1273 > transparency #1.1 0
    1274 
    1275 > view matrix models
    1276 > #4,0.84021,-0.0035817,-0.54224,142.19,-0.39021,0.69038,-0.60919,201.03,0.37654,0.72344,0.57867,-93.731
    1277 
    1278 > view matrix models
    1279 > #4,0.79315,-0.11192,-0.59866,177.39,0.50761,-0.42168,0.75135,74.2,-0.33653,-0.89981,-0.27764,436.47
    1280 
    1281 > view matrix models
    1282 > #4,0.7358,0.3335,-0.58938,106.02,-0.64815,0.094684,-0.7556,375.07,-0.19619,0.93798,0.28583,9.2542
    1283 
    1284 > view matrix models
    1285 > #4,0.79115,-0.59673,-0.13416,211.08,0.60994,0.75351,0.24535,-98.992,-0.045318,-0.27593,0.96011,122.12
    1286 
    1287 > view matrix models
    1288 > #4,0.66555,-0.4336,-0.60749,260.88,0.69641,0.65352,0.29652,-103.07,0.26843,-0.62041,0.73691,152.31
    1289 
    1290 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1291 (#1) using 3401 atoms 
    1292 average map value = 0.1, steps = 416 
    1293 shifted from previous position = 2.7 
    1294 rotated from previous position = 17.5 degrees 
    1295 atoms outside contour = 1774, contour level = 0.072 
    1296  
    1297 Position of F562a.pdb (#4) relative to
    1298 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1299 Matrix rotation and translation 
    1300 0.67732915 -0.28469604 -0.67836083 239.91883502 
    1301 0.71088577 0.49065254 0.50388643 -103.74543128 
    1302 0.18938499 -0.82353401 0.53471962 227.48787848 
    1303 Axis -0.70890735 -0.46341865 0.53168931 
    1304 Axis point 0.00000000 101.86597662 309.82596584 
    1305 Rotation angle (degrees) 69.43005060 
    1306 Shift along axis -1.04978373 
    1307  
    1308 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1309 (#1) using 3401 atoms 
    1310 average map value = 0.1, steps = 44 
    1311 shifted from previous position = 0.00594 
    1312 rotated from previous position = 0.0194 degrees 
    1313 atoms outside contour = 1776, contour level = 0.072 
    1314  
    1315 Position of F562a.pdb (#4) relative to
    1316 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1317 Matrix rotation and translation 
    1318 0.67756361 -0.28454385 -0.67819052 239.83133941 
    1319 0.71064745 0.49081816 0.50406126 -103.75597407 
    1320 0.18944069 -0.82348792 0.53477088 227.46549023 
    1321 Axis -0.70904026 -0.46339937 0.53152886 
    1322 Axis point 0.00000000 101.90886125 309.76335536 
    1323 Rotation angle (degrees) 69.41623953 
    1324 Shift along axis -1.06514982 
    1325  
    1326 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1327 (#1) using 3401 atoms 
    1328 average map value = 0.09997, steps = 40 
    1329 shifted from previous position = 0.0133 
    1330 rotated from previous position = 0.00996 degrees 
    1331 atoms outside contour = 1778, contour level = 0.072 
    1332  
    1333 Position of F562a.pdb (#4) relative to
    1334 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1335 Matrix rotation and translation 
    1336 0.67763562 -0.28462709 -0.67808363 239.81516361 
    1337 0.71058849 0.49090368 0.50406111 -103.75178064 
    1338 0.18940430 -0.82340817 0.53490655 227.43306000 
    1339 Axis -0.70903930 -0.46335011 0.53157309 
    1340 Axis point 0.00000000 101.93201901 309.76345143 
    1341 Rotation angle (degrees) 69.40726713 
    1342 Shift along axis -1.06768104 
    1343  
    1344 
    1345 > view matrix models
    1346 > #4,0.67386,0.21665,-0.70638,152.68,-0.73712,0.13162,-0.66282,370.99,-0.050625,0.96733,0.2484,-19.457
    1347 
    1348 > view matrix models
    1349 > #4,0.26977,0.74198,-0.61375,121.96,-0.64983,-0.33008,-0.68467,441.19,-0.7106,0.58353,0.39312,157.04
    1350 
    1351 > view matrix models
    1352 > #4,0.83537,0.35405,-0.42048,63.612,-0.53507,0.34852,-0.76957,306.25,-0.12592,0.86786,0.48059,-14.673
    1353 
    1354 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1355 (#1) using 3401 atoms 
    1356 average map value = 0.1062, steps = 108 
    1357 shifted from previous position = 1.02 
    1358 rotated from previous position = 11.1 degrees 
    1359 atoms outside contour = 1639, contour level = 0.072 
    1360  
    1361 Position of F562a.pdb (#4) relative to
    1362 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1363 Matrix rotation and translation 
    1364 0.88907475 0.29063713 -0.35366111 56.95234558 
    1365 -0.45699328 0.51877555 -0.72251581 256.52548266 
    1366 -0.02651919 0.80399130 0.59404945 -35.16228912 
    1367 Axis 0.88188843 -0.18899530 -0.43191847 
    1368 Axis point 0.00000000 161.74872048 251.74241852 
    1369 Rotation angle (degrees) 59.93713751 
    1370 Shift along axis 16.93074519 
    1371  
    1372 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1373 (#1) using 3401 atoms 
    1374 average map value = 0.1062, steps = 44 
    1375 shifted from previous position = 0.0122 
    1376 rotated from previous position = 0.077 degrees 
    1377 atoms outside contour = 1637, contour level = 0.072 
    1378  
    1379 Position of F562a.pdb (#4) relative to
    1380 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1381 Matrix rotation and translation 
    1382 0.88924092 0.29042756 -0.35341541 56.93133633 
    1383 -0.45670512 0.51991995 -0.72187513 256.18534624 
    1384 -0.02590471 0.80332752 0.59497383 -35.27785394 
    1385 Axis 0.88179482 -0.18935008 -0.43195422 
    1386 Axis point -0.00000000 161.74523741 251.76190662 
    1387 Rotation angle (degrees) 59.86313127 
    1388 Shift along axis 16.93146051 
    1389  
    1390 
    1391 > view matrix models
    1392 > #4,0.83879,0.21495,-0.50022,97.467,-0.52296,0.062549,-0.85006,366.96,-0.15144,0.97462,0.16488,7.9202
    1393 
    1394 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1395 (#1) using 3401 atoms 
    1396 average map value = 0.1097, steps = 264 
    1397 shifted from previous position = 0.803 
    1398 rotated from previous position = 13.4 degrees 
    1399 atoms outside contour = 1566, contour level = 0.072 
    1400  
    1401 Position of F562a.pdb (#4) relative to
    1402 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1403 Matrix rotation and translation 
    1404 0.90125965 0.23249395 -0.36561951 66.81826163 
    1405 -0.42074684 0.26813163 -0.86664730 312.38684742 
    1406 -0.10345610 0.93490749 0.33947732 -14.03685609 
    1407 Axis 0.93143071 -0.13554240 -0.33773523 
    1408 Axis point 0.00000000 165.03559591 224.93775063 
    1409 Rotation angle (degrees) 75.25993272 
    1410 Shift along axis 24.63566001 
    1411  
    1412 
    1413 > view matrix models
    1414 > #4,0.85035,0.35218,-0.39099,57.593,-0.48265,0.22596,-0.84616,329.25,-0.20965,0.90825,0.36212,8.0544
    1415 
    1416 > ui mousemode right "translate selected models"
    1417 
    1418 > view matrix models
    1419 > #4,0.85035,0.35218,-0.39099,60.231,-0.48265,0.22596,-0.84616,326.26,-0.20965,0.90825,0.36212,12.759
    1420 
    1421 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1422 (#1) using 3401 atoms 
    1423 average map value = 0.1101, steps = 168 
    1424 shifted from previous position = 2.33 
    1425 rotated from previous position = 5.98 degrees 
    1426 atoms outside contour = 1596, contour level = 0.072 
    1427  
    1428 Position of F562a.pdb (#4) relative to
    1429 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1430 Matrix rotation and translation 
    1431 0.88028089 0.25385290 -0.40082949 74.19694561 
    1432 -0.45618497 0.22068248 -0.86208731 322.45385437 
    1433 -0.13038732 0.94173137 0.31006645 -3.17418883 
    1434 Axis 0.92158142 -0.13817047 -0.36276246 
    1435 Axis point 0.00000000 162.85511452 230.82234394 
    1436 Rotation angle (degrees) 78.14035717 
    1437 Shift along axis 24.97640109 
    1438  
    1439 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1440 (#1) using 3401 atoms 
    1441 average map value = 0.1101, steps = 64 
    1442 shifted from previous position = 0.011 
    1443 rotated from previous position = 0.0221 degrees 
    1444 atoms outside contour = 1600, contour level = 0.072 
    1445  
    1446 Position of F562a.pdb (#4) relative to
    1447 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1448 Matrix rotation and translation 
    1449 0.88011312 0.25412437 -0.40102585 74.19170998 
    1450 -0.45646647 0.22069435 -0.86193525 322.48434036 
    1451 -0.13053461 0.94165537 0.31023525 -3.15440043 
    1452 Axis 0.92146618 -0.13819573 -0.36304548 
    1453 Axis point 0.00000000 162.86097718 230.89097488 
    1454 Rotation angle (degrees) 78.13997962 
    1455 Shift along axis 24.94438268 
    1456  
    1457 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1458 (#1) using 3401 atoms 
    1459 average map value = 0.1101, steps = 64 
    1460 shifted from previous position = 0.00421 
    1461 rotated from previous position = 0.0136 degrees 
    1462 atoms outside contour = 1600, contour level = 0.072 
    1463  
    1464 Position of F562a.pdb (#4) relative to
    1465 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1466 Matrix rotation and translation 
    1467 0.88018838 0.25419012 -0.40081894 74.13944294 
    1468 -0.45629950 0.22079847 -0.86199700 322.44263683 
    1469 -0.13061091 0.94161321 0.31033107 -3.14778151 
    1470 Axis 0.92150340 -0.13805512 -0.36300449 
    1471 Axis point 0.00000000 162.82540766 230.87431985 
    1472 Rotation angle (degrees) 78.13192347 
    1473 Shift along axis 24.94755119 
    1474  
    1475 
    1476 > view matrix models
    1477 > #4,0.88019,0.25419,-0.40082,73.448,-0.4563,0.2208,-0.862,321.07,-0.13061,0.94161,0.31033,-5.8994
    1478 
    1479 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1480 (#1) using 3401 atoms 
    1481 average map value = 0.1115, steps = 160 
    1482 shifted from previous position = 2.99 
    1483 rotated from previous position = 8.44 degrees 
    1484 atoms outside contour = 1603, contour level = 0.072 
    1485  
    1486 Position of F562a.pdb (#4) relative to
    1487 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1488 Matrix rotation and translation 
    1489 0.87327534 0.17162879 -0.45599755 97.28727310 
    1490 -0.48720393 0.31672140 -0.81383039 304.58441441 
    1491 0.00474745 0.93286180 0.36020320 -32.68286674 
    1492 Axis 0.90839597 -0.23961801 -0.34263678 
    1493 Axis point 0.00000000 182.33141527 229.00675692 
    1494 Rotation angle (degrees) 74.03202850 
    1495 Shift along axis 26.58980844 
    1496  
    1497 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1498 (#1) using 3401 atoms 
    1499 average map value = 0.1115, steps = 80 
    1500 shifted from previous position = 0.0187 
    1501 rotated from previous position = 0.0503 degrees 
    1502 atoms outside contour = 1606, contour level = 0.072 
    1503  
    1504 Position of F562a.pdb (#4) relative to
    1505 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1506 Matrix rotation and translation 
    1507 0.87307788 0.17102576 -0.45660182 97.51562460 
    1508 -0.48755025 0.31670719 -0.81362849 304.62173537 
    1509 0.00545764 0.93297736 0.35989370 -32.78455753 
    1510 Axis 0.90828067 -0.24028299 -0.34247673 
    1511 Axis point 0.00000000 182.48861826 229.00019788 
    1512 Rotation angle (degrees) 74.04755731 
    1513 Shift along axis 26.60408358 
    1514  
    1515 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1516 (#1) using 3401 atoms 
    1517 average map value = 0.1115, steps = 64 
    1518 shifted from previous position = 0.00983 
    1519 rotated from previous position = 0.00562 degrees 
    1520 atoms outside contour = 1605, contour level = 0.072 
    1521  
    1522 Position of F562a.pdb (#4) relative to
    1523 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1524 Matrix rotation and translation 
    1525 0.87308357 0.17093159 -0.45662622 97.52642834 
    1526 -0.48753906 0.31671935 -0.81363046 304.61327140 
    1527 0.00554721 0.93299049 0.35985828 -32.79571036 
    1528 Axis 0.90828615 -0.24034163 -0.34242104 
    1529 Axis point 0.00000000 182.49871036 228.98437979 
    1530 Rotation angle (degrees) 74.04808080 
    1531 Shift along axis 26.60059602 
    1532  
    1533 
    1534 > ui mousemode right "rotate selected models"
    1535 
    1536 > transparency #1.1 50
    1537 
    1538 > ui mousemode right "translate selected models"
    1539 
    1540 > view matrix models
    1541 > #4,0.87308,0.17093,-0.45663,98.781,-0.48754,0.31672,-0.81363,307.95,0.0055472,0.93299,0.35986,-31.624
    1542 
    1543 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1544 (#1) using 3401 atoms 
    1545 average map value = 0.1045, steps = 152 
    1546 shifted from previous position = 1.66 
    1547 rotated from previous position = 10.1 degrees 
    1548 atoms outside contour = 1670, contour level = 0.072 
    1549  
    1550 Position of F562a.pdb (#4) relative to
    1551 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1552 Matrix rotation and translation 
    1553 0.85430945 0.22816829 -0.46700601 94.00588935 
    1554 -0.50530889 0.15416741 -0.84905556 345.08239658 
    1555 -0.12173045 0.96133847 0.24700214 -1.12292161 
    1556 Axis 0.91267386 -0.17406375 -0.36976782 
    1557 Axis point 0.00000000 176.18270876 236.27702715 
    1558 Rotation angle (degrees) 82.66101368 
    1559 Shift along axis 26.14560144 
    1560  
    1561 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1562 (#1) using 3401 atoms 
    1563 average map value = 0.1045, steps = 60 
    1564 shifted from previous position = 0.00837 
    1565 rotated from previous position = 0.0183 degrees 
    1566 atoms outside contour = 1667, contour level = 0.072 
    1567  
    1568 Position of F562a.pdb (#4) relative to
    1569 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1570 Matrix rotation and translation 
    1571 0.85416080 0.22824487 -0.46724044 94.04888675 
    1572 -0.50553655 0.15397090 -0.84895570 345.14108146 
    1573 -0.12182835 0.96135179 0.24690203 -1.09962552 
    1574 Axis 0.91260386 -0.17412755 -0.36991051 
    1575 Axis point 0.00000000 176.20594034 236.31033169 
    1576 Rotation angle (degrees) 82.67387511 
    1577 Shift along axis 26.13756946 
    1578  
    1579 
    1580 > view matrix models
    1581 > #4,0.85416,0.22824,-0.46724,92.304,-0.50554,0.15397,-0.84896,343.85,-0.12183,0.96135,0.2469,-1.3966
    1582 
    1583 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1584 (#1) using 3401 atoms 
    1585 average map value = 0.1115, steps = 132 
    1586 shifted from previous position = 2.46 
    1587 rotated from previous position = 10.1 degrees 
    1588 atoms outside contour = 1603, contour level = 0.072 
    1589  
    1590 Position of F562a.pdb (#4) relative to
    1591 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1592 Matrix rotation and translation 
    1593 0.87327321 0.17148581 -0.45605541 97.32164807 
    1594 -0.48720576 0.31684479 -0.81378127 304.55640572 
    1595 0.00494684 0.93284619 0.36024093 -32.71905415 
    1596 Axis 0.90838381 -0.23975747 -0.34257148 
    1597 Axis point 0.00000000 182.35784967 228.99751317 
    1598 Rotation angle (degrees) 74.02729082 
    1599 Shift along axis 26.59434986 
    1600  
    1601 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1602 (#1) using 3401 atoms 
    1603 average map value = 0.1115, steps = 100 
    1604 shifted from previous position = 0.0199 
    1605 rotated from previous position = 0.0492 degrees 
    1606 atoms outside contour = 1607, contour level = 0.072 
    1607  
    1608 Position of F562a.pdb (#4) relative to
    1609 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1610 Matrix rotation and translation 
    1611 0.87291436 0.17135958 -0.45678926 97.50396396 
    1612 -0.48784609 0.31650499 -0.81352984 304.69020219 
    1613 0.00516995 0.93298473 0.35987885 -32.73221582 
    1614 Axis 0.90818184 -0.24021727 -0.34278478 
    1615 Axis point 0.00000000 182.47945606 229.06508608 
    1616 Rotation angle (degrees) 74.05889597 
    1617 Shift along axis 26.57958591 
    1618  
    1619 
    1620 > volume #1 step 1
    1621 
    1622 > volume #1 level 0.08
    1623 
    1624 > volume #2 step 1
    1625 
    1626 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1627 (#1) using 3401 atoms 
    1628 average map value = 0.1115, steps = 96 
    1629 shifted from previous position = 0.0269 
    1630 rotated from previous position = 0.0588 degrees 
    1631 atoms outside contour = 1705, contour level = 0.08 
    1632  
    1633 Position of F562a.pdb (#4) relative to
    1634 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1635 Matrix rotation and translation 
    1636 0.87339018 0.17133657 -0.45588748 97.30726750 
    1637 -0.48699588 0.31678456 -0.81393032 304.55388891 
    1638 0.00496208 0.93289407 0.36011672 -32.71648369 
    1639 Axis 0.90847710 -0.23967565 -0.34238127 
    1640 Axis point 0.00000000 182.34480224 228.95151912 
    1641 Rotation angle (degrees) 74.02930115 
    1642 Shift along axis 26.60878416 
    1643  
    1644 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1645 (#1) using 3401 atoms 
    1646 average map value = 0.1115, steps = 60 
    1647 shifted from previous position = 0.0234 
    1648 rotated from previous position = 0.0504 degrees 
    1649 atoms outside contour = 1711, contour level = 0.08 
    1650  
    1651 Position of F562a.pdb (#4) relative to
    1652 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1653 Matrix rotation and translation 
    1654 0.87307658 0.17097372 -0.45662380 97.51998587 
    1655 -0.48755237 0.31664803 -0.81365025 304.63116274 
    1656 0.00547621 0.93300698 0.35981662 -32.78056504 
    1657 Axis 0.90828882 -0.24029916 -0.34244377 
    1658 Axis point 0.00000000 182.49216804 228.98849803 
    1659 Rotation angle (degrees) 74.05165523 
    1660 Shift along axis 26.59919907 
    1661  
    1662 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1663 (#1) using 3401 atoms 
    1664 average map value = 0.1115, steps = 84 
    1665 shifted from previous position = 0.0236 
    1666 rotated from previous position = 0.0512 degrees 
    1667 atoms outside contour = 1709, contour level = 0.08 
    1668  
    1669 Position of F562a.pdb (#4) relative to
    1670 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1671 Matrix rotation and translation 
    1672 0.87330072 0.17150987 -0.45599367 97.31366850 
    1673 -0.48715626 0.31696366 -0.81376461 304.52650710 
    1674 0.00496476 0.93280138 0.36035670 -32.73218629 
    1675 Axis 0.90838730 -0.23974404 -0.34257162 
    1676 Axis point 0.00000000 182.35082823 229.00016180 
    1677 Rotation angle (degrees) 74.01947881 
    1678 Shift along axis 26.60320358 
    1679  
    1680 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1681 (#1) using 5602 atoms 
    1682 average map value = 0.09224, steps = 36 
    1683 shifted from previous position = 0.0101 
    1684 rotated from previous position = 0.0146 degrees 
    1685 atoms outside contour = 3383, contour level = 0.08 
    1686  
    1687 Position of D2NS1.pdb (#3) relative to
    1688 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1689 Matrix rotation and translation 
    1690 -0.06781116 0.24433459 0.96731706 -24.10970616 
    1691 -0.87336663 0.45417416 -0.17594486 287.52120019 
    1692 -0.48231982 -0.85675345 0.18259559 387.95373087 
    1693 Axis -0.34859656 0.74226213 -0.57230007 
    1694 Axis point 265.34079550 0.00000000 317.90521257 
    1695 Rotation angle (degrees) 102.44607735 
    1696 Shift along axis -0.20528738 
    1697  
    1698 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1699 (#1) using 5602 atoms 
    1700 average map value = 0.09224, steps = 40 
    1701 shifted from previous position = 0.00617 
    1702 rotated from previous position = 0.0174 degrees 
    1703 atoms outside contour = 3388, contour level = 0.08 
    1704  
    1705 Position of D2NS1.pdb (#3) relative to
    1706 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1707 Matrix rotation and translation 
    1708 -0.06800223 0.24456045 0.96724657 -24.09574276 
    1709 -0.87334229 0.45411451 -0.17621946 287.57652794 
    1710 -0.48233700 -0.85672063 0.18270418 387.93151574 
    1711 Axis -0.34844475 0.74224675 -0.57241245 
    1712 Axis point 265.30857487 0.00000000 317.93174566 
    1713 Rotation angle (degrees) 102.45024724 
    1714 Shift along axis -0.20805003 
    1715  
    1716 
    1717 > ui mousemode right "rotate selected models"
    1718 
    1719 > view matrix models
    1720 > #4,0.8783,0.21948,-0.42476,83.959,-0.47606,0.31931,-0.81939,302.68,-0.044211,0.92188,0.38494,-24.427
    1721 
    1722 > view matrix models
    1723 > #4,0.88185,0.18737,-0.43271,90.075,-0.47057,0.40846,-0.78213,281.03,0.030198,0.89334,0.44837,-40.684
    1724 
    1725 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1726 (#1) using 3401 atoms 
    1727 average map value = 0.1115, steps = 108 
    1728 shifted from previous position = 0.192 
    1729 rotated from previous position = 5.8 degrees 
    1730 atoms outside contour = 1706, contour level = 0.08 
    1731  
    1732 Position of F562a.pdb (#4) relative to
    1733 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1734 Matrix rotation and translation 
    1735 0.87316782 0.17153805 -0.45623751 97.35347505 
    1736 -0.48739404 0.31688450 -0.81365305 304.56284709 
    1737 0.00500214 0.93282310 0.36029997 -32.73417130 
    1738 Axis 0.90830421 -0.23988070 -0.34269623 
    1739 Axis point 0.00000000 182.38522859 229.02890887 
    1740 Rotation angle (degrees) 74.02748836 
    1741 Shift along axis 26.58569939 
    1742  
    1743 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1744 (#1) using 3401 atoms 
    1745 average map value = 0.1115, steps = 100 
    1746 shifted from previous position = 0.0157 
    1747 rotated from previous position = 0.0308 degrees 
    1748 atoms outside contour = 1714, contour level = 0.08 
    1749  
    1750 Position of F562a.pdb (#4) relative to
    1751 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1752 Matrix rotation and translation 
    1753 0.87319228 0.17106442 -0.45636852 97.46138911 
    1754 -0.48734683 0.31669009 -0.81375701 304.60534678 
    1755 0.00532251 0.93297608 0.35989904 -32.76360108 
    1756 Axis 0.90836070 -0.24009506 -0.34239627 
    1757 Axis point 0.00000000 182.44525999 228.97324319 
    1758 Rotation angle (degrees) 74.04449916 
    1759 Shift along axis 26.61399150 
    1760  
    1761 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1762 (#1) using 3401 atoms 
    1763 average map value = 0.1115, steps = 76 
    1764 shifted from previous position = 0.0215 
    1765 rotated from previous position = 0.0496 degrees 
    1766 atoms outside contour = 1707, contour level = 0.08 
    1767  
    1768 Position of F562a.pdb (#4) relative to
    1769 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1770 Matrix rotation and translation 
    1771 0.87344661 0.17154945 -0.45569927 97.23463453 
    1772 -0.48689717 0.31676739 -0.81399606 304.54231699 
    1773 0.00471009 0.93286078 0.36020634 -32.68225206 
    1774 Axis 0.90851141 -0.23945131 -0.34244721 
    1775 Axis point 0.00000000 182.29150588 228.95203805 
    1776 Rotation angle (degrees) 74.02546087 
    1777 Shift along axis 26.60766517 
    1778  
    1779 
    1780 > close #5
    1781 
    1782 > open "D:/OneDrive - Nanyang Technological
    1783 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562b.pdb"
    1784 
    1785 Chain information for F562b.pdb #5 
    1786 --- 
    1787 Chain | Description 
    1788 B | No description available 
    1789 C | No description available 
    1790  
    1791 
    1792 > select #5
    1793 
    1794 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    1795 
    1796 > view matrix models
    1797 > #5,0.88246,-0.46571,0.066244,91.139,0.4452,0.87234,0.20206,-101.84,-0.15189,-0.14881,0.97713,59.494
    1798 
    1799 > ui mousemode right "translate selected models"
    1800 
    1801 > view matrix models
    1802 > #5,0.88246,-0.46571,0.066244,31.321,0.4452,0.87234,0.20206,-110.9,-0.15189,-0.14881,0.97713,2.868
    1803 
    1804 > view matrix models
    1805 > #5,0.88246,-0.46571,0.066244,29.937,0.4452,0.87234,0.20206,-111.7,-0.15189,-0.14881,0.97713,-4.3706
    1806 
    1807 > view matrix models
    1808 > #5,0.91945,-0.24365,-0.30863,71.496,-0.34812,-0.86933,-0.35081,481.22,-0.18283,0.42999,-0.88413,336.53
    1809 
    1810 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1811 (#1) using 3401 atoms 
    1812 average map value = 0.1014, steps = 252 
    1813 shifted from previous position = 4.97 
    1814 rotated from previous position = 12.4 degrees 
    1815 atoms outside contour = 1810, contour level = 0.08 
    1816  
    1817 Position of F562b.pdb (#5) relative to
    1818 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1819 Matrix rotation and translation 
    1820 0.96186420 -0.19777272 -0.18895294 31.32789418 
    1821 -0.26901427 -0.80896731 -0.52268846 497.86596548 
    1822 -0.04948323 0.55358635 -0.83132038 280.55853441 
    1823 Axis 0.98957826 -0.12823509 -0.06550286 
    1824 Axis point 0.00000000 209.55045747 214.71270936 
    1825 Rotation angle (degrees) 147.05697484 
    1826 Shift along axis -51.21986933 
    1827  
    1828 
    1829 > view matrix models
    1830 > #5,0.96186,-0.19777,-0.18895,31.586,-0.26901,-0.80897,-0.52269,497.84,-0.049483,0.55359,-0.83132,280.45
    1831 
    1832 > view matrix models
    1833 > #5,0.96186,-0.19777,-0.18895,30.409,-0.26901,-0.80897,-0.52269,498.49,-0.049483,0.55359,-0.83132,281.14
    1834 
    1835 > view matrix models
    1836 > #5,0.88111,-0.30725,-0.35949,105.37,-0.46365,-0.71093,-0.52878,515.6,-0.093104,0.63259,-0.76887,259.2
    1837 
    1838 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1839 (#1) using 3401 atoms 
    1840 average map value = 0.1109, steps = 80 
    1841 shifted from previous position = 3.4 
    1842 rotated from previous position = 5.08 degrees 
    1843 atoms outside contour = 1772, contour level = 0.08 
    1844  
    1845 Position of F562b.pdb (#5) relative to
    1846 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1847 Matrix rotation and translation 
    1848 0.88807867 -0.23238898 -0.39662534 101.69393944 
    1849 -0.43540490 -0.70196949 -0.56361460 519.59851714 
    1850 -0.14744106 0.67322671 -0.72458742 250.51818794 
    1851 Axis 0.96785351 -0.19499177 -0.15886409 
    1852 Axis point 0.00000000 224.56879044 228.99496698 
    1853 Rotation angle (degrees) 140.28561169 
    1854 Shift along axis -42.69094177 
    1855  
    1856 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1857 (#1) using 3401 atoms 
    1858 average map value = 0.1109, steps = 40 
    1859 shifted from previous position = 0.0247 
    1860 rotated from previous position = 0.0823 degrees 
    1861 atoms outside contour = 1771, contour level = 0.08 
    1862  
    1863 Position of F562b.pdb (#5) relative to
    1864 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1865 Matrix rotation and translation 
    1866 0.88749875 -0.23316934 -0.39746451 102.13143422 
    1867 -0.43663025 -0.70123937 -0.56357554 519.69347155 
    1868 -0.14730923 0.67371761 -0.72415784 250.30786189 
    1869 Axis 0.96767878 -0.19564479 -0.15912543 
    1870 Axis point 0.00000000 224.69705024 229.03906748 
    1871 Rotation angle (degrees) 140.25962425 
    1872 Shift along axis -42.67524524 
    1873  
    1874 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1875 (#1) using 3401 atoms 
    1876 average map value = 0.1109, steps = 40 
    1877 shifted from previous position = 0.0089 
    1878 rotated from previous position = 0.0313 degrees 
    1879 atoms outside contour = 1770, contour level = 0.08 
    1880  
    1881 Position of F562b.pdb (#5) relative to
    1882 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1883 Matrix rotation and translation 
    1884 0.88726809 -0.23348649 -0.39779316 102.30830437 
    1885 -0.43710961 -0.70099140 -0.56351243 519.72597500 
    1886 -0.14727705 0.67386581 -0.72402648 250.24321586 
    1887 Axis 0.96761002 -0.19589960 -0.15923003 
    1888 Axis point 0.00000000 224.74651301 229.05595353 
    1889 Rotation angle (degrees) 140.25296234 
    1890 Shift along axis -42.66580653 
    1891  
    1892 
    1893 > view matrix models
    1894 > #5,0.90434,-0.19289,-0.38074,87.744,-0.3816,-0.76498,-0.51883,511.31,-0.19118,0.61449,-0.76541,278.75
    1895 
    1896 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1897 (#1) using 3401 atoms 
    1898 average map value = 0.1109, steps = 100 
    1899 shifted from previous position = 0.228 
    1900 rotated from previous position = 5.49 degrees 
    1901 atoms outside contour = 1772, contour level = 0.08 
    1902  
    1903 Position of F562b.pdb (#5) relative to
    1904 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1905 Matrix rotation and translation 
    1906 0.88741151 -0.23323538 -0.39762052 102.19303295 
    1907 -0.43675670 -0.70132020 -0.56337694 519.68635289 
    1908 -0.14745987 0.67361061 -0.72422672 250.37123988 
    1909 Axis 0.96765550 -0.19569262 -0.15920817 
    1910 Axis point 0.00000000 224.70331960 229.05340664 
    1911 Rotation angle (degrees) 140.27024302 
    1912 Shift along axis -42.67227987 
    1913  
    1914 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1915 (#1) using 3401 atoms 
    1916 average map value = 0.1109, steps = 80 
    1917 shifted from previous position = 0.0119 
    1918 rotated from previous position = 0.0244 degrees 
    1919 atoms outside contour = 1769, contour level = 0.08 
    1920  
    1921 Position of F562b.pdb (#5) relative to
    1922 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1923 Matrix rotation and translation 
    1924 0.88757691 -0.23309386 -0.39733424 102.06718757 
    1925 -0.43649500 -0.70124393 -0.56367462 519.68560309 
    1926 -0.14723913 0.67373898 -0.72415222 250.29116827 
    1927 Axis 0.96770087 -0.19558315 -0.15906683 
    1928 Axis point 0.00000000 224.68268474 229.02792313 
    1929 Rotation angle (degrees) 140.25607412 
    1930 Shift along axis -42.68426633 
    1931  
    1932 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1933 (#1) using 3401 atoms 
    1934 average map value = 0.1109, steps = 64 
    1935 shifted from previous position = 0.0443 
    1936 rotated from previous position = 0.146 degrees 
    1937 atoms outside contour = 1761, contour level = 0.08 
    1938  
    1939 Position of F562b.pdb (#5) relative to
    1940 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1941 Matrix rotation and translation 
    1942 0.88644690 -0.23468134 -0.39891925 102.92117215 
    1943 -0.43878232 -0.70033958 -0.56302270 519.80857088 
    1944 -0.14724801 0.67412844 -0.72378787 250.13865633 
    1945 Axis 0.96736944 -0.19679007 -0.15959331 
    1946 Axis point 0.00000000 224.90663730 229.11626097 
    1947 Rotation angle (degrees) 140.24985998 
    1948 Shift along axis -42.65082531 
    1949  
    1950 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1951 (#1) using 3401 atoms 
    1952 average map value = 0.1109, steps = 28 
    1953 shifted from previous position = 0.0228 
    1954 rotated from previous position = 0.0509 degrees 
    1955 atoms outside contour = 1770, contour level = 0.08 
    1956  
    1957 Position of F562b.pdb (#5) relative to
    1958 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1959 Matrix rotation and translation 
    1960 0.88682818 -0.23410569 -0.39840974 102.63155782 
    1961 -0.43798841 -0.70069517 -0.56319841 519.75407402 
    1962 -0.14731582 0.67395906 -0.72393179 250.21245718 
    1963 Axis 0.96748195 -0.19636048 -0.15944037 
    1964 Axis point 0.00000000 224.82302925 229.08819200 
    1965 Rotation angle (degrees) 140.25515764 
    1966 Shift along axis -42.65894548 
    1967  
    1968 Average map value = 0.1109 for 3401 atoms, 1770 outside contour 
    1969 Average map value = 0.1109 for 3401 atoms, 1770 outside contour 
    1970 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1971 (#1) using 3401 atoms 
    1972 average map value = 0.1109, steps = 40 
    1973 shifted from previous position = 0.0277 
    1974 rotated from previous position = 0.119 degrees 
    1975 atoms outside contour = 1770, contour level = 0.08 
    1976  
    1977 Position of F562b.pdb (#5) relative to
    1978 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1979 Matrix rotation and translation 
    1980 0.88773516 -0.23286893 -0.39711253 101.94821925 
    1981 -0.43614356 -0.70150514 -0.56362163 519.65415902 
    1982 -0.14732651 0.67354481 -0.72431506 250.37946507 
    1983 Axis 0.96774956 -0.19539029 -0.15900765 
    1984 Axis point 0.00000000 224.64447067 229.01845950 
    1985 Rotation angle (degrees) 140.26798555 
    1986 Shift along axis -42.68728231 
    1987  
    1988 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    1989 (#1) using 3401 atoms 
    1990 average map value = 0.1109, steps = 36 
    1991 shifted from previous position = 0.0101 
    1992 rotated from previous position = 0.0384 degrees 
    1993 atoms outside contour = 1772, contour level = 0.08 
    1994  
    1995 Position of F562b.pdb (#5) relative to
    1996 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    1997 Matrix rotation and translation 
    1998 0.88743039 -0.23323831 -0.39757668 102.17484111 
    1999 -0.43673470 -0.70130263 -0.56341586 519.68061974 
    2000 -0.14741140 0.67362788 -0.72422052 250.35767544 
    2001 Axis 0.96766061 -0.19568838 -0.15918228 
    2002 Axis point 0.00000000 224.69868010 229.04697101 
    2003 Rotation angle (degrees) 140.26833165 
    2004 Shift along axis -42.67739283 
    2005  
    2006 
    2007 > ~select #5
    2008 
    2009 Nothing selected 
    2010 
    2011 > show #!2 models
    2012 
    2013 > select #2
    2014 
    2015 2 models selected 
    2016 
    2017 > view matrix models
    2018 > #2,0.19536,0.75362,0.62761,-85.152,-0.79186,-0.25635,0.5543,213.6,0.57862,-0.60527,0.54668,70.661
    2019 
    2020 > view matrix models
    2021 > #2,0.11282,0.94881,0.29501,-45.954,-0.85716,-0.057225,0.51186,202.13,0.50254,-0.31062,0.80683,-2.2981
    2022 
    2023 > view matrix models
    2024 > #2,0.11282,0.94881,0.29501,-10.942,-0.85716,-0.057225,0.51186,230.24,0.50254,-0.31062,0.80683,26.411
    2025 
    2026 > view matrix models
    2027 > #2,-0.3673,0.80202,0.47101,56.376,-0.91933,-0.38991,-0.052965,380.04,0.14117,-0.45246,0.88054,91.186
    2028 
    2029 > view matrix models
    2030 > #2,-0.37949,0.87152,0.31056,74.515,-0.81999,-0.16136,-0.54916,412.77,-0.42849,-0.46305,0.77587,198.78
    2031 
    2032 > view matrix models
    2033 > #2,-0.37949,0.87152,0.31056,77.692,-0.81999,-0.16136,-0.54916,412.77,-0.42849,-0.46305,0.77587,195.9
    2034 
    2035 > view matrix models
    2036 > #2,-0.4416,0.17153,0.88066,94.799,-0.84825,0.23999,-0.47209,346.93,-0.29232,-0.9555,0.039518,365.71
    2037 
    2038 > view matrix models
    2039 > #2,-0.16701,0.27438,0.94701,26.293,-0.9691,-0.22254,-0.10643,372.5,0.18155,-0.93552,0.30307,245.76
    2040 
    2041 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
    2042 cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points 
    2043 correlation = 0.3616, correlation about mean = 0.238, overlap = 5797 
    2044 steps = 816, shift = 17.1, angle = 92.5 degrees 
    2045  
    2046 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
    2047 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2048 Matrix rotation and translation 
    2049 -0.23884246 0.36253629 0.90084502 32.04958536 
    2050 -0.12095024 0.90936326 -0.39803210 133.21868643 
    2051 -0.96349643 -0.20402438 -0.17334571 390.21884814 
    2052 Axis 0.10022302 0.96310562 -0.24976572 
    2053 Axis point 169.19260085 0.00000000 200.88498104 
    2054 Rotation angle (degrees) 104.56110947 
    2055 Shift along axis 34.05247827 
    2056  
    2057 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
    2058 cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points 
    2059 correlation = 0.3616, correlation about mean = 0.238, overlap = 5797 
    2060 steps = 40, shift = 0.000646, angle = 0.0027 degrees 
    2061  
    2062 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
    2063 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2064 Matrix rotation and translation 
    2065 -0.23884389 0.36253338 0.90084582 32.04982504 
    2066 -0.12099611 0.90935469 -0.39803771 133.22769414 
    2067 -0.96349031 -0.20406771 -0.17332869 390.22127920 
    2068 Axis 0.10020344 0.96310196 -0.24978768 
    2069 Axis point 169.19590472 0.00000000 200.88843406 
    2070 Rotation angle (degrees) 104.56090162 
    2071 Shift along axis 34.05088824 
    2072  
    2073 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
    2074 cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points 
    2075 correlation = 0.3616, correlation about mean = 0.238, overlap = 5797 
    2076 steps = 40, shift = 2.75e-05, angle = 5.91e-05 degrees 
    2077  
    2078 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
    2079 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2080 Matrix rotation and translation 
    2081 -0.23884450 0.36253261 0.90084597 32.05002579 
    2082 -0.12099600 0.90935500 -0.39803705 133.22750949 
    2083 -0.96349017 -0.20406771 -0.17332945 390.22138385 
    2084 Axis 0.10020311 0.96310210 -0.24978726 
    2085 Axis point 169.19595961 -0.00000000 200.88835343 
    2086 Rotation angle (degrees) 104.56093288 
    2087 Shift along axis 34.05087684 
    2088  
    2089 
    2090 > hide #!1 models
    2091 
    2092 > ui mousemode right "rotate selected models"
    2093 
    2094 > view matrix models
    2095 > #2,-0.24143,0.39089,0.88821,30.445,-0.11992,0.89625,-0.42703,139.68,-0.96298,-0.20961,-0.16951,390.31
    2096 
    2097 > view matrix models
    2098 > #2,-0.24371,0.41583,0.87618,29.184,-0.11889,0.8838,-0.45252,145.47,-0.96253,-0.21445,-0.16596,390.36
    2099 
    2100 > view matrix models
    2101 > #2,-0.23248,0.44368,0.86551,25.173,-0.098419,0.87459,-0.47477,147.23,-0.96761,-0.19556,-0.15966,387.41
    2102 
    2103 > view matrix models
    2104 > #2,-0.015904,0.29362,0.95579,-1.8481,0.11672,0.94992,-0.28987,72.596,-0.99304,0.10695,-0.049378,329.9
    2105 
    2106 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
    2107 cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points 
    2108 correlation = 0.3636, correlation about mean = 0.2345, overlap = 5800 
    2109 steps = 160, shift = 4.43, angle = 14.2 degrees 
    2110  
    2111 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
    2112 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2113 Matrix rotation and translation 
    2114 -0.23589350 0.38613188 0.89177153 30.30521757 
    2115 0.14116968 0.92155092 -0.36168365 84.35973344 
    2116 -0.96147045 0.04057228 -0.27189798 372.10342069 
    2117 Axis 0.21036827 0.96919218 -0.12810818 
    2118 Axis point 149.90554609 -0.00000000 183.31483684 
    2119 Rotation angle (degrees) 107.04485499 
    2120 Shift along axis 40.46655914 
    2121  
    2122 
    2123 > transparency sel 50
    2124 
    2125 > view matrix models
    2126 > #2,-0.32117,0.35848,0.87655,50.083,0.35637,0.9033,-0.23885,33.297,-0.87741,0.23567,-0.41786,354.8
    2127 
    2128 > view matrix models
    2129 > #2,-0.25849,0.33315,0.90675,38.999,0.20781,0.93585,-0.2846,59.301,-0.9434,0.11486,-0.31114,365.02
    2130 
    2131 > hide #3 models
    2132 
    2133 > hide #4 models
    2134 
    2135 > hide #5 models
    2136 
    2137 > show #5 models
    2138 
    2139 > show #4 models
    2140 
    2141 > show #3 models
    2142 
    2143 > open "D:/OneDrive - Nanyang Technological
    2144 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
    2145 
    2146 Chain information for D2NS1-F562.pdb #6 
    2147 --- 
    2148 Chain | Description 
    2149 B | No description available 
    2150 C E | No description available 
    2151 D | No description available 
    2152 F | No description available 
    2153  
    2154 
    2155 > close #6
    2156 
    2157 > save "D:/OneDrive - Nanyang Technological
    2158 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1.pdb" models #3
    2159 > relModel #1
    2160 
    2161 > save "D:/OneDrive - Nanyang Technological
    2162 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562a.pdb" models #4
    2163 > relModel #1
    2164 
    2165 > save "D:/OneDrive - Nanyang Technological
    2166 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562b.pdb" models #5
    2167 > relModel #1
    2168 
    2169 > open "D:/OneDrive - Nanyang Technological
    2170 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
    2171 
    2172 Chain information for D2NS1-F562.pdb #6 
    2173 --- 
    2174 Chain | Description 
    2175 B | No description available 
    2176 C | No description available 
    2177  
    2178 
    2179 > close #6
    2180 
    2181 > open "D:/OneDrive - Nanyang Technological
    2182 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
    2183 
    2184 Chain information for D2NS1-F562.pdb #6 
    2185 --- 
    2186 Chain | Description 
    2187 A B | No description available 
    2188 C E | No description available 
    2189 D F | No description available 
    2190  
    2191 
    2192 > hide atoms
    2193 
    2194 > show cartoons
    2195 
    2196 > hide #3 models
    2197 
    2198 > hide #5 models
    2199 
    2200 > hide #4 models
    2201 
    2202 Fit molecule D2NS1-F562.pdb (#6) to map
    2203 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    2204 average map value = 0.1026, steps = 40 
    2205 shifted from previous position = 0.0103 
    2206 rotated from previous position = 0.00699 degrees 
    2207 atoms outside contour = 6863, contour level = 0.08 
    2208  
    2209 Position of D2NS1-F562.pdb (#6) relative to
    2210 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2211 Matrix rotation and translation 
    2212 1.00000000 -0.00007640 -0.00005950 0.01644925 
    2213 0.00007639 0.99999999 -0.00007418 0.00540007 
    2214 0.00005950 0.00007417 1.00000000 -0.02042262 
    2215 Axis 0.60809281 -0.48779755 0.62631995 
    2216 Axis point -36.04322257 258.47150214 0.00000000 
    2217 Rotation angle (degrees) 0.00698874 
    2218 Shift along axis -0.00542257 
    2219  
    2220 Fit molecule D2NS1-F562.pdb (#6) to map
    2221 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 12404 atoms 
    2222 average map value = 0.1322, steps = 204 
    2223 shifted from previous position = 3.17 
    2224 rotated from previous position = 16.9 degrees 
    2225 atoms outside contour = 7037, contour level = 0.14151 
    2226  
    2227 Position of D2NS1-F562.pdb (#6) relative to
    2228 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    2229 Matrix rotation and translation 
    2230 -0.15126719 0.47107682 -0.86902521 263.21094843 
    2231 0.40313494 0.83210747 0.38089281 -155.24920226 
    2232 0.90255217 -0.29271785 -0.31577809 100.07490639 
    2233 Axis -0.35517923 -0.93411153 -0.03582417 
    2234 Axis point 121.90346818 0.00000000 160.98219047 
    2235 Rotation angle (degrees) 108.50992410 
    2236 Shift along axis 47.94790735 
    2237  
    2238 
    2239 > show #3 models
    2240 
    2241 > mmaker #6 to #3
    2242 
    2243 Parameters 
    2244 --- 
    2245 Chain pairing | bb 
    2246 Alignment algorithm | Needleman-Wunsch 
    2247 Similarity matrix | BLOSUM-62 
    2248 SS fraction | 0.3 
    2249 Gap open (HH/SS/other) | 18/18/6 
    2250 Gap extend | 1 
    2251 SS matrix |  |  | H | S | O 
    2252 ---|---|---|--- 
    2253 H | 6 | -9 | -6 
    2254 S |  | 6 | -6 
    2255 O |  |  | 4 
    2256 Iteration cutoff | 2 
    2257  
    2258 Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
    2259 alignment score = 1871.9 
    2260 RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
    2261 0.023) 
    2262  
    2263 
    2264 > hide #6 models
    2265 
    2266 > hide #3 models
    2267 
    2268 > ui mousemode right "map eraser"
    2269 
    2270 > open "D:/OneDrive - Nanyang Technological
    2271 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J59_004_volume_map_sharp
    2272 > (3).mrc"
    2273 
    2274 Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc as #8, grid size
    2275 352,352,352, pixel 0.85, shown at level 0.366, step 2, values float32 
    2276 
    2277 > close #7
    2278 
    2279 > hide #!2 models
    2280 
    2281 > surface dust #8 size 8.5
    2282 
    2283 > select #8
    2284 
    2285 2 models selected 
    2286 
    2287 > close #7
    2288 
    2289 > ui mousemode right "translate selected models"
    2290 
    2291 > view matrix models #8,1,0,0,35.396,0,1,0,60.903,0,0,1,32.921
    2292 
    2293 > ui mousemode right "rotate selected models"
    2294 
    2295 > view matrix models
    2296 > #8,-0.3457,-0.50036,0.79381,208.17,-0.017535,0.84927,0.52767,14.154,-0.93818,0.1685,-0.30237,329.15
    2297 
    2298 > view matrix models
    2299 > #8,-0.51948,-0.14515,0.84206,178.05,0.63577,0.59277,0.49439,-45.989,-0.57091,0.79219,-0.21565,171.93
    2300 
    2301 > view matrix models
    2302 > #8,-0.55842,-0.30769,0.77039,216.83,0.59819,0.49406,0.63093,-44.478,-0.57475,0.81316,-0.09184,152.9
    2303 
    2304 > view matrix models
    2305 > #8,-0.55842,-0.30769,0.77039,191.12,0.59819,0.49406,0.63093,-46.563,-0.57475,0.81316,-0.09184,158.22
    2306 
    2307 > show #6 models
    2308 
    2309 > ~select #8
    2310 
    2311 Nothing selected 
    2312 Fit molecule D2NS1-F562.pdb (#6) to map
    2313 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    2314 average map value = 0.1026, steps = 168 
    2315 shifted from previous position = 1.67 
    2316 rotated from previous position = 11.8 degrees 
    2317 atoms outside contour = 6854, contour level = 0.08 
    2318  
    2319 Position of D2NS1-F562.pdb (#6) relative to
    2320 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2321 Matrix rotation and translation 
    2322 -1.00000000 0.00007634 0.00003096 356.91445101 
    2323 -0.00007636 -0.99999975 -0.00069729 357.06728170 
    2324 0.00003091 -0.00069729 0.99999976 0.11956672 
    2325 Axis -0.00001547 0.00034864 -0.99999994 
    2326 Axis point 178.46403997 178.52684922 0.00000000 
    2327 Rotation angle (degrees) 179.99562555 
    2328 Shift along axis -0.00059852 
    2329  
    2330 Fit molecule D2NS1-F562.pdb (#6) to map
    2331 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    2332 average map value = 0.1026, steps = 40 
    2333 shifted from previous position = 0.00373 
    2334 rotated from previous position = 0.0435 degrees 
    2335 atoms outside contour = 6861, contour level = 0.08 
    2336  
    2337 Position of D2NS1-F562.pdb (#6) relative to
    2338 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2339 Matrix rotation and translation 
    2340 -1.00000000 0.00004453 0.00006393 356.91507698 
    2341 -0.00004452 -1.00000000 0.00006135 356.92005524 
    2342 0.00006393 0.00006135 1.00000000 -0.02104448 
    2343 Axis -0.00003196 -0.00003068 -1.00000000 
    2344 Axis point 178.46151168 178.45605515 0.00000000 
    2345 Rotation angle (degrees) 179.99744898 
    2346 Shift along axis -0.00131278 
    2347  
    2348 
    2349 > select #8
    2350 
    2351 2 models selected 
    2352 
    2353 > view matrix models
    2354 > #8,-0.55842,-0.30769,0.77039,144.53,0.59819,0.49406,0.63093,-60.652,-0.57475,0.81316,-0.09184,256.77
    2355 
    2356 > view matrix models
    2357 > #8,-0.55842,-0.30769,0.77039,188.5,0.59819,0.49406,0.63093,-43.585,-0.57475,0.81316,-0.09184,207.1
    2358 
    2359 > view matrix models
    2360 > #8,0.20416,-0.32979,0.92171,53.292,0.8306,0.55667,0.015197,-5.7187,-0.5181,0.76247,0.38758,141.12
    2361 
    2362 > view matrix models
    2363 > #8,-0.17775,-0.55408,0.81327,158.88,0.42359,0.70287,0.57144,-38.275,-0.88824,0.44606,0.10977,280.75
    2364 
    2365 > view matrix models
    2366 > #8,-0.44365,-0.53212,0.72113,209.28,0.54415,0.47941,0.68853,-40.877,-0.71209,0.69787,0.076868,222.08
    2367 
    2368 > view matrix models
    2369 > #8,-0.44365,-0.53212,0.72113,201.21,0.54415,0.47941,0.68853,-58.258,-0.71209,0.69787,0.076868,191.6
    2370 
    2371 > view matrix models
    2372 > #8,-0.44365,-0.53212,0.72113,198.44,0.54415,0.47941,0.68853,-54.781,-0.71209,0.69787,0.076868,186.46
    2373 
    2374 > view matrix models
    2375 > #8,-0.078986,-0.30105,0.95033,78.334,0.99624,-0.057911,0.064456,35.555,0.03563,0.95185,0.30449,4.0251
    2376 
    2377 > view matrix models
    2378 > #8,-0.078986,-0.30105,0.95033,83.821,0.99624,-0.057911,0.064456,34.166,0.03563,0.95185,0.30449,22.679
    2379 
    2380 > view matrix models
    2381 > #8,-0.13528,-0.37298,0.91792,107.12,0.9291,0.27408,0.24829,-27.377,-0.34419,0.88644,0.30946,90.098
    2382 
    2383 > view matrix models
    2384 > #8,-0.13528,-0.37298,0.91792,107.41,0.9291,0.27408,0.24829,-25.4,-0.34419,0.88644,0.30946,74.434
    2385 
    2386 > view matrix models
    2387 > #8,0.021026,-0.64563,0.76336,142.78,0.95068,0.24925,0.18463,-16.653,-0.30947,0.72183,0.61903,50.881
    2388 
    2389 > view matrix models
    2390 > #8,0.18242,-0.5728,0.79914,102.63,0.95907,0.28269,-0.016302,4.2907,-0.21658,0.76941,0.60092,32.168
    2391 
    2392 > view matrix models
    2393 > #8,0.18242,-0.5728,0.79914,103.51,0.95907,0.28269,-0.016302,-14.792,-0.21658,0.76941,0.60092,29.021
    2394 
    2395 > view matrix models
    2396 > #8,0.18242,-0.5728,0.79914,103.75,0.95907,0.28269,-0.016302,-13.773,-0.21658,0.76941,0.60092,25.236
    2397 
    2398 > view matrix models
    2399 > #8,0.19689,-0.59123,0.7821,106.42,0.95308,0.30251,-0.011255,-16.342,-0.22993,0.74762,0.62305,27.429
    2400 
    2401 > view matrix models
    2402 > #8,0.16349,-0.53138,0.83121,96.478,0.91695,0.39269,0.070685,-34.591,-0.36397,0.75062,0.55145,57.366
    2403 
    2404 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    2405 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    2406 correlation = 0.2099, correlation about mean = -0.0466, overlap = 1148 
    2407 steps = 220, shift = 8.88, angle = 20.7 degrees 
    2408  
    2409 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    2410 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2411 Matrix rotation and translation 
    2412 0.16970377 -0.22411591 0.95967322 38.04053966 
    2413 0.82808228 0.56039048 -0.01556391 -26.95927500 
    2414 -0.53430362 0.79732965 0.28068680 115.40605181 
    2415 Axis 0.40645268 0.74699927 0.52610674 
    2416 Axis point 84.17805896 0.00000000 56.92499809 
    2417 Rotation angle (degrees) 89.69114416 
    2418 Shift along axis 56.03902271 
    2419  
    2420 
    2421 > hide #!8 models
    2422 
    2423 > hide #7 models
    2424 
    2425 > show #!8 models
    2426 
    2427 > hide #!8 models
    2428 
    2429 > show #!8 models
    2430 
    2431 > view matrix models
    2432 > #8,0.17985,-0.20944,0.96114,34.185,0.82577,0.56311,-0.031812,-24.805,-0.53457,0.7994,0.27422,116.02
    2433 
    2434 > view matrix models
    2435 > #8,-0.19365,-0.33381,0.92253,114.87,-0.70512,-0.60645,-0.36745,423.6,0.68213,-0.72166,-0.11794,196.81
    2436 
    2437 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    2438 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    2439 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    2440 steps = 196, shift = 4.16, angle = 13 degrees 
    2441  
    2442 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    2443 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2444 Matrix rotation and translation 
    2445 -0.07683115 -0.17561277 0.98145662 66.44166832 
    2446 -0.66408769 -0.72522667 -0.18175198 411.16957530 
    2447 0.74369650 -0.66573749 -0.06090228 170.05104945 
    2448 Axis -0.66519466 0.32677996 -0.67136497 
    2449 Axis point 7.75299271 239.88960504 0.00000000 
    2450 Rotation angle (degrees) 158.66671698 
    2451 Shift along axis -24.00098327 
    2452  
    2453 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    2454 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    2455 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    2456 steps = 44, shift = 0.00106, angle = 0.00247 degrees 
    2457  
    2458 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    2459 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2460 Matrix rotation and translation 
    2461 -0.07685176 -0.17562808 0.98145227 66.44848746 
    2462 -0.66411122 -0.72519937 -0.18177500 411.17240045 
    2463 0.74367337 -0.66576320 -0.06090373 170.05786271 
    2464 Axis -0.66518608 0.32679973 -0.67136385 
    2465 Axis point 7.75566835 239.89404572 0.00000000 
    2466 Rotation angle (degrees) 158.66630362 
    2467 Shift along axis -24.00027887 
    2468  
    2469 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    2470 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    2471 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    2472 steps = 44, shift = 0.00214, angle = 0.00428 degrees 
    2473  
    2474 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    2475 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2476 Matrix rotation and translation 
    2477 -0.07680221 -0.17565442 0.98145143 66.44396733 
    2478 -0.66407552 -0.72523465 -0.18176462 411.17025225 
    2479 0.74371036 -0.66571781 -0.06094818 170.05404481 
    2480 Axis -0.66520863 0.32678246 -0.67134991 
    2481 Axis point 7.74491366 239.89221167 -0.00000000 
    2482 Rotation angle (degrees) 158.66868085 
    2483 Shift along axis -24.00164195 
    2484  
    2485 
    2486 > select up
    2487 
    2488 24808 atoms, 25460 bonds, 3176 residues, 11 models selected 
    2489 
    2490 > select up
    2491 
    2492 24808 atoms, 25460 bonds, 3176 residues, 11 models selected 
    2493 
    2494 > select up
    2495 
    2496 24808 atoms, 25460 bonds, 3176 residues, 11 models selected 
    2497 
    2498 > select down
    2499 
    2500 2 models selected 
    2501 
    2502 > volume flip #8
    2503 
    2504 Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip as #9, grid size
    2505 352,352,352, pixel 0.85, shown at step 1, values float32 
    2506 
    2507 > hide #!9 models
    2508 
    2509 > show #!9 models
    2510 
    2511 > select #9
    2512 
    2513 2 models selected 
    2514 
    2515 > view matrix models
    2516 > #9,0.04932,0.5784,-0.81426,225.85,0.77832,-0.53317,-0.33159,193.54,-0.62593,-0.6174,-0.47647,432.54
    2517 
    2518 > view matrix models
    2519 > #9,0.49864,0.44515,-0.74377,167.72,0.18866,-0.89322,-0.40812,346.38,-0.84603,0.063187,-0.52938,372.95
    2520 
    2521 > view matrix models
    2522 > #9,0.41566,0.19473,-0.88843,240.37,-0.83603,-0.30285,-0.45753,418.6,-0.35815,0.93293,0.036921,80.781
    2523 
    2524 > view matrix models
    2525 > #9,0.18699,-0.28999,-0.93858,354,0.30934,-0.88945,0.33644,207.89,-0.93239,-0.35325,-0.076615,374.31
    2526 
    2527 > view matrix models
    2528 > #9,0.12166,-0.27135,-0.95476,363.51,0.35041,-0.88823,0.29709,207.97,-0.92866,-0.37071,-0.01298,366.08
    2529 
    2530 > ui mousemode right "translate selected models"
    2531 
    2532 > view matrix models
    2533 > #9,0.12166,-0.27135,-0.95476,343.55,0.35041,-0.88823,0.29709,204.63,-0.92866,-0.37071,-0.01298,384.14
    2534 
    2535 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    2536 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    2537 correlation = 0.2626, correlation about mean = -0.03988, overlap = 1580 
    2538 steps = 48, shift = 0.0161, angle = 0.00778 degrees 
    2539  
    2540 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    2541 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2542 Matrix rotation and translation 
    2543 -0.07667600 -0.17562499 0.98146657 66.40220937 
    2544 -0.66405605 -0.72527845 -0.18166098 411.15872420 
    2545 0.74374077 -0.66567786 -0.06101339 170.05477366 
    2546 Axis -0.66525588 0.32674168 -0.67132294 
    2547 Axis point 7.71835621 239.88762888 0.00000000 
    2548 Rotation angle (degrees) 158.66732589 
    2549 Shift along axis -23.99344049 
    2550  
    2551 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    2552 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    2553 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    2554 steps = 84, shift = 0.0157, angle = 0.009 degrees 
    2555  
    2556 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    2557 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2558 Matrix rotation and translation 
    2559 -0.07682622 -0.17562423 0.98145496 66.44206918 
    2560 -0.66408132 -0.72523107 -0.18175771 411.17012882 
    2561 0.74370270 -0.66572968 -0.06091201 170.05004664 
    2562 Axis -0.66519758 0.32677973 -0.67136219 
    2563 Axis point 7.75121505 239.88987802 0.00000000 
    2564 Rotation angle (degrees) 158.66744100 
    2565 Shift along axis -24.00021217 
    2566  
    2567 
    2568 > view matrix models
    2569 > #9,0.12166,-0.27135,-0.95476,338.02,0.35041,-0.88823,0.29709,203.08,-0.92866,-0.37071,-0.01298,379.52
    2570 
    2571 > ui mousemode right "rotate selected models"
    2572 
    2573 > view matrix models
    2574 > #9,0.30016,-0.86169,-0.40914,310.95,-0.62921,-0.50123,0.59402,242.86,-0.71693,0.079138,-0.69264,391.26
    2575 
    2576 > view matrix models
    2577 > #9,0.079463,-0.47579,-0.87596,361.79,-0.033015,-0.87952,0.47472,229.87,-0.99629,-0.0088031,-0.085597,347.7
    2578 
    2579 > view matrix models
    2580 > #9,0.41919,-0.72698,-0.54387,295.14,-0.54116,-0.68106,0.49326,272.69,-0.729,0.087548,-0.6789,389.59
    2581 
    2582 > view matrix models
    2583 > #9,-0.24911,-0.67335,-0.6961,410.62,-0.72999,-0.34178,0.59185,234.54,-0.63644,0.65558,-0.4064,247.91
    2584 
    2585 > view matrix models
    2586 > #9,0.38176,-0.48586,-0.78626,304.1,-0.52937,-0.81227,0.24491,330.41,-0.75764,0.32273,-0.56729,341.04
    2587 
    2588 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    2589 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    2590 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    2591 steps = 40, shift = 0.000846, angle = 0.00177 degrees 
    2592  
    2593 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    2594 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2595 Matrix rotation and translation 
    2596 -0.07680654 -0.17560484 0.98145997 66.43537485 
    2597 -0.66409320 -0.72522729 -0.18172939 411.16781129 
    2598 0.74369413 -0.66573891 -0.06091578 170.05270073 
    2599 Axis -0.66520310 0.32677576 -0.67135865 
    2600 Axis point 7.74972828 239.88942606 0.00000000 
    2601 Rotation angle (degrees) 158.66589087 
    2602 Shift along axis -23.99969612 
    2603  
    2604 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    2605 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    2606 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    2607 steps = 40, shift = 0.00125, angle = 0.00125 degrees 
    2608  
    2609 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    2610 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2611 Matrix rotation and translation 
    2612 -0.07681767 -0.17562278 0.98145589 66.43984164 
    2613 -0.66408848 -0.72522635 -0.18175040 411.16938528 
    2614 0.74369719 -0.66573520 -0.06091887 170.05309874 
    2615 Axis -0.66520021 0.32678120 -0.67135886 
    2616 Axis point 7.74944501 239.89073787 0.00000000 
    2617 Rotation angle (degrees) 158.66693629 
    2618 Shift along axis -24.00002709 
    2619  
    2620 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip in map
    2621 cryosparc_P35_J96_006_volume_map_sharp.mrc using 435032 points 
    2622 correlation = 0.2522, correlation about mean = -0.0372, overlap = 1.179e+04 
    2623 steps = 324, shift = 5.58, angle = 29.2 degrees 
    2624  
    2625 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip (#9)
    2626 relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2627 Matrix rotation and translation 
    2628 0.07209466 -0.25700523 -0.96371709 344.01508219 
    2629 -0.25749943 -0.93827144 0.23095609 315.15876008 
    2630 -0.96358516 0.23150590 -0.13382306 321.33072132 
    2631 Axis 0.73215596 -0.17567940 -0.65809148 
    2632 Axis point 0.00000000 198.81231893 315.31278484 
    2633 Rotation angle (degrees) 179.97848683 
    2634 Shift along axis -14.95921604 
    2635  
    2636 
    2637 > hide #!9 models
    2638 
    2639 > show #!9 models
    2640 
    2641 > hide #!9 models
    2642 
    2643 > show #!8 models
    2644 
    2645 > show #!9 models
    2646 
    2647 > hide #!8 models
    2648 
    2649 > save "D:/OneDrive - Nanyang Technological
    2650 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
    2651 
    2652 > save "D:/OneDrive - Nanyang Technological
    2653 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
    2654 > includeMaps true
    2655 
    2656 > show #!8 models
    2657 
    2658 > hide #!8 models
    2659 
    2660 > hide #!9 models
    2661 
    2662 > show #!8 models
    2663 
    2664 > hide #!8 models
    2665 
    2666 > show #!2 models
    2667 
    2668 > ~select #9
    2669 
    2670 Nothing selected 
    2671 
    2672 > show #7 models
    2673 
    2674 > hide #6 models
    2675 
    2676 > hide #!1 models
    2677 
    2678 > select #7
    2679 
    2680 1 model selected 
    2681 
    2682 > view matrix models
    2683 > #7,0.28314,0.80804,0.51663,178.11,-0.89657,0.0317,0.44178,178.55,0.34059,-0.58828,0.73343,173.27
    2684 
    2685 > view matrix models
    2686 > #7,-0.85167,0.44193,-0.28171,178.2,0.13709,-0.33096,-0.93363,178.47,-0.50584,-0.83376,0.22128,173.34
    2687 
    2688 > view matrix models
    2689 > #7,-0.052894,0.17656,-0.98287,178.14,0.95344,0.30156,0.0028629,178.4,0.2969,-0.93695,-0.18429,173.28
    2690 
    2691 > ui mousemode right "translate selected models"
    2692 
    2693 > view matrix models
    2694 > #7,-0.052894,0.17656,-0.98287,123.75,0.95344,0.30156,0.0028629,168.98,0.2969,-0.93695,-0.18429,135.65
    2695 
    2696 > view matrix models
    2697 > #7,-0.052894,0.17656,-0.98287,171.65,0.95344,0.30156,0.0028629,239.46,0.2969,-0.93695,-0.18429,240.81
    2698 
    2699 > view matrix models
    2700 > #7,-0.052894,0.17656,-0.98287,168.29,0.95344,0.30156,0.0028629,214.9,0.2969,-0.93695,-0.18429,234.8
    2701 
    2702 > transparency #2.1 0
    2703 
    2704 > volume erase #2 center 168.29,214.9,234.8 radius 57.895
    2705 
    2706 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
    2707 352,352,352, pixel 0.85, shown at step 1, values float32 
    2708 
    2709 > view matrix models
    2710 > #7,-0.052894,0.17656,-0.98287,158.31,0.95344,0.30156,0.0028629,232.11,0.2969,-0.93695,-0.18429,231.78
    2711 
    2712 > volume erase #10 center 158.31,232.11,231.78 radius 57.895
    2713 
    2714 > view matrix models
    2715 > #7,-0.052894,0.17656,-0.98287,179.95,0.95344,0.30156,0.0028629,219.57,0.2969,-0.93695,-0.18429,237.28
    2716 
    2717 > view matrix models
    2718 > #7,-0.052894,0.17656,-0.98287,196.31,0.95344,0.30156,0.0028629,220.25,0.2969,-0.93695,-0.18429,246.32
    2719 
    2720 > volume erase #10 center 196.31,220.25,246.32 radius 57.895
    2721 
    2722 > view matrix models
    2723 > #7,-0.052894,0.17656,-0.98287,185.48,0.95344,0.30156,0.0028629,234.46,0.2969,-0.93695,-0.18429,244.14
    2724 
    2725 > view matrix models
    2726 > #7,-0.052894,0.17656,-0.98287,151.71,0.95344,0.30156,0.0028629,160.15,0.2969,-0.93695,-0.18429,262.05
    2727 
    2728 > view matrix models
    2729 > #7,-0.052894,0.17656,-0.98287,147.93,0.95344,0.30156,0.0028629,158.34,0.2969,-0.93695,-0.18429,267.59
    2730 
    2731 > view matrix models
    2732 > #7,-0.052894,0.17656,-0.98287,139.18,0.95344,0.30156,0.0028629,153.5,0.2969,-0.93695,-0.18429,267
    2733 
    2734 > volume erase #10 center 139.18,153.5,267 radius 57.895
    2735 
    2736 > view matrix models
    2737 > #7,-0.052894,0.17656,-0.98287,140,0.95344,0.30156,0.0028629,152.53,0.2969,-0.93695,-0.18429,263.01
    2738 
    2739 > view matrix models
    2740 > #7,-0.052894,0.17656,-0.98287,156.67,0.95344,0.30156,0.0028629,178.21,0.2969,-0.93695,-0.18429,266.42
    2741 
    2742 > volume erase #10 center 156.67,178.21,266.42 radius 57.895
    2743 
    2744 > view matrix models
    2745 > #7,-0.052894,0.17656,-0.98287,158.47,0.95344,0.30156,0.0028629,179.86,0.2969,-0.93695,-0.18429,260.63
    2746 
    2747 > view matrix models
    2748 > #7,-0.052894,0.17656,-0.98287,146.27,0.95344,0.30156,0.0028629,179.75,0.2969,-0.93695,-0.18429,264.96
    2749 
    2750 > view matrix models
    2751 > #7,-0.052894,0.17656,-0.98287,136.73,0.95344,0.30156,0.0028629,165.7,0.2969,-0.93695,-0.18429,256.45
    2752 
    2753 > volume erase #10 center 136.73,165.7,256.45 radius 57.895
    2754 
    2755 > view matrix models
    2756 > #7,-0.052894,0.17656,-0.98287,170.65,0.95344,0.30156,0.0028629,257.57,0.2969,-0.93695,-0.18429,281.54
    2757 
    2758 > view matrix models
    2759 > #7,-0.052894,0.17656,-0.98287,198.12,0.95344,0.30156,0.0028629,237.97,0.2969,-0.93695,-0.18429,234.34
    2760 
    2761 > volume erase #10 center 198.12,237.97,234.34 radius 57.895
    2762 
    2763 > close #7
    2764 
    2765 > show #!1 models
    2766 
    2767 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc copy in map
    2768 cryosparc_P35_J96_006_volume_map_sharp.mrc using 252601 points 
    2769 correlation = 0.4197, correlation about mean = 0.1732, overlap = 5606 
    2770 steps = 100, shift = 2.13, angle = 5.64 degrees 
    2771  
    2772 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) relative to
    2773 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2774 Matrix rotation and translation 
    2775 -0.26232817 0.42310640 0.86727444 32.84932501 
    2776 0.23389320 0.89982892 -0.36824168 75.35914970 
    2777 -0.93620401 0.10624943 -0.33501218 371.04180450 
    2778 Axis 0.25313923 0.96214902 -0.10094453 
    2779 Axis point 142.07695422 0.00000000 181.57625532 
    2780 Rotation angle (degrees) 110.41122784 
    2781 Shift along axis 43.36754334 
    2782  
    2783 
    2784 > select #10
    2785 
    2786 2 models selected 
    2787 
    2788 > view matrix models
    2789 > #10,-0.26233,0.42311,0.86727,32.251,0.23389,0.89983,-0.36824,72.484,-0.9362,0.10625,-0.33501,370.49
    2790 
    2791 > ui mousemode right "rotate selected models"
    2792 
    2793 > view matrix models
    2794 > #10,-0.13878,0.40417,0.9041,8.8226,0.22067,0.9026,-0.36963,74.459,-0.96543,0.14821,-0.21445,349.11
    2795 
    2796 > view matrix models
    2797 > #10,0.081829,0.24713,0.96552,-14.455,0.27881,0.92441,-0.26024,43.68,-0.95685,0.29049,0.0067426,290.35
    2798 
    2799 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc copy in map
    2800 cryosparc_P35_J96_006_volume_map_sharp.mrc using 252601 points 
    2801 correlation = 0.4197, correlation about mean = 0.1733, overlap = 5606 
    2802 steps = 228, shift = 2.88, angle = 23.2 degrees 
    2803  
    2804 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) relative to
    2805 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2806 Matrix rotation and translation 
    2807 -0.26246485 0.42303734 0.86726677 32.87464761 
    2808 0.23392580 0.89986112 -0.36814227 75.32527217 
    2809 -0.93615756 0.10625167 -0.33514125 371.06459232 
    2810 Axis 0.25309913 0.96216476 -0.10089498 
    2811 Axis point 142.08264269 0.00000000 181.57434136 
    2812 Rotation angle (degrees) 110.41836671 
    2813 Shift along axis 43.35731307 
    2814  
    2815 
    2816 > show #6 models
    2817 
    2818 > save "D:/OneDrive - Nanyang Technological
    2819 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
    2820 > includeMaps true
    2821 
    2822 > hide #!10 models
    2823 
    2824 > show #!8 models
    2825 
    2826 > hide #!1 models
    2827 
    2828 > ~select #10
    2829 
    2830 Nothing selected 
    2831 
    2832 > hide #6 models
    2833 
    2834 > select #7
    2835 
    2836 1 model selected 
    2837 
    2838 > view matrix models
    2839 > #7,0.92464,0.25458,-0.28325,178.06,0.04684,0.66208,0.74796,178.47,0.37795,-0.70486,0.60026,173.27
    2840 
    2841 > ui mousemode right "translate selected models"
    2842 
    2843 > view matrix models
    2844 > #7,0.92464,0.25458,-0.28325,204.47,0.04684,0.66208,0.74796,168.78,0.37795,-0.70486,0.60026,117.92
    2845 
    2846 > view matrix models
    2847 > #7,0.92464,0.25458,-0.28325,205.35,0.04684,0.66208,0.74796,172.6,0.37795,-0.70486,0.60026,132.71
    2848 
    2849 > view matrix models
    2850 > #7,0.92464,0.25458,-0.28325,202.38,0.04684,0.66208,0.74796,170.72,0.37795,-0.70486,0.60026,135.25
    2851 
    2852 > view matrix models
    2853 > #7,0.92464,0.25458,-0.28325,208.14,0.04684,0.66208,0.74796,169.1,0.37795,-0.70486,0.60026,122.9
    2854 
    2855 > volume #8 level 0.8304
    2856 
    2857 > view matrix models
    2858 > #7,0.92464,0.25458,-0.28325,209.46,0.04684,0.66208,0.74796,167.64,0.37795,-0.70486,0.60026,121.48
    2859 
    2860 > volume erase #8 center 209.46,167.64,121.48 radius 64.178
    2861 
    2862 Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy as #11, grid size
    2863 352,352,352, pixel 0.85, shown at step 1, values float32 
    2864 
    2865 > view matrix models
    2866 > #7,0.92464,0.25458,-0.28325,202.68,0.04684,0.66208,0.74796,128.68,0.37795,-0.70486,0.60026,117.72
    2867 
    2868 > volume erase #11 center 202.68,128.68,117.72 radius 64.178
    2869 
    2870 > view matrix models
    2871 > #7,0.92464,0.25458,-0.28325,183.78,0.04684,0.66208,0.74796,136.58,0.37795,-0.70486,0.60026,112.38
    2872 
    2873 > volume erase #11 center 183.78,136.58,112.38 radius 64.178
    2874 
    2875 > view matrix models
    2876 > #7,0.92464,0.25458,-0.28325,262.78,0.04684,0.66208,0.74796,132.37,0.37795,-0.70486,0.60026,184.94
    2877 
    2878 > view matrix models
    2879 > #7,0.92464,0.25458,-0.28325,269.47,0.04684,0.66208,0.74796,136.95,0.37795,-0.70486,0.60026,179.85
    2880 
    2881 > view matrix models
    2882 > #7,0.92464,0.25458,-0.28325,267.59,0.04684,0.66208,0.74796,127.26,0.37795,-0.70486,0.60026,154.16
    2883 
    2884 > view matrix models
    2885 > #7,0.92464,0.25458,-0.28325,261.44,0.04684,0.66208,0.74796,136.21,0.37795,-0.70486,0.60026,158.39
    2886 
    2887 > volume erase #11 center 261.44,136.21,158.39 radius 64.178
    2888 
    2889 > view matrix models
    2890 > #7,0.92464,0.25458,-0.28325,234.76,0.04684,0.66208,0.74796,204.63,0.37795,-0.70486,0.60026,115.7
    2891 
    2892 > view matrix models
    2893 > #7,0.92464,0.25458,-0.28325,232.48,0.04684,0.66208,0.74796,207.24,0.37795,-0.70486,0.60026,119.09
    2894 
    2895 > volume erase #11 center 232.48,207.24,119.09 radius 64.178
    2896 
    2897 > view matrix models
    2898 > #7,0.92464,0.25458,-0.28325,211.86,0.04684,0.66208,0.74796,185.05,0.37795,-0.70486,0.60026,105.87
    2899 
    2900 > view matrix models
    2901 > #7,0.92464,0.25458,-0.28325,195.04,0.04684,0.66208,0.74796,187.39,0.37795,-0.70486,0.60026,114.92
    2902 
    2903 > view matrix models
    2904 > #7,0.92464,0.25458,-0.28325,201.04,0.04684,0.66208,0.74796,190.35,0.37795,-0.70486,0.60026,113.3
    2905 
    2906 > volume erase #11 center 201.04,190.35,113.3 radius 64.178
    2907 
    2908 > show #!1 models
    2909 
    2910 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
    2911 cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points 
    2912 correlation = 0.3648, correlation about mean = -0.1049, overlap = 2621 
    2913 steps = 72, shift = 2.57, angle = 2.92 degrees 
    2914  
    2915 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
    2916 to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2917 Matrix rotation and translation 
    2918 -0.05111081 -0.21510165 0.97525327 67.52834138 
    2919 -0.64952035 -0.73462917 -0.19606954 411.11615250 
    2920 0.75862440 -0.64346813 -0.10216541 168.35220279 
    2921 Axis -0.67771084 0.32814528 -0.65804915 
    2922 Axis point 0.00000000 241.21252430 -1.00026216 
    2923 Rotation angle (degrees) 160.72632370 
    2924 Shift along axis -21.64288928 
    2925  
    2926 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
    2927 cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points 
    2928 correlation = 0.3649, correlation about mean = -0.1049, overlap = 2621 
    2929 steps = 40, shift = 0.0141, angle = 0.00956 degrees 
    2930  
    2931 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
    2932 to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2933 Matrix rotation and translation 
    2934 -0.05107225 -0.21496635 0.97528512 67.48907810 
    2935 -0.64946346 -0.73471119 -0.19595064 411.10839498 
    2936 0.75867570 -0.64341970 -0.10208944 168.33302170 
    2937 Axis -0.67772214 0.32806961 -0.65807524 
    2938 Axis point 0.00000000 241.19521972 -0.99729201 
    2939 Rotation angle (degrees) 160.72350203 
    2940 Shift along axis -21.64246440 
    2941  
    2942 Correlation = 0.3649, Correlation about mean = -0.1049, Overlap = 2621 
    2943  
    2944 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
    2945 cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points 
    2946 correlation = 0.3649, correlation about mean = -0.1049, overlap = 2621 
    2947 steps = 28, shift = 0.011, angle = 0.00422 degrees 
    2948  
    2949 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
    2950 to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    2951 Matrix rotation and translation 
    2952 -0.05110002 -0.21502631 0.97527045 67.51163904 
    2953 -0.64943800 -0.73471600 -0.19601698 411.10850225 
    2954 0.75869563 -0.64339417 -0.10210226 168.32377829 
    2955 Axis -0.67771626 0.32808172 -0.65807526 
    2956 Axis point 0.00000000 241.19615320 -1.00289431 
    2957 Rotation angle (degrees) 160.72744238 
    2958 Shift along axis -21.64626553 
    2959  
    2960 
    2961 > close #7
    2962 
    2963 > volume #8 level 0.4211
    2964 
    2965 > hide #!8 models
    2966 
    2967 > volume #11 level 0.6377
    2968 
    2969 > volume #11 level 0.4713
    2970 
    2971 > show #!10 models
    2972 
    2973 > hide #!10 models
    2974 
    2975 > show #!10 models
    2976 
    2977 > select #11
    2978 
    2979 2 models selected 
    2980 
    2981 > ui mousemode right "rotate selected models"
    2982 
    2983 > view matrix models
    2984 > #11,-0.14971,0.63965,-0.75394,191.13,-0.95888,-0.2799,-0.047058,377.99,-0.24113,0.71589,0.65525,40.47
    2985 
    2986 > view matrix models
    2987 > #11,-0.069022,0.30969,-0.94833,249.55,0.96027,0.27828,0.020987,-16.584,0.2704,-0.9092,-0.3166,311.78
    2988 
    2989 > ui mousemode right "translate selected models"
    2990 
    2991 > view matrix models
    2992 > #11,-0.069022,0.30969,-0.94833,292.24,0.96027,0.27828,0.020987,-16.748,0.2704,-0.9092,-0.3166,306.11
    2993 
    2994 > view matrix models
    2995 > #11,-0.069022,0.30969,-0.94833,288.83,0.96027,0.27828,0.020987,-15.141,0.2704,-0.9092,-0.3166,305.54
    2996 
    2997 > ui mousemode right "rotate selected models"
    2998 
    2999 > view matrix models
    3000 > #11,-0.12042,0.37081,-0.92087,284.98,0.89214,0.44729,0.063446,-33.276,0.43542,-0.8139,-0.38467,274.73
    3001 
    3002 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
    3003 cryosparc_P35_J96_006_volume_map_sharp.mrc using 185886 points 
    3004 correlation = 0.3705, correlation about mean = -0.01342, overlap = 9885 
    3005 steps = 84, shift = 3.3, angle = 7.24 degrees 
    3006  
    3007 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
    3008 to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    3009 Matrix rotation and translation 
    3010 -0.08967779 0.29999028 -0.94971770 295.49237204 
    3011 0.84493489 0.52775912 0.08692132 -41.96570345 
    3012 0.52729773 -0.79465472 -0.30080053 248.18221209 
    3013 Axis -0.48858097 -0.81858128 0.30201543 
    3014 Axis point 60.64458577 -0.00000000 223.51625228 
    3015 Rotation angle (degrees) 115.55387500 
    3016 Shift along axis -35.06475327 
    3017  
    3018 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
    3019 cryosparc_P35_J96_006_volume_map_sharp.mrc using 185886 points 
    3020 correlation = 0.3706, correlation about mean = -0.01331, overlap = 9885 
    3021 steps = 40, shift = 0.0143, angle = 0.0103 degrees 
    3022  
    3023 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
    3024 to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    3025 Matrix rotation and translation 
    3026 -0.08981970 0.29998685 -0.94970537 295.52003565 
    3027 0.84486634 0.52788229 0.08683967 -41.94876855 
    3028 0.52738342 -0.79457419 -0.30086302 248.17026594 
    3029 Axis -0.48850161 -0.81863956 0.30198584 
    3030 Axis point 60.66605513 0.00000000 223.51111811 
    3031 Rotation angle (degrees) 115.55645450 
    3032 Shift along axis -35.07718649 
    3033  
    3034 
    3035 > save "D:/OneDrive - Nanyang Technological
    3036 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
    3037 > includeMaps true
    3038 
    3039 > close #9
    3040 
    3041 > show #!2 models
    3042 
    3043 > hide #!11 models
    3044 
    3045 > ~select #11
    3046 
    3047 Nothing selected 
    3048 
    3049 > show #6 models
    3050 
    3051 > hide #!2 models
    3052 
    3053 > show #!2 models
    3054 
    3055 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
    3056 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 434908 points 
    3057 correlation = 0.8681, correlation about mean = 0.7943, overlap = 2.493e+04 
    3058 steps = 100, shift = 2.6, angle = 5.47 degrees 
    3059  
    3060 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
    3061 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3062 Matrix rotation and translation 
    3063 0.99999417 -0.00078818 -0.00332112 0.86833791 
    3064 0.00079720 0.99999599 0.00271726 -0.70720618 
    3065 0.00331897 -0.00271989 0.99999079 0.00769659 
    3066 Axis -0.62300052 -0.76083593 0.18165636 
    3067 Axis point -1.67706066 0.00000000 261.17922578 
    3068 Rotation angle (degrees) 0.25002110 
    3069 Shift along axis -0.00150896 
    3070  
    3071 
    3072 > hide #!1 models
    3073 
    3074 Fit molecule D2NS1-F562.pdb (#6) to map
    3075 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 12404 atoms 
    3076 average map value = 0.1247, steps = 124 
    3077 shifted from previous position = 2.69 
    3078 rotated from previous position = 12.5 degrees 
    3079 atoms outside contour = 7351, contour level = 0.14151 
    3080  
    3081 Position of D2NS1-F562.pdb (#6) relative to
    3082 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3083 Matrix rotation and translation 
    3084 0.25275147 -0.43670415 -0.86336907 353.51447381 
    3085 -0.44938591 -0.84323715 0.29496333 308.88812835 
    3086 -0.85683660 0.31343349 -0.40937812 323.84932290 
    3087 Axis 0.79143097 -0.27991074 -0.54340316 
    3088 Axis point 0.00000000 215.73050893 284.44415750 
    3089 Rotation angle (degrees) 179.33140963 
    3090 Shift along axis 17.34045325 
    3091  
    3092 Fit molecule D2NS1-F562.pdb (#6) to map
    3093 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 12404 atoms 
    3094 average map value = 0.1247, steps = 36 
    3095 shifted from previous position = 0.00249 
    3096 rotated from previous position = 0.00661 degrees 
    3097 atoms outside contour = 7351, contour level = 0.14151 
    3098  
    3099 Position of D2NS1-F562.pdb (#6) relative to
    3100 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3101 Matrix rotation and translation 
    3102 0.25279114 -0.43660663 -0.86340677 353.49888697 
    3103 -0.44933375 -0.84329450 0.29487884 308.90364784 
    3104 -0.85685225 0.31341505 -0.40935948 323.85331097 
    3105 Axis 0.79144345 -0.27985911 -0.54341158 
    3106 Axis point 0.00000000 215.71863017 284.44492018 
    3107 Rotation angle (degrees) 179.32902903 
    3108 Shift along axis 17.33923677 
    3109  
    3110 
    3111 > transparency #2.1#10.1 50
    3112 
    3113 > hide #!2 models
    3114 
    3115 > show #!8 models
    3116 
    3117 > select #8
    3118 
    3119 2 models selected 
    3120 
    3121 > view matrix models
    3122 > #8,0.33902,0.03981,-0.93994,229.8,-0.92382,-0.17477,-0.34061,394.45,-0.17784,0.9838,-0.022475,72.918
    3123 
    3124 > view matrix models
    3125 > #8,-0.19081,0.15972,-0.96855,298.63,-0.9771,-0.1256,0.17178,326.79,-0.094217,0.97914,0.18003,33.4
    3126 
    3127 > ui mousemode right "translate selected models"
    3128 
    3129 > view matrix models
    3130 > #8,-0.19081,0.15972,-0.96855,333.9,-0.9771,-0.1256,0.17178,339.76,-0.094217,0.97914,0.18003,31.589
    3131 
    3132 > view matrix models
    3133 > #8,-0.19081,0.15972,-0.96855,336.31,-0.9771,-0.1256,0.17178,330.87,-0.094217,0.97914,0.18003,34.463
    3134 
    3135 > view matrix models
    3136 > #8,-0.19081,0.15972,-0.96855,332.19,-0.9771,-0.1256,0.17178,338.81,-0.094217,0.97914,0.18003,28.17
    3137 
    3138 > view matrix models
    3139 > #8,-0.19081,0.15972,-0.96855,344.81,-0.9771,-0.1256,0.17178,333.8,-0.094217,0.97914,0.18003,27.752
    3140 
    3141 > ui mousemode right "rotate selected models"
    3142 
    3143 > view matrix models
    3144 > #8,0.39538,0.22669,-0.8901,233.97,0.79273,0.40527,0.45534,-53.893,0.46395,-0.88565,-0.019473,233.43
    3145 
    3146 > ui mousemode right "translate selected models"
    3147 
    3148 > view matrix models
    3149 > #8,0.39538,0.22669,-0.8901,225.01,0.79273,0.40527,0.45534,-60.792,0.46395,-0.88565,-0.019473,244.4
    3150 
    3151 > view matrix models
    3152 > #8,0.39538,0.22669,-0.8901,226.27,0.79273,0.40527,0.45534,-67.659,0.46395,-0.88565,-0.019473,244.84
    3153 
    3154 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    3155 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 47154 points 
    3156 correlation = 0.3601, correlation about mean = -0.01926, overlap = 2801 
    3157 steps = 244, shift = 6.57, angle = 20.9 degrees 
    3158  
    3159 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    3160 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3161 Matrix rotation and translation 
    3162 -0.50275518 0.77664634 0.37954926 71.44698114 
    3163 0.77480667 0.59955666 -0.20051529 -35.12156246 
    3164 -0.38329076 0.19326720 -0.90318100 318.59922133 
    3165 Axis 0.45869577 0.88859079 -0.00214294 
    3166 Axis point 85.22138435 0.00000000 150.24137730 
    3167 Rotation angle (degrees) 154.58056842 
    3168 Shift along axis 0.88099311 
    3169  
    3170 
    3171 > save "D:/OneDrive - Nanyang Technological
    3172 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
    3173 > includeMaps true
    3174 
    3175 ——— End of log from Tue Feb 22 21:05:12 2022 ———
    3176 
    3177 opened ChimeraX session 
    3178 
    3179 > hide #!10 models
    3180 
    3181 > show #!10 models
    3182 
    3183 > hide #!8 models
    3184 
    3185 > show #!1 models
    3186 
    3187 > show #!2 models
    3188 
    3189 > close #11
    3190 
    3191 > close #8
    3192 
    3193 > open "D:/OneDrive - Nanyang Technological
    3194 > University/Temporal/202109_zvNS1/3_Structures/2n5e.pdb"
    3195 
    3196 2n5e.pdb title: 
    3197 The 3D solution structure of discoidal high-density lipoprotein particles
    3198 [more info...] 
    3199  
    3200 Chain information for 2n5e.pdb 
    3201 --- 
    3202 Chain | Description 
    3203 7.1/A 7.2/A 7.3/A 7.4/A 7.5/A 7.6/A 7.7/A 7.8/A 7.9/A 7.10/A 7.1/B 7.2/B 7.3/B
    3204 7.4/B 7.5/B 7.6/B 7.7/B 7.8/B 7.9/B 7.10/B | apolipoprotein A-I 
    3205  
    3206 
    3207 > close #7.2-10
    3208 
    3209 > hide #7.1 models
    3210 
    3211 > show #7.1 models
    3212 
    3213 > hide #7.1 models
    3214 
    3215 > hide #!2 models
    3216 
    3217 > hide #!1 models
    3218 
    3219 > ui tool show "Fit in Map"
    3220 
    3221 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3222 copy (#10) using 5602 atoms 
    3223 average map value = 0.1754, steps = 352 
    3224 shifted from previous position = 4.55 
    3225 rotated from previous position = 50.7 degrees 
    3226 atoms outside contour = 2605, contour level = 0.14151 
    3227  
    3228 Position of D2NS1.pdb (#3) relative to
    3229 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3230 Matrix rotation and translation 
    3231 -0.51892205 0.80965860 -0.27417668 164.22917225 
    3232 -0.84272074 -0.43077092 0.32289035 300.54198392 
    3233 0.14332362 0.39860929 0.90585262 -107.70830576 
    3234 Axis 0.04438420 -0.24472630 -0.96857580 
    3235 Axis point 169.29706156 116.85077370 0.00000000 
    3236 Rotation angle (degrees) 121.46114137 
    3237 Shift along axis 38.06231174 
    3238  
    3239 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3240 copy (#10) using 5602 atoms 
    3241 average map value = 0.1754, steps = 40 
    3242 shifted from previous position = 0.00569 
    3243 rotated from previous position = 0.00161 degrees 
    3244 atoms outside contour = 2609, contour level = 0.14151 
    3245  
    3246 Position of D2NS1.pdb (#3) relative to
    3247 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3248 Matrix rotation and translation 
    3249 -0.51894067 0.80965192 -0.27416117 164.23500046 
    3250 -0.84270669 -0.43078495 0.32290828 300.54258112 
    3251 0.14333881 0.39860769 0.90585092 -107.71085737 
    3252 Axis 0.04437330 -0.24472913 -0.96857558 
    3253 Axis point 169.29862447 116.85084764 0.00000000 
    3254 Rotation angle (degrees) 121.46229524 
    3255 Shift along axis 38.06223078 
    3256  
    3257 
    3258 > show #4 models
    3259 
    3260 > hide #!7 models
    3261 
    3262 > hide #6 models
    3263 
    3264 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3265 copy (#10) using 3401 atoms 
    3266 average map value = 0.2415, steps = 184 
    3267 shifted from previous position = 2.68 
    3268 rotated from previous position = 43.1 degrees 
    3269 atoms outside contour = 1055, contour level = 0.14151 
    3270  
    3271 Position of F562a.pdb (#4) relative to
    3272 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3273 Matrix rotation and translation 
    3274 0.23696585 -0.97040692 -0.04644960 286.31819473 
    3275 0.13996862 0.08141367 -0.98680321 234.14224375 
    3276 0.96138231 0.22733718 0.15511878 -33.92541253 
    3277 Axis 0.62926604 -0.52234025 0.57548668 
    3278 Axis point 0.00000000 269.88096267 6.34604794 
    3279 Rotation angle (degrees) 105.26304401 
    3280 Shift along axis 38.34477607 
    3281  
    3282 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3283 copy (#10) using 3401 atoms 
    3284 average map value = 0.2415, steps = 40 
    3285 shifted from previous position = 0.0163 
    3286 rotated from previous position = 0.0184 degrees 
    3287 atoms outside contour = 1053, contour level = 0.14151 
    3288  
    3289 Position of F562a.pdb (#4) relative to
    3290 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3291 Matrix rotation and translation 
    3292 0.23699244 -0.97040417 -0.04637137 286.30251238 
    3293 0.14028426 0.08141314 -0.98675843 234.09383454 
    3294 0.96132975 0.22734912 0.15542673 -33.96007421 
    3295 Axis 0.62921931 -0.52224780 0.57562166 
    3296 Axis point 0.00000000 269.87054516 6.30278577 
    3297 Rotation angle (degrees) 105.25312557 
    3298 Shift along axis 38.34392482 
    3299  
    3300 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3301 copy (#10) using 3401 atoms 
    3302 average map value = 0.2415, steps = 44 
    3303 shifted from previous position = 0.0177 
    3304 rotated from previous position = 0.024 degrees 
    3305 atoms outside contour = 1055, contour level = 0.14151 
    3306  
    3307 Position of F562a.pdb (#4) relative to
    3308 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3309 Matrix rotation and translation 
    3310 0.23699037 -0.97040260 -0.04641486 286.30808679 
    3311 0.13987427 0.08136006 -0.98682101 234.17141287 
    3312 0.96139000 0.22737483 0.15501591 -33.91830894 
    3313 Axis 0.62930653 -0.52233598 0.57544628 
    3314 Axis point 0.00000000 269.87165306 6.36745226 
    3315 Rotation angle (degrees) 105.26696289 
    3316 Shift along axis 38.34122922 
    3317  
    3318 
    3319 > show #3 models
    3320 
    3321 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3322 copy (#10) using 3401 atoms 
    3323 average map value = 0.2415, steps = 44 
    3324 shifted from previous position = 0.0174 
    3325 rotated from previous position = 0.02 degrees 
    3326 atoms outside contour = 1053, contour level = 0.14151 
    3327  
    3328 Position of F562a.pdb (#4) relative to
    3329 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3330 Matrix rotation and translation 
    3331 0.23696878 -0.97040926 -0.04638578 286.31082660 
    3332 0.14021616 0.08140780 -0.98676855 234.10798884 
    3333 0.96134552 0.22732931 0.15535816 -33.95179699 
    3334 Axis 0.62922296 -0.52227064 0.57559694 
    3335 Axis point 0.00000000 269.87770153 6.30937551 
    3336 Rotation angle (degrees) 105.25602295 
    3337 Shift along axis 38.34306534 
    3338  
    3339 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3340 copy (#10) using 3401 atoms 
    3341 average map value = 0.2415, steps = 28 
    3342 shifted from previous position = 0.0182 
    3343 rotated from previous position = 0.0232 degrees 
    3344 atoms outside contour = 1055, contour level = 0.14151 
    3345  
    3346 Position of F562a.pdb (#4) relative to
    3347 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3348 Matrix rotation and translation 
    3349 0.23695180 -0.97040946 -0.04646826 286.32373425 
    3350 0.13981736 0.08139458 -0.98682623 234.17404048 
    3351 0.96140779 0.22733318 0.15496668 -33.91113966 
    3352 Axis 0.62929239 -0.52237681 0.57542468 
    3353 Axis point 0.00000000 269.88626156 6.36736238 
    3354 Rotation angle (degrees) 105.26854490 
    3355 Shift along axis 38.34095150 
    3356  
    3357 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3358 copy (#10) using 3401 atoms 
    3359 average map value = 0.2415, steps = 40 
    3360 shifted from previous position = 0.00386 
    3361 rotated from previous position = 0.0076 degrees 
    3362 atoms outside contour = 1055, contour level = 0.14151 
    3363  
    3364 Position of F562a.pdb (#4) relative to
    3365 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3366 Matrix rotation and translation 
    3367 0.23701158 -0.97039892 -0.04638334 286.30019564 
    3368 0.13991374 0.08134082 -0.98681700 234.16833276 
    3369 0.96137903 0.22739739 0.15505086 -33.92599735 
    3370 Axis 0.62931286 -0.52231123 0.57546182 
    3371 Axis point 0.00000000 269.86512738 6.36383820 
    3372 Rotation angle (degrees) 105.26586629 
    3373 Shift along axis 38.34052770 
    3374  
    3375 
    3376 > show #!2 models
    3377 
    3378 > show #6 models
    3379 
    3380 > hide #!2 models
    3381 
    3382 > hide #!10 models
    3383 
    3384 > hide #6 models
    3385 
    3386 > show #6 models
    3387 
    3388 > mmaker #6 to #3
    3389 
    3390 Parameters 
    3391 --- 
    3392 Chain pairing | bb 
    3393 Alignment algorithm | Needleman-Wunsch 
    3394 Similarity matrix | BLOSUM-62 
    3395 SS fraction | 0.3 
    3396 Gap open (HH/SS/other) | 18/18/6 
    3397 Gap extend | 1 
    3398 SS matrix |  |  | H | S | O 
    3399 ---|---|---|--- 
    3400 H | 6 | -9 | -6 
    3401 S |  | 6 | -6 
    3402 O |  |  | 4 
    3403 Iteration cutoff | 2 
    3404  
    3405 Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
    3406 alignment score = 1871.9 
    3407 RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
    3408 0.023) 
    3409  
    3410 
    3411 > hide #6 models
    3412 
    3413 > show #6 models
    3414 
    3415 > hide #6 models
    3416 
    3417 > show #6 models
    3418 
    3419 > hide #6 models
    3420 
    3421 > show #!2 models
    3422 
    3423 > show #!1 models
    3424 
    3425 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    3426 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points 
    3427 correlation = 0.4911, correlation about mean = 0.2779, overlap = 6002 
    3428 steps = 1308, shift = 0.661, angle = 22 degrees 
    3429  
    3430 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    3431 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3432 Matrix rotation and translation 
    3433 -0.27793747 -0.14035072 -0.95029069 409.92559615 
    3434 0.39452131 0.88530641 -0.24614115 -49.02432671 
    3435 0.87584454 -0.44332178 -0.19068848 109.24693947 
    3436 Axis -0.10307165 -0.95457032 0.27959209 
    3437 Axis point 169.03926821 0.00000000 207.85299225 
    3438 Rotation angle (degrees) 106.95735055 
    3439 Shift along axis 35.09003774 
    3440  
    3441 
    3442 > show #!10 models
    3443 
    3444 > hide #!2 models
    3445 
    3446 > hide #!1 models
    3447 
    3448 > show #!2 models
    3449 
    3450 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3451 copy (#10) using 5602 atoms 
    3452 average map value = 0.1754, steps = 44 
    3453 shifted from previous position = 0.00219 
    3454 rotated from previous position = 0.0172 degrees 
    3455 atoms outside contour = 2607, contour level = 0.14151 
    3456  
    3457 Position of D2NS1.pdb (#3) relative to
    3458 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3459 Matrix rotation and translation 
    3460 -0.51889139 0.80974271 -0.27398626 164.17754795 
    3461 -0.84268736 -0.43067692 0.32310277 300.48501792 
    3462 0.14363056 0.39854000 0.90583449 -107.74724207 
    3463 Axis 0.04421738 -0.24478525 -0.96856853 
    3464 Axis point 169.27126594 116.83993981 0.00000000 
    3465 Rotation angle (degrees) 121.45756347 
    3466 Shift along axis 38.06578928 
    3467  
    3468 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3469 copy (#10) using 5602 atoms 
    3470 average map value = 0.1754, steps = 44 
    3471 shifted from previous position = 0.00282 
    3472 rotated from previous position = 0.00397 degrees 
    3473 atoms outside contour = 2606, contour level = 0.14151 
    3474  
    3475 Position of D2NS1.pdb (#3) relative to
    3476 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3477 Matrix rotation and translation 
    3478 -0.51894411 0.80971407 -0.27397106 164.19040191 
    3479 -0.84265984 -0.43073928 0.32309143 300.49449446 
    3480 0.14360158 0.39853079 0.90584314 -107.74009884 
    3481 Axis 0.04422032 -0.24476870 -0.96857258 
    3482 Axis point 169.27313448 116.84271119 0.00000000 
    3483 Rotation angle (degrees) 121.46113819 
    3484 Shift along axis 38.06301215 
    3485  
    3486 
    3487 > select #3
    3488 
    3489 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    3490 
    3491 > ui mousemode right "rotate selected models"
    3492 
    3493 > view matrix models
    3494 > #3,-0.14665,-0.10019,0.9841,42.803,-0.93066,-0.32317,-0.17158,431.35,0.33522,-0.94102,-0.045847,294.18
    3495 
    3496 > view matrix models
    3497 > #3,-0.24212,-0.16715,0.95574,75.904,-0.91312,-0.29375,-0.2827,443.12,0.328,-0.94116,-0.081503,301.82
    3498 
    3499 > view matrix models
    3500 > #3,-0.22781,0.0025001,0.9737,41.665,-0.95433,-0.19906,-0.22277,423.77,0.19327,-0.97998,0.047735,309.02
    3501 
    3502 > view matrix models
    3503 > #3,-0.31679,-0.24249,0.91698,108.61,-0.87534,-0.29756,-0.38109,454.64,0.36527,-0.92339,-0.118,298.78
    3504 
    3505 > view matrix models
    3506 > #3,-0.20831,0.16138,0.96466,13.134,-0.97765,-0.063166,-0.20055,401.06,0.028569,-0.98487,0.17093,316.86
    3507 
    3508 > view matrix models
    3509 > #3,-0.18189,0.029376,0.98288,27.434,-0.97841,0.094327,-0.18388,371.75,-0.098114,-0.99511,0.011585,369.25
    3510 
    3511 > ui mousemode right "translate selected models"
    3512 
    3513 > view matrix models
    3514 > #3,-0.18189,0.029376,0.98288,26.801,-0.97841,0.094327,-0.18388,370.7,-0.098114,-0.99511,0.011585,365.44
    3515 
    3516 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3517 copy (#10) using 5602 atoms 
    3518 average map value = 0.1754, steps = 220 
    3519 shifted from previous position = 5.16 
    3520 rotated from previous position = 26.4 degrees 
    3521 atoms outside contour = 2605, contour level = 0.14151 
    3522  
    3523 Position of D2NS1.pdb (#3) relative to
    3524 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3525 Matrix rotation and translation 
    3526 -0.51865164 0.80982057 -0.27420999 164.16314366 
    3527 -0.84285174 -0.43044060 0.32298891 300.49787860 
    3528 0.14353196 0.39863709 0.90580740 -107.73453379 
    3529 Axis 0.04433389 -0.24481919 -0.96855463 
    3530 Axis point 169.29026360 116.83700867 0.00000000 
    3531 Rotation angle (degrees) 121.44248630 
    3532 Shift along axis 38.05712471 
    3533  
    3534 
    3535 > hide #!2 models
    3536 
    3537 > view matrix models
    3538 > #3,-0.095949,-0.048917,0.99418,23.903,-0.93262,-0.34465,-0.10697,422.69,0.34788,-0.93745,-0.012552,284.37
    3539 
    3540 > view matrix models
    3541 > #3,-0.095949,-0.048917,0.99418,24.499,-0.93262,-0.34465,-0.10697,420.51,0.34788,-0.93745,-0.012552,282.55
    3542 
    3543 > ui mousemode right "map eraser"
    3544 
    3545 > volume erase #10 center 197.01,182.51,231.59 radius 31.633
    3546 
    3547 > volume erase #10 center 213.27,171.82,231.83 radius 31.633
    3548 
    3549 > volume erase #10 center 199.27,226.74,192.59 radius 31.633
    3550 
    3551 > volume erase #10 center 201.83,210.63,213.73 radius 31.633
    3552 
    3553 > close #8
    3554 
    3555 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3556 copy (#10) using 5602 atoms 
    3557 average map value = 0.1735, steps = 84 
    3558 shifted from previous position = 4.01 
    3559 rotated from previous position = 2.96 degrees 
    3560 atoms outside contour = 2586, contour level = 0.14151 
    3561  
    3562 Position of D2NS1.pdb (#3) relative to
    3563 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3564 Matrix rotation and translation 
    3565 -0.47450864 0.83236882 -0.28636287 154.63058051 
    3566 -0.86693279 -0.38553270 0.31589884 297.74905925 
    3567 0.15254210 0.39815408 0.90454642 -108.87748698 
    3568 Axis 0.04681588 -0.24980441 -0.96716391 
    3569 Axis point 169.11832797 115.96117517 0.00000000 
    3570 Rotation angle (degrees) 118.53838807 
    3571 Shift along axis 38.16251411 
    3572  
    3573 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3574 copy (#10) using 5602 atoms 
    3575 average map value = 0.1735, steps = 48 
    3576 shifted from previous position = 0.00277 
    3577 rotated from previous position = 0.00477 degrees 
    3578 atoms outside contour = 2584, contour level = 0.14151 
    3579  
    3580 Position of D2NS1.pdb (#3) relative to
    3581 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3582 Matrix rotation and translation 
    3583 -0.47448892 0.83239630 -0.28631566 154.61369255 
    3584 -0.86692974 -0.38549828 0.31594921 297.73456104 
    3585 0.15262076 0.39812996 0.90454377 -108.88430164 
    3586 Axis 0.04677274 -0.24981834 -0.96716240 
    3587 Axis point 169.11102884 115.95863363 0.00000000 
    3588 Rotation angle (degrees) 118.53670909 
    3589 Shift along axis 38.16095498 
    3590  
    3591 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    3592 copy (#10) using 5602 atoms 
    3593 average map value = 0.1735, steps = 60 
    3594 shifted from previous position = 0.0162 
    3595 rotated from previous position = 0.0207 degrees 
    3596 atoms outside contour = 2591, contour level = 0.14151 
    3597  
    3598 Position of D2NS1.pdb (#3) relative to
    3599 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3600 Matrix rotation and translation 
    3601 -0.47456944 0.83227118 -0.28654585 154.70120447 
    3602 -0.86694397 -0.38562941 0.31575007 297.80757285 
    3603 0.15228918 0.39826452 0.90454042 -108.84769154 
    3604 Axis 0.04696579 -0.24977725 -0.96716366 
    3605 Axis point 169.15292707 115.96995015 0.00000000 
    3606 Rotation angle (degrees) 118.54372018 
    3607 Shift along axis 38.15363917 
    3608  
    3609 
    3610 > show #!2 models
    3611 
    3612 > show #!7 models
    3613 
    3614 > show #7.1 models
    3615 
    3616 > select #7.1
    3617 
    3618 5464 atoms, 5510 bonds, 334 residues, 1 model selected 
    3619 
    3620 > close #8
    3621 
    3622 > close #8
    3623 
    3624 > ui mousemode right "translate selected models"
    3625 
    3626 > view matrix models #7.1,1,0,0,169.78,0,1,0,228.66,0,0,1,242.62
    3627 
    3628 > view matrix models #7.1,1,0,0,141.19,0,1,0,179.49,0,0,1,253.16
    3629 
    3630 > view matrix models #7.1,1,0,0,139.34,0,1,0,181.33,0,0,1,279.32
    3631 
    3632 > view matrix models #7.1,1,0,0,140.66,0,1,0,199.74,0,0,1,261.78
    3633 
    3634 > view matrix models #7.1,1,0,0,152.52,0,1,0,194.28,0,0,1,257.24
    3635 
    3636 > ui mousemode right "rotate selected models"
    3637 
    3638 > view matrix models
    3639 > #7.1,0.96441,0.048869,0.25985,165.75,0.098602,0.8454,-0.52495,167.67,-0.24533,0.53189,0.8105,246.45
    3640 
    3641 > view matrix models
    3642 > #7.1,0.52404,0.070357,0.84878,205.22,0.25659,0.93724,-0.23611,177.31,-0.81212,0.34152,0.4731,245.12
    3643 
    3644 > ui mousemode right "translate selected models"
    3645 
    3646 > view matrix models
    3647 > #7.1,0.52404,0.070357,0.84878,218.96,0.25659,0.93724,-0.23611,166.4,-0.81212,0.34152,0.4731,253.15
    3648 
    3649 > view matrix models
    3650 > #7.1,0.52404,0.070357,0.84878,218.06,0.25659,0.93724,-0.23611,172.5,-0.81212,0.34152,0.4731,255.75
    3651 
    3652 > view matrix models
    3653 > #7.1,0.52404,0.070357,0.84878,220.15,0.25659,0.93724,-0.23611,172.23,-0.81212,0.34152,0.4731,250.53
    3654 
    3655 > view matrix models
    3656 > #7.1,0.52404,0.070357,0.84878,218.93,0.25659,0.93724,-0.23611,169.22,-0.81212,0.34152,0.4731,253.47
    3657 
    3658 > view matrix models
    3659 > #7.1,0.52404,0.070357,0.84878,218.24,0.25659,0.93724,-0.23611,170.23,-0.81212,0.34152,0.4731,253.64
    3660 
    3661 > view matrix models
    3662 > #7.1,0.52404,0.070357,0.84878,216.82,0.25659,0.93724,-0.23611,165.96,-0.81212,0.34152,0.4731,248.26
    3663 
    3664 > ui mousemode right "rotate selected models"
    3665 
    3666 > view matrix models
    3667 > #7.1,0.73952,-0.17388,0.65029,205.07,0.14405,0.98456,0.099452,184.79,-0.65754,0.020126,0.75315,262.95
    3668 
    3669 > view matrix models
    3670 > #7.1,0.73125,-0.084624,0.67684,205.42,0.062378,0.99641,0.057187,184.4,-0.67925,0.00040129,0.73391,262.74
    3671 
    3672 > view matrix models
    3673 > #7.1,0.69799,-0.10334,0.70861,208.03,0.074484,0.99464,0.071682,184.87,-0.71222,0.0027467,0.70195,261.87
    3674 
    3675 > view matrix models
    3676 > #7.1,0.63726,0.053079,0.76882,210.42,0.18684,0.95722,-0.22096,168.07,-0.74766,0.28445,0.60008,253.89
    3677 
    3678 > ui mousemode right "translate selected models"
    3679 
    3680 > view matrix models
    3681 > #7.1,0.63726,0.053079,0.76882,208.69,0.18684,0.95722,-0.22096,171.97,-0.74766,0.28445,0.60008,254.92
    3682 
    3683 > view matrix models
    3684 > #7.1,0.63726,0.053079,0.76882,209.09,0.18684,0.95722,-0.22096,174.45,-0.74766,0.28445,0.60008,259.11
    3685 
    3686 > ui mousemode right "rotate selected models"
    3687 
    3688 > view matrix models
    3689 > #7.1,0.62362,0.070465,0.77855,209.66,0.22628,0.93702,-0.26606,171.53,-0.74826,0.34209,0.5684,256.78
    3690 
    3691 > view matrix models
    3692 > #7.1,0.61203,0.086506,0.78609,210.1,0.26096,0.91623,-0.30401,169.1,-0.74654,0.3912,0.53819,254.58
    3693 
    3694 > ui mousemode right "rotate selected models"
    3695 
    3696 > ~select #7.1
    3697 
    3698 Nothing selected 
    3699 
    3700 > save "D:/OneDrive - Nanyang Technological
    3701 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
    3702 > includeMaps true
    3703 
    3704 ——— End of log from Tue Feb 22 21:54:19 2022 ———
    3705 
    3706 opened ChimeraX session 
    3707 
    3708 > open "D:/OneDrive - Nanyang Technological
    3709 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/2n5e.pdb"
    3710 
    3711 2n5e.pdb title: 
    3712 The 3D solution structure of discoidal high-density lipoprotein particles
    3713 [more info...] 
    3714  
    3715 Chain information for 2n5e.pdb 
    3716 --- 
    3717 Chain | Description 
    3718 8.1/A 8.2/A 8.3/A 8.4/A 8.5/A 8.6/A 8.7/A 8.8/A 8.9/A 8.10/A 8.1/B 8.2/B 8.3/B
    3719 8.4/B 8.5/B 8.6/B 8.7/B 8.8/B 8.9/B 8.10/B | apolipoprotein A-I 
    3720  
    3721 
    3722 > mmaker #8 to #7
    3723 
    3724 Parameters 
    3725 --- 
    3726 Chain pairing | bb 
    3727 Alignment algorithm | Needleman-Wunsch 
    3728 Similarity matrix | BLOSUM-62 
    3729 SS fraction | 0.3 
    3730 Gap open (HH/SS/other) | 18/18/6 
    3731 Gap extend | 1 
    3732 SS matrix |  |  | H | S | O 
    3733 ---|---|---|--- 
    3734 H | 6 | -9 | -6 
    3735 S |  | 6 | -6 
    3736 O |  |  | 4 
    3737 Iteration cutoff | 2 
    3738  
    3739 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.1), sequence
    3740 alignment score = 889.9 
    3741 RMSD between 167 pruned atom pairs is 0.000 angstroms; (across all 167 pairs:
    3742 0.000) 
    3743  
    3744 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.2), sequence
    3745 alignment score = 889.9 
    3746 RMSD between 99 pruned atom pairs is 0.967 angstroms; (across all 167 pairs:
    3747 2.405) 
    3748  
    3749 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.3), sequence
    3750 alignment score = 882.7 
    3751 RMSD between 146 pruned atom pairs is 0.614 angstroms; (across all 167 pairs:
    3752 6.590) 
    3753  
    3754 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.4), sequence
    3755 alignment score = 879.1 
    3756 RMSD between 90 pruned atom pairs is 0.877 angstroms; (across all 167 pairs:
    3757 6.733) 
    3758  
    3759 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.5), sequence
    3760 alignment score = 886.3 
    3761 RMSD between 83 pruned atom pairs is 0.781 angstroms; (across all 167 pairs:
    3762 7.288) 
    3763  
    3764 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.6), sequence
    3765 alignment score = 889.9 
    3766 RMSD between 150 pruned atom pairs is 0.625 angstroms; (across all 167 pairs:
    3767 4.094) 
    3768  
    3769 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.7), sequence
    3770 alignment score = 886.3 
    3771 RMSD between 150 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    3772 2.428) 
    3773  
    3774 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.8), sequence
    3775 alignment score = 882.7 
    3776 RMSD between 114 pruned atom pairs is 1.220 angstroms; (across all 167 pairs:
    3777 8.487) 
    3778  
    3779 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.9), sequence
    3780 alignment score = 886.3 
    3781 RMSD between 137 pruned atom pairs is 0.954 angstroms; (across all 167 pairs:
    3782 7.152) 
    3783  
    3784 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.10), sequence
    3785 alignment score = 886.3 
    3786 RMSD between 149 pruned atom pairs is 0.855 angstroms; (across all 167 pairs:
    3787 1.629) 
    3788  
    3789 
    3790 > close #7
    3791 
    3792 > save "D:/OneDrive - Nanyang Technological
    3793 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
    3794 > includeMaps true
    3795 
    3796 ——— End of log from Tue Feb 22 22:03:06 2022 ———
    3797 
    3798 opened ChimeraX session 
    3799 
    3800 > open "D:/OneDrive - Nanyang Technological
    3801 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb"
    3802 
    3803 Chain information for ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb #7 
    3804 --- 
    3805 Chain | Description 
    3806 B C | No description available 
    3807  
    3808 
    3809 > select #7
    3810 
    3811 4272 atoms, 4342 bonds, 530 residues, 1 model selected 
    3812 
    3813 > view matrix models #7,1,0,0,155.3,0,1,0,-32.66,0,0,1,15.862
    3814 
    3815 > view matrix models #7,1,0,0,227.55,0,1,0,182.45,0,0,1,257.42
    3816 
    3817 > view matrix models #7,1,0,0,226.69,0,1,0,184.64,0,0,1,255.63
    3818 
    3819 > view matrix models #7,1,0,0,204.58,0,1,0,234.23,0,0,1,235.65
    3820 
    3821 > ui mousemode right "rotate selected models"
    3822 
    3823 > view matrix models
    3824 > #7,0.67294,0.6481,-0.35654,204.55,-0.4966,0.03861,-0.86712,237.02,-0.54821,0.76058,0.34783,236.07
    3825 
    3826 > ui mousemode right "translate selected models"
    3827 
    3828 > view matrix models
    3829 > #7,0.67294,0.6481,-0.35654,202.23,-0.4966,0.03861,-0.86712,223.37,-0.54821,0.76058,0.34783,214.9
    3830 
    3831 > view matrix models
    3832 > #7,0.67294,0.6481,-0.35654,204.71,-0.4966,0.03861,-0.86712,212.44,-0.54821,0.76058,0.34783,207.19
    3833 
    3834 > view matrix models
    3835 > #7,0.67294,0.6481,-0.35654,168.77,-0.4966,0.03861,-0.86712,212.73,-0.54821,0.76058,0.34783,213.42
    3836 
    3837 > view matrix models
    3838 > #7,0.67294,0.6481,-0.35654,168.7,-0.4966,0.03861,-0.86712,204.73,-0.54821,0.76058,0.34783,218.41
    3839 
    3840 > view matrix models
    3841 > #7,0.67294,0.6481,-0.35654,169.65,-0.4966,0.03861,-0.86712,208.53,-0.54821,0.76058,0.34783,221.42
    3842 
    3843 > ui mousemode right "rotate selected models"
    3844 
    3845 > view matrix models
    3846 > #7,0.74751,0.56918,-0.34243,169.65,-0.52825,0.19685,-0.82595,208.32,-0.40271,0.7983,0.44782,221.09
    3847 
    3848 > view matrix models
    3849 > #7,0.17157,-0.18647,-0.96736,171.99,0.92678,0.36358,0.094287,205.38,0.33413,-0.91271,0.23519,222.64
    3850 
    3851 > view matrix models
    3852 > #7,-0.43014,-0.90269,-0.011358,172.47,-0.7035,0.32728,0.63086,206.67,-0.56575,0.27935,-0.77582,223.35
    3853 
    3854 > view matrix models
    3855 > #7,-0.56096,-0.12743,-0.81798,172.58,-0.79405,0.36224,0.48812,206.9,0.2341,0.92333,-0.30439,221.07
    3856 
    3857 > view matrix models
    3858 > #7,-0.46527,-0.14524,-0.87317,172.56,-0.84174,0.37778,0.38568,207.05,0.27385,0.91443,-0.29802,221.03
    3859 
    3860 > ui mousemode right "translate selected models"
    3861 
    3862 > view matrix models
    3863 > #7,-0.46527,-0.14524,-0.87317,175.91,-0.84174,0.37778,0.38568,203.89,0.27385,0.91443,-0.29802,211.39
    3864 
    3865 > view matrix models
    3866 > #7,-0.46527,-0.14524,-0.87317,174.08,-0.84174,0.37778,0.38568,206.07,0.27385,0.91443,-0.29802,215.64
    3867 
    3868 > hide #!8 models
    3869 
    3870 > view matrix models
    3871 > #7,-0.46527,-0.14524,-0.87317,174.65,-0.84174,0.37778,0.38568,206.88,0.27385,0.91443,-0.29802,212.06
    3872 
    3873 > save "D:/OneDrive - Nanyang Technological
    3874 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220302_D2NS1ts-
    3875 > Ab56-apoa1.cxs" includeMaps true
    3876 
    3877 ——— End of log from Wed Mar 2 00:08:07 2022 ———
    3878 
    3879 opened ChimeraX session 
    3880 
    3881 > open "D:/OneDrive - Nanyang Technological
    3882 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb"
    3883 
    3884 Chain information for ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb
    3885 #9 
    3886 --- 
    3887 Chain | Description 
    3888 B C | No description available 
    3889  
    3890 
    3891 > mmaker #9 to #10
    3892 
    3893 No 'to' model specified 
    3894 
    3895 > mmaker #9 to #7
    3896 
    3897 Parameters 
    3898 --- 
    3899 Chain pairing | bb 
    3900 Alignment algorithm | Needleman-Wunsch 
    3901 Similarity matrix | BLOSUM-62 
    3902 SS fraction | 0.3 
    3903 Gap open (HH/SS/other) | 18/18/6 
    3904 Gap extend | 1 
    3905 SS matrix |  |  | H | S | O 
    3906 ---|---|---|--- 
    3907 H | 6 | -9 | -6 
    3908 S |  | 6 | -6 
    3909 O |  |  | 4 
    3910 Iteration cutoff | 2 
    3911  
    3912 Matchmaker ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb, chain B (#7) with
    3913 ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb, chain B (#9),
    3914 sequence alignment score = 1084.5 
    3915 RMSD between 74 pruned atom pairs is 0.985 angstroms; (across all 207 pairs:
    3916 10.547) 
    3917  
    3918 
    3919 > hide #7 models
    3920 
    3921 > select #9
    3922 
    3923 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    3924 
    3925 > ui mousemode right "rotate selected models"
    3926 
    3927 > view matrix models
    3928 > #9,0.52533,-0.58815,-0.61491,177.85,0.0047201,0.72466,-0.68909,201.87,0.85089,0.35909,0.38346,210.74
    3929 
    3930 > view matrix models
    3931 > #9,0.45946,-0.88174,0.10689,181.58,0.8882,0.45638,-0.053134,204.22,-0.0019327,0.11935,0.99285,214.69
    3932 
    3933 > ui mousemode right "translate selected models"
    3934 
    3935 > view matrix models
    3936 > #9,0.45946,-0.88174,0.10689,177.6,0.8882,0.45638,-0.053134,197.13,-0.0019327,0.11935,0.99285,218.41
    3937 
    3938 > view matrix models
    3939 > #9,0.45946,-0.88174,0.10689,175.75,0.8882,0.45638,-0.053134,203.48,-0.0019327,0.11935,0.99285,218.85
    3940 
    3941 > view matrix models
    3942 > #9,0.45946,-0.88174,0.10689,169.69,0.8882,0.45638,-0.053134,196.29,-0.0019327,0.11935,0.99285,214.81
    3943 
    3944 > view matrix models
    3945 > #9,0.45946,-0.88174,0.10689,169.27,0.8882,0.45638,-0.053134,199.29,-0.0019327,0.11935,0.99285,212.88
    3946 
    3947 > view matrix models
    3948 > #9,0.45946,-0.88174,0.10689,173.56,0.8882,0.45638,-0.053134,203.27,-0.0019327,0.11935,0.99285,212.35
    3949 
    3950 > view matrix models
    3951 > #9,0.45946,-0.88174,0.10689,176.72,0.8882,0.45638,-0.053134,202,-0.0019327,0.11935,0.99285,212.91
    3952 
    3953 > view matrix models
    3954 > #9,0.45946,-0.88174,0.10689,172.24,0.8882,0.45638,-0.053134,200.71,-0.0019327,0.11935,0.99285,209.78
    3955 
    3956 > view matrix models
    3957 > #9,0.45946,-0.88174,0.10689,171.54,0.8882,0.45638,-0.053134,200.71,-0.0019327,0.11935,0.99285,209.45
    3958 
    3959 > ui tool show "Fit in Map"
    3960 
    3961 Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
    3962 map cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 3334 atoms 
    3963 average map value = 0.1014, steps = 288 
    3964 shifted from previous position = 26.2 
    3965 rotated from previous position = 35.6 degrees 
    3966 atoms outside contour = 2236, contour level = 0.14151 
    3967  
    3968 Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
    3969 relative to cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    3970 Matrix rotation and translation 
    3971 0.15030095 -0.25689088 -0.95468145 159.80559539 
    3972 0.91205850 0.40867945 0.03362089 142.63963221 
    3973 0.38152180 -0.87577859 0.29572442 147.85545078 
    3974 Axis -0.45590440 -0.66987165 0.58602316 
    3975 Axis point -104.50370211 0.00000000 221.35941513 
    3976 Rotation angle (degrees) 94.16607036 
    3977 Shift along axis -81.75960077 
    3978  
    3979 
    3980 > view matrix models
    3981 > #9,0.67727,-0.51922,0.52127,172.73,0.71543,0.63007,-0.30194,194.77,-0.17166,0.57742,0.7982,218.78
    3982 
    3983 > view matrix models
    3984 > #9,0.67727,-0.51922,0.52127,173.99,0.71543,0.63007,-0.30194,197.51,-0.17166,0.57742,0.7982,212.36
    3985 
    3986 > view matrix models
    3987 > #9,0.67727,-0.51922,0.52127,174.96,0.71543,0.63007,-0.30194,195,-0.17166,0.57742,0.7982,208.97
    3988 
    3989 > ui mousemode right "rotate selected models"
    3990 
    3991 > view matrix models
    3992 > #9,0.66193,-0.59819,0.45168,174.95,0.73725,0.62836,-0.24824,195.18,-0.13532,0.49732,0.85695,209.41
    3993 
    3994 > view matrix models
    3995 > #9,0.64956,-0.67275,0.35424,174.82,0.71372,0.70012,0.020895,196.02,-0.26207,0.23925,0.93492,210.62
    3996 
    3997 > save "D:/OneDrive - Nanyang Technological
    3998 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220302_D2NS1ts-
    3999 > Ab56-apoa1.cxs" includeMaps true
    4000 
    4001 ——— End of log from Wed Mar 2 00:18:18 2022 ———
    4002 
    4003 opened ChimeraX session 
    4004 
    4005 > show #!1 models
    4006 
    4007 > hide #!2 models
    4008 
    4009 > hide #9 models
    4010 
    4011 > hide #!10 models
    4012 
    4013 > show #6 models
    4014 
    4015 > hide #4 models
    4016 
    4017 > hide #3 models
    4018 
    4019 > ui tool show "Fit in Map"
    4020 
    4021 Fit molecule D2NS1-F562.pdb (#6) to map
    4022 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    4023 average map value = 0.07482, steps = 364 
    4024 shifted from previous position = 2.61 
    4025 rotated from previous position = 17.1 degrees 
    4026 atoms outside contour = 8195, contour level = 0.08 
    4027  
    4028 Position of D2NS1-F562.pdb (#6) relative to
    4029 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    4030 Matrix rotation and translation 
    4031 -0.99640848 0.07252019 0.04371456 331.26650068 
    4032 -0.01695668 -0.67668277 0.73607941 166.80204366 
    4033 0.08296151 0.73269451 0.67548215 -88.38561339 
    4034 Axis -0.03462299 -0.40144391 -0.91522895 
    4035 Axis point 169.54681270 98.35816249 0.00000000 
    4036 Rotation angle (degrees) 177.19813771 
    4037 Shift along axis 2.46197109 
    4038  
    4039 
    4040 > ui mousemode right "translate selected models"
    4041 
    4042 > view matrix models
    4043 > #9,0.64956,-0.67275,0.35424,175.54,0.71372,0.70012,0.020895,189.47,-0.26207,0.23925,0.93492,190.81
    4044 
    4045 > ~select #9
    4046 
    4047 Nothing selected 
    4048 
    4049 > select #6
    4050 
    4051 12404 atoms, 12730 bonds, 1588 residues, 1 model selected 
    4052 
    4053 > view matrix models
    4054 > #6,-0.99797,0.039575,0.049905,338.25,-0.014392,-0.90338,0.42859,266.52,0.062045,0.42701,0.90212,-62.663
    4055 
    4056 > ui mousemode right "rotate selected models"
    4057 
    4058 > view matrix models
    4059 > #6,-0.99623,0.082033,0.028348,334.24,-0.086585,-0.91673,-0.39002,429.14,-0.006007,-0.391,0.92037,92.117
    4060 
    4061 > view matrix models
    4062 > #6,-0.99623,0.082033,0.028348,335.42,-0.086585,-0.91673,-0.39002,430.38,-0.006007,-0.391,0.92037,88.929
    4063 
    4064 Fit molecule D2NS1-F562.pdb (#6) to map
    4065 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    4066 average map value = 0.09493, steps = 84 
    4067 shifted from previous position = 3.13 
    4068 rotated from previous position = 3.82 degrees 
    4069 atoms outside contour = 7003, contour level = 0.08 
    4070  
    4071 Position of D2NS1-F562.pdb (#6) relative to
    4072 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    4073 Matrix rotation and translation 
    4074 -0.99820989 0.05968746 0.00379835 345.43779112 
    4075 -0.05973880 -0.99809742 -0.01525811 372.27574829 
    4076 0.00288041 -0.01545771 0.99987637 1.80150722 
    4077 Axis -0.00167123 0.00768605 -0.99996907 
    4078 Axis point 178.28007958 180.98306790 0.00000000 
    4079 Rotation angle (degrees) 176.57654715 
    4080 Shift along axis 0.48257203 
    4081  
    4082 Fit molecule D2NS1-F562.pdb (#6) to map
    4083 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    4084 average map value = 0.09495, steps = 48 
    4085 shifted from previous position = 0.019 
    4086 rotated from previous position = 0.00432 degrees 
    4087 atoms outside contour = 7012, contour level = 0.08 
    4088  
    4089 Position of D2NS1-F562.pdb (#6) relative to
    4090 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    4091 Matrix rotation and translation 
    4092 -0.99820895 0.05970074 0.00383565 345.40975009 
    4093 -0.05975246 -0.99809759 -0.01519388 372.26991158 
    4094 0.00292127 -0.01539585 0.99987721 1.78218185 
    4095 Axis -0.00169079 0.00765450 -0.99996927 
    4096 Axis point 178.26722509 180.97930211 0.00000000 
    4097 Rotation angle (degrees) 176.57577490 
    4098 Shift along axis 0.48339683 
    4099  
    4100 
    4101 > set bgColor white
    4102 
    4103 > lighting full
    4104 
    4105 > ~select #6
    4106 
    4107 Nothing selected 
    4108 
    4109 > hide #6 models
    4110 
    4111 > show #6 models
    4112 
    4113 > color #6 bychain
    4114 
    4115 Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
    4116 models, 1 maps. 
    4117 
    4118 Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
    4119 models, 1 maps. 
    4120 
    4121 > select #1
    4122 
    4123 2 models selected 
    4124 
    4125 Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
    4126 models, 1 maps. 
    4127 
    4128 > ~select #1
    4129 
    4130 Nothing selected 
    4131 
    4132 > hide #!1 models
    4133 
    4134 > show #!2 models
    4135 
    4136 > hide #!2 models
    4137 
    4138 > show #!2 models
    4139 
    4140 > show #3 models
    4141 
    4142 > show #4 models
    4143 
    4144 > hide #6 models
    4145 
    4146 > volume #2 color #a7a49f80
    4147 
    4148 > volume #2 color #b8b5af80
    4149 
    4150 > color #3-4 bychain
    4151 
    4152 Color zone shortcut requires 1 displayed atomic model and 1 map, got 12 atomic
    4153 models, 1 maps. 
    4154 
    4155 > hide #4 models
    4156 
    4157 > show #4 models
    4158 
    4159 > hide #4 models
    4160 
    4161 > select #3
    4162 
    4163 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    4164 
    4165 > select #2
    4166 
    4167 2 models selected 
    4168 
    4169 > ~select #2
    4170 
    4171 Nothing selected 
    4172 
    4173 Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
    4174 models, 1 maps. 
    4175 
    4176 > show #4 models
    4177 
    4178 > ui tool show "Segment Map"
    4179 
    4180 > show #9 models
    4181 
    4182 > ui mousemode right "translate selected models"
    4183 
    4184 > select #9
    4185 
    4186 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    4187 
    4188 > view matrix models
    4189 > #9,0.64956,-0.67275,0.35424,173.28,0.71372,0.70012,0.020895,203.74,-0.26207,0.23925,0.93492,217.24
    4190 
    4191 > ui mousemode right "rotate selected models"
    4192 
    4193 > view matrix models
    4194 > #9,0.42545,-0.83111,0.35811,174.01,0.88507,0.46469,0.026952,204.31,-0.18881,0.30548,0.93329,216.96
    4195 
    4196 > view matrix models
    4197 > #9,0.36854,-0.89204,0.26163,173.89,0.89839,0.4141,0.14638,204.91,-0.23892,0.18109,0.954,217.47
    4198 
    4199 > view matrix models
    4200 > #9,0.39748,-0.85333,0.3374,174.03,0.89601,0.44024,0.057848,204.49,-0.1979,0.27932,0.93958,217.07
    4201 
    4202 > view matrix models
    4203 > #9,0.4249,-0.82293,0.37715,174.06,0.89397,0.44699,-0.03185,204.13,-0.14237,0.3507,0.9256,216.74
    4204 
    4205 > view matrix models
    4206 > #9,0.30959,-0.88763,0.34097,174.24,0.94929,0.30918,-0.057041,204.4,-0.05479,0.34134,0.93834,216.73
    4207 
    4208 > ~select #9
    4209 
    4210 Nothing selected 
    4211 
    4212 > ui mousemode right "translate selected models"
    4213 
    4214 > select #9
    4215 
    4216 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    4217 
    4218 > ~select #9
    4219 
    4220 Nothing selected 
    4221 
    4222 > select #9
    4223 
    4224 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    4225 
    4226 > view matrix models
    4227 > #9,0.30959,-0.88763,0.34097,171.78,0.94929,0.30918,-0.057041,200.45,-0.05479,0.34134,0.93834,215.77
    4228 
    4229 > ~select #9
    4230 
    4231 Nothing selected 
    4232 
    4233 > movie record
    4234 
    4235 > turn y 2 180
    4236 
    4237 > wait 180
    4238 
    4239 > movie encode "C:\Users\dahailuo\OneDrive - Nanyang Technological
    4240 > University\Temporal\202112_FlaviNS1\Data_EM_Alvin\movie2.mp4"
    4241 
    4242 Movie saved to \C:Users\\...\Data_EM_Alvin\movie2.mp4 
    4243  
    4244 
    4245 > show #6 models
    4246 
    4247 > mmaker #6 to #3
    4248 
    4249 Parameters 
    4250 --- 
    4251 Chain pairing | bb 
    4252 Alignment algorithm | Needleman-Wunsch 
    4253 Similarity matrix | BLOSUM-62 
    4254 SS fraction | 0.3 
    4255 Gap open (HH/SS/other) | 18/18/6 
    4256 Gap extend | 1 
    4257 SS matrix |  |  | H | S | O 
    4258 ---|---|---|--- 
    4259 H | 6 | -9 | -6 
    4260 S |  | 6 | -6 
    4261 O |  |  | 4 
    4262 Iteration cutoff | 2 
    4263  
    4264 Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
    4265 alignment score = 1871.9 
    4266 RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
    4267 0.023) 
    4268  
    4269 
    4270 > mmaker #6 to #4
    4271 
    4272 Parameters 
    4273 --- 
    4274 Chain pairing | bb 
    4275 Alignment algorithm | Needleman-Wunsch 
    4276 Similarity matrix | BLOSUM-62 
    4277 SS fraction | 0.3 
    4278 Gap open (HH/SS/other) | 18/18/6 
    4279 Gap extend | 1 
    4280 SS matrix |  |  | H | S | O 
    4281 ---|---|---|--- 
    4282 H | 6 | -9 | -6 
    4283 S |  | 6 | -6 
    4284 O |  |  | 4 
    4285 Iteration cutoff | 2 
    4286  
    4287 Matchmaker F562a.pdb, chain B (#4) with D2NS1-F562.pdb, chain C (#6), sequence
    4288 alignment score = 1200 
    4289 RMSD between 228 pruned atom pairs is 0.000 angstroms; (across all 228 pairs:
    4290 0.000) 
    4291  
    4292 
    4293 > hide #!2 models
    4294 
    4295 > hide #9 models
    4296 
    4297 > hide #3 models
    4298 
    4299 > hide #4 models
    4300 
    4301 > show #!2 models
    4302 
    4303 > hide #6 models
    4304 
    4305 > show #!1 models
    4306 
    4307 > show #!10 models
    4308 
    4309 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    4310 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points 
    4311 correlation = 0.493, correlation about mean = 0.2808, overlap = 5991 
    4312 steps = 48, shift = 0.0601, angle = 0.109 degrees 
    4313  
    4314 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    4315 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    4316 Matrix rotation and translation 
    4317 -0.27792284 -0.14164293 -0.95010322 410.09306464 
    4318 0.39540197 0.88452622 -0.24752902 -48.83916554 
    4319 0.87545196 -0.44446666 -0.18982414 109.38604242 
    4320 Axis -0.10294301 -0.95425209 0.28072349 
    4321 Axis point 169.05771360 0.00000000 208.04394464 
    4322 Rotation angle (degrees) 106.95439226 
    4323 Shift along axis 35.09589160 
    4324  
    4325 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    4326 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points 
    4327 correlation = 0.493, correlation about mean = 0.2809, overlap = 5991 
    4328 steps = 48, shift = 0.0078, angle = 0.0885 degrees 
    4329  
    4330 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    4331 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    4332 Matrix rotation and translation 
    4333 -0.27794843 -0.14312388 -0.94987377 410.31424613 
    4334 0.39534589 0.88416435 -0.24890760 -48.51539453 
    4335 0.87546917 -0.44471217 -0.18916865 109.30275225 
    4336 Axis -0.10234637 -0.95410041 0.28145627 
    4337 Axis point 169.16249688 0.00000000 208.15543264 
    4338 Rotation angle (degrees) 106.94636481 
    4339 Shift along axis 35.05832906 
    4340  
    4341 
    4342 > hide #!2 models
    4343 
    4344 > select #1
    4345 
    4346 2 models selected 
    4347 
    4348 > ui mousemode right "rotate selected models"
    4349 
    4350 > view matrix models
    4351 > #1,0.74046,0.62541,0.24616,-107.44,-0.65719,0.75044,0.070241,152.95,-0.1408,-0.21378,0.96668,70.267
    4352 
    4353 > view matrix models
    4354 > #1,0.72193,-0.13867,0.67793,-42.597,0.2204,0.97477,-0.035306,-25.414,-0.65593,0.1749,0.73428,133.11
    4355 
    4356 > view matrix models
    4357 > #1,0.74615,0.64297,-0.17276,-38.999,0.62682,-0.76589,-0.14322,231.4,-0.22441,-0.0014231,-0.97449,383.68
    4358 
    4359 > view matrix models
    4360 > #1,0.80841,0.29993,0.50648,-106.59,0.51816,-0.77083,-0.37058,291.07,0.27926,0.56202,-0.77856,159.28
    4361 
    4362 > view matrix models
    4363 > #1,0.96135,-0.23483,0.14371,24.411,0.25186,0.96097,-0.11451,-14.839,-0.11121,0.14628,0.98297,-2.0945
    4364 
    4365 > view matrix models
    4366 > #1,0.99141,-0.075528,-0.10677,34.022,0.051461,0.97582,-0.21244,35.244,0.12024,0.20512,0.97132,-51.881
    4367 
    4368 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    4369 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points 
    4370 correlation = 0.493, correlation about mean = 0.2808, overlap = 5991 
    4371 steps = 716, shift = 1.66, angle = 12.6 degrees 
    4372  
    4373 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    4374 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    4375 Matrix rotation and translation 
    4376 -0.27785362 -0.14026525 -0.95032783 409.88132947 
    4377 0.39567157 0.88475643 -0.24627224 -49.16134094 
    4378 0.87535212 -0.44444535 -0.19033380 109.50506725 
    4379 Axis -0.10359229 -0.95434929 0.28015367 
    4380 Axis point 168.94433960 0.00000000 207.96495201 
    4381 Rotation angle (degrees) 106.96068830 
    4382 Shift along axis 35.13479072 
    4383  
    4384 
    4385 > show #!2 models
    4386 
    4387 > hide #!2 models
    4388 
    4389 > show #!2 models
    4390 
    4391 > ~select #1
    4392 
    4393 Nothing selected 
    4394 
    4395 > select #1
    4396 
    4397 2 models selected 
    4398 
    4399 > view matrix models
    4400 > #1,0.9987,0.030982,-0.040533,2.2432,0.0036821,0.74864,0.66296,-67.414,0.050884,-0.66225,0.74755,154.04
    4401 
    4402 > view matrix models
    4403 > #1,0.87306,0.20075,-0.44437,64.348,0.48063,-0.20061,0.85367,-16.172,0.082229,-0.95888,-0.27163,378
    4404 
    4405 > view matrix models
    4406 > #1,0.83244,0.37492,-0.40802,34.215,0.55119,-0.48475,0.67912,52.19,0.056831,-0.79023,-0.61017,411.1
    4407 
    4408 > view matrix models
    4409 > #1,0.68639,0.56283,-0.46053,35.845,0.69489,-0.69435,0.1871,149.22,-0.21447,-0.44844,-0.8677,443.15
    4410 
    4411 > hide #!10 models
    4412 
    4413 > show #!10 models
    4414 
    4415 > hide #!10 models
    4416 
    4417 > show #!10 models
    4418 
    4419 > hide #!1 models
    4420 
    4421 > hide #!2 models
    4422 
    4423 > show #!1 models
    4424 
    4425 > view matrix models
    4426 > #1,0.82844,0.50873,-0.23428,-19.057,0.47101,-0.40647,0.7829,34.547,0.30305,-0.75893,-0.57635,355.71
    4427 
    4428 > view matrix models
    4429 > #1,0.84453,-0.094928,-0.52703,136.53,-0.025459,-0.99017,0.13755,339.15,-0.5349,-0.10275,-0.83864,433.6
    4430 
    4431 > view matrix models
    4432 > #1,0.97799,-0.18464,-0.097184,54.238,-0.1969,-0.66248,-0.72274,460.34,0.069068,0.72597,-0.68425,151.17
    4433 
    4434 > view matrix models
    4435 > #1,0.97796,-0.19168,-0.082782,53.003,-0.16644,-0.47632,-0.86337,446.06,0.12606,0.85812,-0.49773,85.086
    4436 
    4437 > view matrix models
    4438 > #1,0.99726,0.035713,-0.06472,5.846,-0.039623,-0.48086,-0.8759,426.41,-0.062402,0.87607,-0.47813,112.12
    4439 
    4440 > view matrix models
    4441 > #1,-0.96752,0.24305,-0.069446,320.31,-0.20699,-0.60408,0.76957,193.12,0.14509,0.75896,0.63477,-96.862
    4442 
    4443 > view matrix models
    4444 > #1,-0.85416,0.24266,-0.45992,367.81,-0.51768,-0.48048,0.70792,237.19,-0.049202,0.84277,0.53603,-60.033
    4445 
    4446 > view matrix models
    4447 > #1,-0.98697,0.14048,-0.078425,343.64,-0.16057,-0.82904,0.53564,265.52,0.010232,0.54125,0.8408,-69.644
    4448 
    4449 > view matrix models
    4450 > #1,-0.99016,0.10292,-0.094853,353.76,-0.13794,-0.83244,0.53668,261.91,-0.023726,0.54448,0.83844,-63.751
    4451 
    4452 > ui mousemode right "translate selected models"
    4453 
    4454 > view matrix models
    4455 > #1,-0.99016,0.10292,-0.094853,357.93,-0.13794,-0.83244,0.53668,248.71,-0.023726,0.54448,0.83844,-68.308
    4456 
    4457 > view matrix models
    4458 > #1,-0.99016,0.10292,-0.094853,358.29,-0.13794,-0.83244,0.53668,250.68,-0.023726,0.54448,0.83844,-68.894
    4459 
    4460 > ui mousemode right "rotate selected models"
    4461 
    4462 > view matrix models
    4463 > #1,-0.9422,-0.030752,0.33364,299.34,0.13856,-0.9424,0.30443,261.21,0.30506,0.33307,0.89219,-99.156
    4464 
    4465 > view matrix models
    4466 > #1,-0.77548,-0.32284,0.54259,285.5,0.28029,-0.94609,-0.16233,317.46,0.56574,0.026196,0.82416,-79.125
    4467 
    4468 > ui mousemode right "translate selected models"
    4469 
    4470 > view matrix models
    4471 > #1,-0.77548,-0.32284,0.54259,268.3,0.28029,-0.94609,-0.16233,334.8,0.56574,0.026196,0.82416,-67.645
    4472 
    4473 > view matrix models
    4474 > #1,-0.77548,-0.32284,0.54259,265.58,0.28029,-0.94609,-0.16233,338.57,0.56574,0.026196,0.82416,-65.98
    4475 
    4476 > view matrix models
    4477 > #1,-0.77548,-0.32284,0.54259,285.03,0.28029,-0.94609,-0.16233,352.61,0.56574,0.026196,0.82416,-59.271
    4478 
    4479 > ui mousemode right "rotate selected models"
    4480 
    4481 > view matrix models
    4482 > #1,-0.91194,-0.17978,0.36883,313.96,0.10929,-0.97286,-0.20397,395.12,0.39549,-0.1457,0.90684,-12.537
    4483 
    4484 > view matrix models
    4485 > #1,-0.91113,-0.10679,0.39805,295.73,0.021642,-0.97691,-0.21254,412.97,0.41156,-0.18504,0.8924,-5.8812
    4486 
    4487 > view matrix models
    4488 > #1,-0.99135,-0.088862,0.096564,359.09,0.037913,-0.89841,-0.43753,435.05,0.12563,-0.43008,0.894,88.599
    4489 
    4490 > ui mousemode right "translate selected models"
    4491 
    4492 > view matrix models
    4493 > #1,-0.99135,-0.088862,0.096564,361.35,0.037913,-0.89841,-0.43753,415.99,0.12563,-0.43008,0.894,90.946
    4494 
    4495 > ui mousemode right "rotate selected models"
    4496 
    4497 > view matrix models
    4498 > #1,-0.99008,-0.020034,0.1391,341.47,-0.013738,-0.97125,-0.23766,403.58,0.13986,-0.23721,0.96134,42.319
    4499 
    4500 > ui mousemode right "translate selected models"
    4501 
    4502 > view matrix models
    4503 > #1,-0.99008,-0.020034,0.1391,341.46,-0.013738,-0.97125,-0.23766,399.55,0.13986,-0.23721,0.96134,42.616
    4504 
    4505 > view matrix models
    4506 > #1,-0.99008,-0.020034,0.1391,338.93,-0.013738,-0.97125,-0.23766,400.44,0.13986,-0.23721,0.96134,32.494
    4507 
    4508 > view matrix models
    4509 > #1,-0.99008,-0.020034,0.1391,335.49,-0.013738,-0.97125,-0.23766,400.28,0.13986,-0.23721,0.96134,33.65
    4510 
    4511 > view matrix models
    4512 > #1,-0.99008,-0.020034,0.1391,333.14,-0.013738,-0.97125,-0.23766,400.18,0.13986,-0.23721,0.96134,33.756
    4513 
    4514 > ui mousemode right "rotate selected models"
    4515 
    4516 > view matrix models
    4517 > #1,-0.99347,-0.11227,0.020092,370.83,0.11149,-0.99309,-0.036498,346.87,0.024051,-0.03402,0.99913,11.612
    4518 
    4519 > view matrix models
    4520 > #1,-0.99314,-0.11513,0.02023,371.26,0.11367,-0.99155,-0.06254,350.72,0.027259,-0.059812,0.99784,15.866
    4521 
    4522 > view matrix models
    4523 > #1,-0.99502,-0.048682,0.086949,348.18,0.043004,-0.99689,-0.06602,364.89,0.089893,-0.061952,0.99402,5.7314
    4524 
    4525 > view matrix models
    4526 > #1,-0.9999,-0.011841,0.0079016,356.17,0.012535,-0.99545,0.094484,342.25,0.0067469,0.094574,0.9955,-7.6193
    4527 
    4528 > view matrix models
    4529 > #1,-0.99955,0.029264,0.006465,349.02,-0.028596,-0.99584,0.086513,351.05,0.0089699,0.086289,0.99623,-6.6648
    4530 
    4531 > show #!2 models
    4532 
    4533 > hide #!2 models
    4534 
    4535 > view matrix models
    4536 > #1,-0.99431,-0.012476,0.10579,338.32,0.013343,-0.99988,0.0074894,357.98,0.10568,0.0088583,0.99436,-9.7821
    4537 
    4538 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    4539 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points 
    4540 correlation = 0.493, correlation about mean = 0.2808, overlap = 5991 
    4541 steps = 948, shift = 10.3, angle = 23.5 degrees 
    4542  
    4543 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    4544 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    4545 Matrix rotation and translation 
    4546 0.27780939 0.13998726 -0.95038174 260.70800172 
    4547 -0.39575740 -0.88479067 -0.24601119 407.82841194 
    4548 -0.87532735 0.44446484 -0.19040216 263.31428797 
    4549 Axis 0.78717074 -0.08556506 -0.61077070 
    4550 Axis point 0.00000000 178.59809032 292.75645151 
    4551 Rotation angle (degrees) 153.98663078 
    4552 Shift along axis 9.50119898 
    4553  
    4554 
    4555 > hide #!10 models
    4556 
    4557 > show #6 models
    4558 
    4559 > select #6
    4560 
    4561 12404 atoms, 12730 bonds, 1588 residues, 1 model selected 
    4562 
    4563 > ~select #6
    4564 
    4565 Nothing selected 
    4566 
    4567 > select #6
    4568 
    4569 12404 atoms, 12730 bonds, 1588 residues, 1 model selected 
    4570 
    4571 > view matrix models
    4572 > #6,0.80584,-0.033933,0.59116,-60.641,-0.18803,0.93202,0.30982,-22.728,-0.56149,-0.36082,0.74468,228.14
    4573 
    4574 > view matrix models
    4575 > #6,0.84169,0.23741,0.48497,-96.336,-0.031206,0.91804,-0.39525,78.603,-0.53906,0.31754,0.78012,96.759
    4576 
    4577 > view matrix models
    4578 > #6,0.95752,0.28708,0.027255,-43.538,-0.26323,0.90873,-0.32391,108.93,-0.11776,0.30298,0.94569,-5.8011
    4579 
    4580 > ui mousemode right "translate selected models"
    4581 
    4582 > view matrix models
    4583 > #6,0.95752,0.28708,0.027255,-47.959,-0.26323,0.90873,-0.32391,118,-0.11776,0.30298,0.94569,-22.337
    4584 
    4585 > ui mousemode right "rotate selected models"
    4586 
    4587 > view matrix models
    4588 > #6,0.99918,0.040001,0.0063686,-7.5857,-0.036305,0.95416,-0.29708,64.472,-0.01796,0.2966,0.95483,-40.695
    4589 
    4590 Fit molecule D2NS1-F562.pdb (#6) to map
    4591 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    4592 average map value = 0.1026, steps = 96 
    4593 shifted from previous position = 4.3 
    4594 rotated from previous position = 4.93 degrees 
    4595 atoms outside contour = 6857, contour level = 0.08 
    4596  
    4597 Position of D2NS1-F562.pdb (#6) relative to
    4598 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    4599 Matrix rotation and translation 
    4600 -1.00000000 -0.00003889 0.00000390 356.92132489 
    4601 0.00003889 -0.99999983 -0.00059770 357.02795185 
    4602 0.00000392 -0.00059770 0.99999983 0.10572384 
    4603 Axis -0.00000446 -0.00030232 0.99999995 
    4604 Axis point 178.45719114 178.51746241 0.00000000 
    4605 Rotation angle (degrees) 179.99777155 
    4606 Shift along axis -0.00380630 
    4607  
    4608 
    4609 > ~select #6
    4610 
    4611 Nothing selected 
    4612 
    4613 > interfaces #6 & ~solvent
    4614 
    4615 7 buried areas: A B 2354, E F 2040, C D 2040, B C 1572, A F 1542, B D 1312, A
    4616 E 1190 
    4617 
    4618 > open "C:/Users/dahailuo/Downloads/cryosparc_P35_J100_005_volume_map_sharp
    4619 > (1).mrc"
    4620 
    4621 Opened cryosparc_P35_J100_005_volume_map_sharp (1).mrc as #11, grid size
    4622 416,416,416, pixel 0.858, shown at level 0.0415, step 2, values float32 
    4623 
    4624 QWindowsWindow::setGeometry: Unable to set geometry 1920x1102+1920+23 (frame:
    4625 1936x1141+1912-8) on QWidgetWindow/"MainWindowClassWindow" on
    4626 "\\\\.\DISPLAY1". Resulting geometry: 1920x1017+1920+23 (frame:
    4627 1936x1056+1912-8) margins: 8, 31, 8, 8 minimum size: 493x1102 MINMAXINFO
    4628 maxSize=0,0 maxpos=0,0 mintrack=509,1141 maxtrack=0,0) 
    4629 
    4630 > volume #11 step 1
    4631 
    4632 > surface dust #1 size 8.58
    4633 
    4634 > surface dust #11 size 8.58
    4635 
    4636 > volume #11 level 0.045
    4637 
    4638 > volume #11 level 0.05
    4639 
    4640 Fit molecule D2NS1-F562.pdb (#6) to map
    4641 cryosparc_P35_J100_005_volume_map_sharp (1).mrc (#11) using 12404 atoms 
    4642 average map value = 0.08442, steps = 152 
    4643 shifted from previous position = 1.4 
    4644 rotated from previous position = 4.71 degrees 
    4645 atoms outside contour = 5898, contour level = 0.05 
    4646  
    4647 Position of D2NS1-F562.pdb (#6) relative to
    4648 cryosparc_P35_J100_005_volume_map_sharp (1).mrc (#11) coordinates: 
    4649 Matrix rotation and translation 
    4650 0.99897026 0.04182548 -0.01757995 -4.15590074 
    4651 -0.04516063 0.95385198 -0.29686178 69.02604187 
    4652 0.00435228 0.29735001 0.95475862 -45.20466997 
    4653 Axis 0.98879513 -0.03649622 -0.14474879 
    4654 Axis point 0.00000000 183.11150795 204.04343868 
    4655 Rotation angle (degrees) 17.48599398 
    4656 Shift along axis -0.08520266 
    4657  
    4658 
    4659 > transparency #11.1 50
    4660 
    4661 > show #3 models
    4662 
    4663 > mmaker #3 to #6
    4664 
    4665 Parameters 
    4666 --- 
    4667 Chain pairing | bb 
    4668 Alignment algorithm | Needleman-Wunsch 
    4669 Similarity matrix | BLOSUM-62 
    4670 SS fraction | 0.3 
    4671 Gap open (HH/SS/other) | 18/18/6 
    4672 Gap extend | 1 
    4673 SS matrix |  |  | H | S | O 
    4674 ---|---|---|--- 
    4675 H | 6 | -9 | -6 
    4676 S |  | 6 | -6 
    4677 O |  |  | 4 
    4678 Iteration cutoff | 2 
    4679  
    4680 Matchmaker D2NS1-F562.pdb, chain A (#6) with D2NS1.pdb, chain B (#3), sequence
    4681 alignment score = 1871.9 
    4682 RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
    4683 0.023) 
    4684  
    4685 
    4686 > hide #6 models
    4687 
    4688 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
    4689 (1).mrc (#11) using 5602 atoms 
    4690 average map value = 0.07338, steps = 60 
    4691 shifted from previous position = 1.1 
    4692 rotated from previous position = 2.61 degrees 
    4693 atoms outside contour = 3025, contour level = 0.05 
    4694  
    4695 Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
    4696 (1).mrc (#11) coordinates: 
    4697 Matrix rotation and translation 
    4698 0.14875593 -0.08639183 -0.98509297 342.36735832 
    4699 0.98470147 -0.07847453 0.15557896 -15.12271804 
    4700 -0.09074546 -0.99316577 0.07339661 361.18209695 
    4701 Axis -0.63557683 -0.49482408 0.59261389 
    4702 Axis point 0.00000000 37.80172615 346.76474569 
    4703 Rotation angle (degrees) 115.35090835 
    4704 Shift along axis 3.92385104 
    4705  
    4706 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
    4707 (1).mrc (#11) using 5602 atoms 
    4708 average map value = 0.07339, steps = 44 
    4709 shifted from previous position = 0.0117 
    4710 rotated from previous position = 0.00688 degrees 
    4711 atoms outside contour = 3021, contour level = 0.05 
    4712  
    4713 Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
    4714 (1).mrc (#11) coordinates: 
    4715 Matrix rotation and translation 
    4716 0.14885535 -0.08637602 -0.98507934 342.35458834 
    4717 0.98468094 -0.07852972 0.15568097 -15.13336069 
    4718 -0.09080510 -0.99316278 0.07336326 361.19655370 
    4719 Axis -0.63562980 -0.49478213 0.59259210 
    4720 Axis point 0.00000000 37.81870419 346.75288311 
    4721 Rotation angle (degrees) 115.35056364 
    4722 Shift along axis 3.91916090 
    4723  
    4724 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
    4725 (1).mrc (#11) using 5602 atoms 
    4726 average map value = 0.07338, steps = 28 
    4727 shifted from previous position = 0.0166 
    4728 rotated from previous position = 0.0195 degrees 
    4729 atoms outside contour = 3027, contour level = 0.05 
    4730  
    4731 Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
    4732 (1).mrc (#11) coordinates: 
    4733 Matrix rotation and translation 
    4734 0.14869429 -0.08663603 -0.98508083 342.41395707 
    4735 0.98471526 -0.07839157 0.15553350 -15.12882419 
    4736 -0.09069683 -0.99315105 0.07365544 361.12491138 
    4737 Axis -0.63549687 -0.49480794 0.59271311 
    4738 Axis point 0.00000000 37.79183158 346.80910583 
    4739 Rotation angle (degrees) 115.34202749 
    4740 Shift along axis 3.92633355 
    4741  
    4742 
    4743 > select #3
    4744 
    4745 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    4746 
    4747 > view matrix models
    4748 > #3,0.052602,-0.042076,-0.99773,354.08,0.96197,-0.26603,0.061936,37.093,-0.26803,-0.96305,0.026482,395.65
    4749 
    4750 > view matrix models
    4751 > #3,0.0070452,-0.012575,-0.9999,357.51,0.93425,-0.35645,0.011066,66.236,-0.35656,-0.93423,0.0092369,409.45
    4752 
    4753 > view matrix models
    4754 > #3,-0.0058622,0.0073093,-0.99996,356.45,0.91272,-0.40851,-0.0083368,82.232,-0.40855,-0.91272,-0.0042765,417.39
    4755 
    4756 > view matrix models
    4757 > #3,-0.020074,-0.027951,-0.99941,364.78,0.92365,-0.38315,-0.0078364,75.954,-0.3827,-0.92326,0.033508,407.88
    4758 
    4759 > view matrix models
    4760 > #3,0.0017745,-0.041136,-0.99915,363.11,0.92163,-0.38766,0.017597,72.537,-0.38806,-0.92088,0.037224,407.76
    4761 
    4762 > view matrix models
    4763 > #3,-0.017771,-0.12129,-0.99246,378.83,0.9086,-0.41622,0.034596,76.603,-0.41728,-0.90114,0.1176,395.26
    4764 
    4765 > view matrix models
    4766 > #3,0.012861,-0.10916,-0.99394,371.67,0.88601,-0.45952,0.061933,82.986,-0.46349,-0.88144,0.09081,404.85
    4767 
    4768 > view matrix models
    4769 > #3,0.012034,-0.092833,-0.99561,369.37,0.88338,-0.46553,0.054084,85.858,-0.46851,-0.88015,0.076405,408.08
    4770 
    4771 > view matrix models
    4772 > #3,0.022255,-0.099641,-0.99477,368.56,0.88274,-0.46516,0.066341,83.724,-0.46934,-0.8796,0.077605,407.92
    4773 
    4774 > ui mousemode right "translate selected models"
    4775 
    4776 > view matrix models
    4777 > #3,0.022255,-0.099641,-0.99477,369.16,0.88274,-0.46516,0.066341,83.998,-0.46934,-0.8796,0.077605,407.23
    4778 
    4779 > view matrix models
    4780 > #3,0.022255,-0.099641,-0.99477,368.06,0.88274,-0.46516,0.066341,83.639,-0.46934,-0.8796,0.077605,407.78
    4781 
    4782 > view matrix models
    4783 > #3,0.022255,-0.099641,-0.99477,369.91,0.88274,-0.46516,0.066341,85.463,-0.46934,-0.8796,0.077605,407.43
    4784 
    4785 > ~select #3
    4786 
    4787 Nothing selected 
    4788 
    4789 > show #6 models
    4790 
    4791 > mmaker #6 to #3
    4792 
    4793 Parameters 
    4794 --- 
    4795 Chain pairing | bb 
    4796 Alignment algorithm | Needleman-Wunsch 
    4797 Similarity matrix | BLOSUM-62 
    4798 SS fraction | 0.3 
    4799 Gap open (HH/SS/other) | 18/18/6 
    4800 Gap extend | 1 
    4801 SS matrix |  |  | H | S | O 
    4802 ---|---|---|--- 
    4803 H | 6 | -9 | -6 
    4804 S |  | 6 | -6 
    4805 O |  |  | 4 
    4806 Iteration cutoff | 2 
    4807  
    4808 Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
    4809 alignment score = 1871.9 
    4810 RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
    4811 0.023) 
    4812  
    4813 
    4814 > show #4 models
    4815 
    4816 > hide #4 models
    4817 
    4818 > show #4 models
    4819 
    4820 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J100_005_volume_map_sharp
    4821 (1).mrc (#11) using 3401 atoms 
    4822 average map value = 0.1004, steps = 64 
    4823 shifted from previous position = 1.84 
    4824 rotated from previous position = 3.05 degrees 
    4825 atoms outside contour = 1419, contour level = 0.05 
    4826  
    4827 Position of F562a.pdb (#4) relative to cryosparc_P35_J100_005_volume_map_sharp
    4828 (1).mrc (#11) coordinates: 
    4829 Matrix rotation and translation 
    4830 0.82616267 0.51307542 -0.23282799 17.45941536 
    4831 -0.12390784 -0.23766697 -0.96341127 357.00880636 
    4832 -0.54963816 0.82478363 -0.13277751 149.37621508 
    4833 Axis 0.92916660 0.16461820 -0.33098381 
    4834 Axis point 0.00000000 112.71394709 221.40097809 
    4835 Rotation angle (degrees) 105.79170262 
    4836 Shift along axis 25.55174348 
    4837  
    4838 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J100_005_volume_map_sharp
    4839 (1).mrc (#11) using 3401 atoms 
    4840 average map value = 0.1004, steps = 48 
    4841 shifted from previous position = 0.011 
    4842 rotated from previous position = 0.0276 degrees 
    4843 atoms outside contour = 1418, contour level = 0.05 
    4844  
    4845 Position of F562a.pdb (#4) relative to cryosparc_P35_J100_005_volume_map_sharp
    4846 (1).mrc (#11) coordinates: 
    4847 Matrix rotation and translation 
    4848 0.82596970 0.51342982 -0.23273140 17.41926576 
    4849 -0.12364669 -0.23778983 -0.96341451 356.97717269 
    4850 -0.54998689 0.82452765 -0.13292329 149.51361297 
    4851 Axis 0.92909832 0.16486078 -0.33105473 
    4852 Axis point 0.00000000 112.65571575 221.42366392 
    4853 Rotation angle (degrees) 105.80544612 
    4854 Shift along axis 25.53855668 
    4855  
    4856 
    4857 > hide #6 models
    4858 
    4859 > show #5 models
    4860 
    4861 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J100_005_volume_map_sharp
    4862 (1).mrc (#11) using 3401 atoms 
    4863 average map value = 0.1083, steps = 76 
    4864 shifted from previous position = 0.951 
    4865 rotated from previous position = 3.36 degrees 
    4866 atoms outside contour = 1258, contour level = 0.05 
    4867  
    4868 Position of F562b.pdb (#5) relative to cryosparc_P35_J100_005_volume_map_sharp
    4869 (1).mrc (#11) coordinates: 
    4870 Matrix rotation and translation 
    4871 0.91100184 -0.19027699 -0.36588295 82.97740999 
    4872 -0.38499639 -0.71041595 -0.58914087 517.50161240 
    4873 -0.14782913 0.67757202 -0.72044619 248.76959820 
    4874 Axis 0.97438742 -0.16773248 -0.14978305 
    4875 Axis point 0.00000000 219.97208546 227.46670853 
    4876 Rotation angle (degrees) 139.45804049 
    4877 Shift along axis -43.21115606 
    4878  
    4879 
    4880 > color #3-5 bychain
    4881 
    4882 > hide #!11 models
    4883 
    4884 > save "C:/Users/dahailuo/OneDrive - Nanyang Technological
    4885 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-Fab56
    4886 > .cxs"
    4887 
    4888 > save "C:/Users/dahailuo/OneDrive - Nanyang Technological
    4889 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-
    4890 > Fab5-DL.cxs" includeMaps true
    4891 
    4892 ——— End of log from Thu Mar 3 12:01:46 2022 ———
    4893 
    4894 opened ChimeraX session 
    4895 
    4896 > show #!2 models
    4897 
    4898 > hide #!2 models
    4899 
    4900 > show #!1 models
    4901 
    4902 > hide #!1 models
    4903 
    4904 > show #!2 models
    4905 
    4906 > hide #!2 models
    4907 
    4908 > show #!1 models
    4909 
    4910 > hide #!1 models
    4911 
    4912 > select #5
    4913 
    4914 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    4915 
    4916 > ~select #5
    4917 
    4918 Nothing selected 
    4919 
    4920 > select #4
    4921 
    4922 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    4923 
    4924 > ~select #4
    4925 
    4926 Nothing selected 
    4927 
    4928 > select #4
    4929 
    4930 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    4931 
    4932 > ~select #4
    4933 
    4934 Nothing selected 
    4935 
    4936 > select #4
    4937 
    4938 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    4939 
    4940 > ~select #4
    4941 
    4942 Nothing selected 
    4943 
    4944 > select #3
    4945 
    4946 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    4947 
    4948 > ~select #3
    4949 
    4950 Nothing selected 
    4951 
    4952 > select #3
    4953 
    4954 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    4955 
    4956 > ~select #3
    4957 
    4958 Nothing selected 
    4959 
    4960 > select #3
    4961 
    4962 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    4963 
    4964 > ~select #3
    4965 
    4966 Nothing selected 
    4967 
    4968 > show #!2 models
    4969 
    4970 > show #!1 models
    4971 
    4972 > hide #!1 models
    4973 
    4974 > hide #!2 models
    4975 
    4976 > show #6 models
    4977 
    4978 > hide #6 models
    4979 
    4980 > show #6 models
    4981 
    4982 > hide #6 models
    4983 
    4984 > show #7 models
    4985 
    4986 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    4987 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    4988 
    4989 > show #!1 models
    4990 
    4991 > hide #!1 models
    4992 
    4993 > show #!2 models
    4994 
    4995 > hide #!2 models
    4996 
    4997 > show #!2 models
    4998 
    4999 > hide #!2 models
    5000 
    5001 > show #!2 models
    5002 
    5003 > hide #!2 models
    5004 
    5005 > hide #3 models
    5006 
    5007 > hide #4 models
    5008 
    5009 > hide #5 models
    5010 
    5011 > show #6 models
    5012 
    5013 > hide #6 models
    5014 
    5015 > show #6 models
    5016 
    5017 > hide #6 models
    5018 
    5019 > show #!8 models
    5020 
    5021 > hide #!8 models
    5022 
    5023 > show #!8 models
    5024 
    5025 > show #9 models
    5026 
    5027 > hide #9 models
    5028 
    5029 > show #9 models
    5030 
    5031 > hide #7 models
    5032 
    5033 > hide #!8 models
    5034 
    5035 > hide #9 models
    5036 
    5037 > close #8
    5038 
    5039 > show #9 models
    5040 
    5041 > hide #9 models
    5042 
    5043 > show #7 models
    5044 
    5045 > show #9 models
    5046 
    5047 > hide #7 models
    5048 
    5049 > ui tool show "Show Sequence Viewer"
    5050 
    5051 > sequence chain #9/B
    5052 
    5053 Alignment identifier is 9/B 
    5054 
    5055 > sequence chain #9/C
    5056 
    5057 Alignment identifier is 9/C 
    5058 
    5059 > select #9/B:2-149,151-206
    5060 
    5061 1648 atoms, 1670 bonds, 204 residues, 1 model selected 
    5062 
    5063 > select #9/B:9
    5064 
    5065 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5066 
    5067 > select #9/B:9-11
    5068 
    5069 25 atoms, 24 bonds, 3 residues, 1 model selected 
    5070 
    5071 > select #9/B:2-149,151-206
    5072 
    5073 1648 atoms, 1670 bonds, 204 residues, 1 model selected 
    5074 
    5075 > select #9/B:1
    5076 
    5077 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5078 
    5079 > select #9/B:1-207
    5080 
    5081 1667 atoms, 1690 bonds, 207 residues, 1 model selected 
    5082 
    5083 > select #9/B:64
    5084 
    5085 7 atoms, 7 bonds, 1 residue, 1 model selected 
    5086 
    5087 > select #9/B:64-86
    5088 
    5089 208 atoms, 215 bonds, 23 residues, 1 model selected 
    5090 
    5091 > select #9/B:64
    5092 
    5093 7 atoms, 7 bonds, 1 residue, 1 model selected 
    5094 
    5095 > select #9/B:64-85
    5096 
    5097 201 atoms, 207 bonds, 22 residues, 1 model selected 
    5098 /Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5099 packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an
    5100 ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-
    5101 tuples-or ndarrays with different lengths or shapes) is deprecated. If you
    5102 meant to do this, you must specify 'dtype=object' when creating the ndarray 
    5103 return array(a, dtype, copy=False, order=order) 
    5104 
    5105 > select #9/B:2-149,151-206
    5106 
    5107 1648 atoms, 1670 bonds, 204 residues, 1 model selected 
    5108 
    5109 > select #9/B:64
    5110 
    5111 7 atoms, 7 bonds, 1 residue, 1 model selected 
    5112 
    5113 > select #9/B:64-85
    5114 
    5115 201 atoms, 207 bonds, 22 residues, 1 model selected 
    5116 
    5117 > color sel blue
    5118 
    5119 > color sel cornflower blue
    5120 
    5121 > select #9/B:151-152
    5122 
    5123 10 atoms, 9 bonds, 2 residues, 1 model selected 
    5124 
    5125 > select #9/B:151-172
    5126 
    5127 163 atoms, 164 bonds, 22 residues, 1 model selected 
    5128 
    5129 > color sel cornflower blue
    5130 
    5131 > show #!10 models
    5132 
    5133 > hide #!10 models
    5134 
    5135 > show #!10 models
    5136 
    5137 > hide #!10 models
    5138 
    5139 > show #!11 models
    5140 
    5141 > hide #!11 models
    5142 
    5143 > close #10
    5144 
    5145 > close #11
    5146 
    5147 > show #7 models
    5148 
    5149 > hide #7 models
    5150 
    5151 > show #6 models
    5152 
    5153 > hide #6 models
    5154 
    5155 > show #5 models
    5156 
    5157 > hide #5 models
    5158 
    5159 > show #!2 models
    5160 
    5161 > show #!1 models
    5162 
    5163 > hide #!1 models
    5164 
    5165 > show #3 models
    5166 
    5167 > show #4 models
    5168 
    5169 > show #5 models
    5170 
    5171 > hide #5 models
    5172 
    5173 > select #3
    5174 
    5175 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    5176 
    5177 > ~select #3
    5178 
    5179 Nothing selected 
    5180 
    5181 > hide #4 models
    5182 
    5183 > show #4 models
    5184 
    5185 > hide #4 models
    5186 
    5187 > select #9/C:2-149,151-206
    5188 
    5189 1648 atoms, 1670 bonds, 204 residues, 1 model selected 
    5190 
    5191 > select #9/C:64
    5192 
    5193 7 atoms, 7 bonds, 1 residue, 1 model selected 
    5194 
    5195 > select #9/C:64-85
    5196 
    5197 201 atoms, 207 bonds, 22 residues, 1 model selected 
    5198 
    5199 > color sel medium blue
    5200 
    5201 > select #9/C:151
    5202 
    5203 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5204 
    5205 > select #9/C:151-172
    5206 
    5207 163 atoms, 164 bonds, 22 residues, 1 model selected 
    5208 
    5209 > color sel medium blue
    5210 
    5211 > close #7
    5212 
    5213 > show #6 models
    5214 
    5215 > hide #6 models
    5216 
    5217 > show #6 models
    5218 
    5219 > hide #6 models
    5220 
    5221 > show #6 models
    5222 
    5223 > hide #6 models
    5224 
    5225 > show #6 models
    5226 
    5227 > hide #6 models
    5228 
    5229 > close #6
    5230 
    5231 > show #4 models
    5232 
    5233 > open "/Users/alvinchew/OneDrive - Nanyang Technological
    5234 > University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J142_005_volume_map_sharp.mrc"
    5235 
    5236 Opened cryosparc_P47_J142_005_volume_map_sharp.mrc as #6, grid size
    5237 360,360,360, pixel 0.85, shown at level 0.0449, step 2, values float32 
    5238 
    5239 > volume #6 step 1
    5240 
    5241 > volume #6 level 0.1656
    5242 
    5243 > volume #6 level 0.06061
    5244 
    5245 > close #6
    5246 
    5247 > open "/Users/alvinchew/OneDrive - Nanyang Technological
    5248 > University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J128_002_volume_map_sharp.mrc"
    5249 
    5250 Opened cryosparc_P47_J128_002_volume_map_sharp.mrc as #6, grid size
    5251 360,360,360, pixel 0.85, shown at level 0.0566, step 2, values float32 
    5252 
    5253 > hide #!2 models
    5254 
    5255 > hide #3 models
    5256 
    5257 > hide #4 models
    5258 
    5259 > hide #!6 models
    5260 
    5261 > hide #9 models
    5262 
    5263 > show #9 models
    5264 
    5265 > hide #9 models
    5266 
    5267 > show #9 models
    5268 
    5269 > hide #9 models
    5270 
    5271 > select #9
    5272 
    5273 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    5274 
    5275 > ~select #9
    5276 
    5277 Nothing selected 
    5278 
    5279 > show #!6 models
    5280 
    5281 > volume #6 step 1
    5282 
    5283 > volume #6 level 0.116
    5284 
    5285 > open "/Users/alvinchew/OneDrive - Nanyang Technological
    5286 > University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J132_002_volume_map_sharp.mrc"
    5287 
    5288 Opened cryosparc_P47_J132_002_volume_map_sharp.mrc as #7, grid size
    5289 360,360,360, pixel 0.85, shown at level 0.0558, step 2, values float32 
    5290 
    5291 > volume #7 step 1
    5292 
    5293 > volume #7 level 0.189
    5294 
    5295 > volume #6 level 0.148
    5296 
    5297 > volume #6 level 0.1384
    5298 
    5299 > volume #7 level 0.08193
    5300 
    5301 > volume #7 level 0.04862
    5302 
    5303 > volume #6 level 0.06462
    5304 
    5305 > close #7
    5306 
    5307 > volume #6 level 0.1336
    5308 
    5309 > volume #6 level 0.1256
    5310 
    5311 > show #!2 models
    5312 
    5313 > hide #!2 models
    5314 
    5315 > show #!1 models
    5316 
    5317 > hide #!1 models
    5318 
    5319 > show #!2 models
    5320 
    5321 > select #6
    5322 
    5323 2 models selected 
    5324 
    5325 > view matrix models
    5326 > #6,-0.83996,0.011508,0.54253,184.02,0.50426,0.3859,0.77253,-105.68,-0.20047,0.92247,-0.32995,103.36
    5327 
    5328 > view matrix models
    5329 > #6,0.1848,-0.18014,0.96613,-8.4193,0.46665,-0.84908,-0.24758,260.82,0.86492,0.4966,-0.072852,-31.125
    5330 
    5331 > view matrix models
    5332 > #6,0.25195,-0.19005,0.94889,-14.067,0.4832,-0.82485,-0.29351,262.08,0.83847,0.53245,-0.11599,-25.726
    5333 
    5334 > view matrix models
    5335 > #6,-0.035938,-0.13733,0.98987,13.939,0.38333,-0.91664,-0.11325,261.83,0.92291,0.37538,0.085583,-46.756
    5336 
    5337 > view matrix models
    5338 > #6,0.1558,-0.53982,0.82724,75.077,-0.30263,-0.82328,-0.48024,409.8,0.94029,-0.17552,-0.29163,98.871
    5339 
    5340 > ui mousemode right "translate selected models"
    5341 
    5342 > view matrix models
    5343 > #6,0.1558,-0.53982,0.82724,121.85,-0.30263,-0.82328,-0.48024,428.76,0.94029,-0.17552,-0.29163,116.7
    5344 
    5345 > view matrix models
    5346 > #6,0.1558,-0.53982,0.82724,122.7,-0.30263,-0.82328,-0.48024,438.5,0.94029,-0.17552,-0.29163,113.43
    5347 
    5348 > view matrix models
    5349 > #6,0.1558,-0.53982,0.82724,123.68,-0.30263,-0.82328,-0.48024,449.46,0.94029,-0.17552,-0.29163,118.59
    5350 
    5351 > ui mousemode right "rotate selected models"
    5352 
    5353 > view matrix models
    5354 > #6,0.15847,-0.55227,0.81847,126.67,-0.30396,-0.81597,-0.49173,450.39,0.93941,-0.17086,-0.29717,118.9
    5355 
    5356 > view matrix models
    5357 > #6,0.31733,-0.49565,0.80848,95.704,-0.41983,-0.83787,-0.34888,447.71,0.85032,-0.22872,-0.47397,170.26
    5358 
    5359 > ui mousemode right "translate selected models"
    5360 
    5361 > view matrix models
    5362 > #6,0.31733,-0.49565,0.80848,94.921,-0.41983,-0.83787,-0.34888,440.31,0.85032,-0.22872,-0.47397,180.5
    5363 
    5364 > view matrix models
    5365 > #6,0.31733,-0.49565,0.80848,96.096,-0.41983,-0.83787,-0.34888,439.7,0.85032,-0.22872,-0.47397,180.02
    5366 
    5367 > view matrix models
    5368 > #6,0.31733,-0.49565,0.80848,94.946,-0.41983,-0.83787,-0.34888,439.56,0.85032,-0.22872,-0.47397,179.06
    5369 
    5370 > view matrix models
    5371 > #6,0.31733,-0.49565,0.80848,94.851,-0.41983,-0.83787,-0.34888,439.42,0.85032,-0.22872,-0.47397,178.96
    5372 
    5373 > ui mousemode right "rotate selected models"
    5374 
    5375 > view matrix models
    5376 > #6,0.32806,-0.48111,0.81296,90.235,-0.37939,-0.85524,-0.35303,436.79,0.86512,-0.19262,-0.4631,169.31
    5377 
    5378 > view matrix models
    5379 > #6,0.36269,-0.41122,0.83627,70.284,-0.30986,-0.89953,-0.30795,425.95,0.87889,-0.14743,-0.45367,158.62
    5380 
    5381 > view matrix models
    5382 > #6,0.36637,-0.44198,0.8188,77.421,-0.35476,-0.87986,-0.31621,430.93,0.86019,-0.17462,-0.47915,169.85
    5383 
    5384 > view matrix models
    5385 > #6,0.36072,-0.39988,0.8426,67.762,-0.30034,-0.9051,-0.30097,424.26,0.88299,-0.1445,-0.44659,156.39
    5386 
    5387 > ui mousemode right "translate selected models"
    5388 
    5389 > view matrix models
    5390 > #6,0.36072,-0.39988,0.8426,67.7,-0.30034,-0.9051,-0.30097,421.64,0.88299,-0.1445,-0.44659,155.81
    5391 
    5392 > view matrix models
    5393 > #6,0.36072,-0.39988,0.8426,69.281,-0.30034,-0.9051,-0.30097,420.24,0.88299,-0.1445,-0.44659,157.09
    5394 
    5395 > view matrix models
    5396 > #6,0.36072,-0.39988,0.8426,69.528,-0.30034,-0.9051,-0.30097,421,0.88299,-0.1445,-0.44659,156.78
    5397 
    5398 > ui mousemode right "rotate selected models"
    5399 
    5400 > view matrix models
    5401 > #6,0.36427,-0.41429,0.83407,72.656,-0.28999,-0.90154,-0.32115,422.2,0.88499,-0.12489,-0.44854,153.73
    5402 
    5403 > view matrix models
    5404 > #6,0.35177,-0.40975,0.84164,72.569,-0.29057,-0.90249,-0.31793,421.91,0.88984,-0.13272,-0.43653,152.26
    5405 
    5406 > view matrix models
    5407 > #6,0.3599,-0.44231,0.82148,79.767,-0.28748,-0.89021,-0.35338,425.33,0.8876,-0.10898,-0.44754,150.68
    5408 
    5409 > view matrix models
    5410 > #6,0.37744,-0.43949,0.8151,77.749,-0.29539,-0.89136,-0.34382,425.13,0.87766,-0.11101,-0.46626,155.55
    5411 
    5412 > ui mousemode right "translate selected models"
    5413 
    5414 > view matrix models
    5415 > #6,0.37744,-0.43949,0.8151,76.75,-0.29539,-0.89136,-0.34382,424.99,0.87766,-0.11101,-0.46626,155.59
    5416 
    5417 > view matrix models
    5418 > #6,0.37744,-0.43949,0.8151,75.665,-0.29539,-0.89136,-0.34382,426.6,0.87766,-0.11101,-0.46626,156.42
    5419 
    5420 > view matrix models
    5421 > #6,0.37744,-0.43949,0.8151,77.299,-0.29539,-0.89136,-0.34382,425.99,0.87766,-0.11101,-0.46626,155.38
    5422 
    5423 > view matrix models
    5424 > #6,0.37744,-0.43949,0.8151,77.803,-0.29539,-0.89136,-0.34382,426.26,0.87766,-0.11101,-0.46626,155.31
    5425 
    5426 > ui mousemode right "rotate selected models"
    5427 
    5428 > view matrix models
    5429 > #6,0.3964,-0.4154,0.81873,70.6,-0.31009,-0.89996,-0.30647,423.68,0.86412,-0.13239,-0.48555,163.85
    5430 
    5431 > view matrix models
    5432 > #6,0.36188,-0.4339,0.82509,77.612,-0.3531,-0.88293,-0.30945,427.92,0.86276,-0.17936,-0.47273,169.32
    5433 
    5434 > view matrix models
    5435 > #6,0.34333,-0.43629,0.83173,79.67,-0.33947,-0.88333,-0.32323,428.21,0.87572,-0.17137,-0.45138,162.63
    5436 
    5437 > view matrix models
    5438 > #6,0.36882,-0.43654,0.82061,77.724,-0.34143,-0.88476,-0.31721,427.74,0.86452,-0.16319,-0.47537,166.95
    5439 
    5440 > view matrix models
    5441 > #6,0.37369,-0.42634,0.82377,74.88,-0.33111,-0.89091,-0.31088,426.13,0.86644,-0.15658,-0.47409,165.42
    5442 
    5443 > ui mousemode right "translate selected models"
    5444 
    5445 > view matrix models
    5446 > #6,0.37369,-0.42634,0.82377,75.079,-0.33111,-0.89091,-0.31088,425.43,0.86644,-0.15658,-0.47409,165.61
    5447 
    5448 > view matrix models
    5449 > #6,0.37369,-0.42634,0.82377,74.521,-0.33111,-0.89091,-0.31088,425.67,0.86644,-0.15658,-0.47409,165.89
    5450 
    5451 > view matrix models
    5452 > #6,0.37369,-0.42634,0.82377,74.154,-0.33111,-0.89091,-0.31088,425.74,0.86644,-0.15658,-0.47409,166.14
    5453 
    5454 > view matrix models
    5455 > #6,0.37369,-0.42634,0.82377,74.447,-0.33111,-0.89091,-0.31088,425.75,0.86644,-0.15658,-0.47409,166.59
    5456 
    5457 > ui mousemode right "rotate selected models"
    5458 
    5459 > view matrix models
    5460 > #6,0.5154,-0.37111,0.77242,53.045,-0.24207,-0.9277,-0.2842,413.84,0.82205,-0.040509,-0.56797,170.41
    5461 
    5462 > view matrix models
    5463 > #6,0.49373,-0.37696,0.78367,55.354,-0.26058,-0.92389,-0.28024,415.36,0.82966,-0.065846,-0.55437,171.02
    5464 
    5465 > ui mousemode right "rotate selected models"
    5466 
    5467 > ui mousemode right select
    5468 
    5469 > ~select #6
    5470 
    5471 Nothing selected 
    5472 
    5473 > vop resample #6 onGrid #2
    5474 
    5475 Opened cryosparc_P47_J128_002_volume_map_sharp.mrc resampled as #7, grid size
    5476 352,352,352, pixel 0.85, shown at step 1, values float32 
    5477 
    5478 > close #6
    5479 
    5480 > ui tool show "Fit to Segments"
    5481 
    5482 > ui tool show "Fit in Map"
    5483 
    5484 > volume #7 level 0.09689
    5485 
    5486 Fit map cryosparc_P47_J128_002_volume_map_sharp.mrc resampled in map
    5487 cryosparc_P47_J20_004_volume_map_sharp.mrc using 175454 points 
    5488 correlation = 0.8828, correlation about mean = 0.547, overlap = 7225 
    5489 steps = 168, shift = 7.84, angle = 17 degrees 
    5490  
    5491 Position of cryosparc_P47_J128_002_volume_map_sharp.mrc resampled (#7)
    5492 relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    5493 Matrix rotation and translation 
    5494 0.95949380 0.09544158 -0.26507085 39.26017660 
    5495 -0.07373087 0.99314477 0.09070403 -7.34539260 
    5496 0.27191066 -0.06748605 0.95995324 -23.66014125 
    5497 Axis -0.27050228 -0.91822900 -0.28928192 
    5498 Axis point 103.77985456 0.00000000 135.28320696 
    5499 Rotation angle (degrees) 17.00173416 
    5500 Shift along axis 2.96923623 
    5501  
    5502 
    5503 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    5504 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    5505 
    5506 Traceback (most recent call last): 
    5507 File
    5508 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5509 packages/chimerax/core/session.py", line 281, in process 
    5510 data = sm.take_snapshot(obj, session, self.state_flags) 
    5511 File
    5512 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5513 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    5514 'region browser': self.region_browser.state(), 
    5515 File
    5516 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5517 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    5518 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5519 File
    5520 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5521 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5522 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5523 File
    5524 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5525 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5526 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5527 ValueError:
    5528 is not in list 
    5529  
    5530 The above exception was the direct cause of the following exception: 
    5531  
    5532 Traceback (most recent call last): 
    5533 File
    5534 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5535 packages/chimerax/core/session.py", line 260, in discovery 
    5536 self.processed[key] = self.process(obj, parents) 
    5537 File
    5538 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5539 packages/chimerax/core/session.py", line 284, in process 
    5540 raise RuntimeError(msg) from e 
    5541 RuntimeError: Error while saving session data for 'tools' ->
    5542  ->   
    5543  
    5544 During handling of the above exception, another exception occurred: 
    5545  
    5546 Traceback (most recent call last): 
    5547 File
    5548 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5549 packages/chimerax/core/session.py", line 877, in save 
    5550 session.save(output, version=version, include_maps=include_maps) 
    5551 File
    5552 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5553 packages/chimerax/core/session.py", line 607, in save 
    5554 mgr.discovery(self._state_containers) 
    5555 File
    5556 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5557 packages/chimerax/core/session.py", line 262, in discovery 
    5558 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    5559 ValueError: error processing: 'tools' ->  -> : Error while saving session data for 'tools' ->
    5560  ->   
    5561  
    5562 ValueError: error processing: 'tools' -> -> : Error while saving session data
    5563 for 'tools' -> -> 
    5564  
    5565 File
    5566 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5567 packages/chimerax/core/session.py", line 262, in discovery 
    5568 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    5569  
    5570 See log for complete Python traceback. 
    5571  
    5572 Traceback (most recent call last): 
    5573 File
    5574 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5575 packages/chimerax/core/session.py", line 281, in process 
    5576 data = sm.take_snapshot(obj, session, self.state_flags) 
    5577 File
    5578 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5579 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    5580 'region browser': self.region_browser.state(), 
    5581 File
    5582 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5583 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    5584 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5585 File
    5586 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5587 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5588 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5589 File
    5590 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5591 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5592 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5593 ValueError:
    5594 is not in list 
    5595  
    5596 The above exception was the direct cause of the following exception: 
    5597  
    5598 Traceback (most recent call last): 
    5599 File
    5600 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5601 packages/chimerax/core/session.py", line 260, in discovery 
    5602 self.processed[key] = self.process(obj, parents) 
    5603 File
    5604 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5605 packages/chimerax/core/session.py", line 284, in process 
    5606 raise RuntimeError(msg) from e 
    5607 RuntimeError: Error while saving session data for 'tools' ->
    5608  ->   
    5609  
    5610 During handling of the above exception, another exception occurred: 
    5611  
    5612 Traceback (most recent call last): 
    5613 File
    5614 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5615 packages/chimerax/save_command/dialog.py", line 116, in   
    5616 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    5617 file", 
    5618 File
    5619 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5620 packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog 
    5621 _dlg.display(session, **kw) 
    5622 File
    5623 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5624 packages/chimerax/save_command/dialog.py", line 51, in display 
    5625 run(session, cmd) 
    5626 File
    5627 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5628 packages/chimerax/core/commands/run.py", line 36, in run 
    5629 results = command.run(text, log=log, return_json=return_json) 
    5630 File
    5631 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5632 packages/chimerax/core/commands/cli.py", line 2852, in run 
    5633 result = ci.function(session, **kw_args) 
    5634 File
    5635 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5636 packages/chimerax/save_command/cmd.py", line 75, in cmd_save 
    5637 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    5638 File
    5639 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5640 packages/chimerax/core/commands/cli.py", line 2852, in run 
    5641 result = ci.function(session, **kw_args) 
    5642 File
    5643 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5644 packages/chimerax/save_command/cmd.py", line 87, in provider_save 
    5645 provider_info.bundle_info.run_provider(session, provider_info.format_name, 
    5646 File
    5647 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5648 packages/chimerax/core_formats/__init__.py", line 79, in save 
    5649 return cxs_save(session, path, **kw) 
    5650 File
    5651 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5652 packages/chimerax/core/session.py", line 877, in save 
    5653 session.save(output, version=version, include_maps=include_maps) 
    5654 File
    5655 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5656 packages/chimerax/core/session.py", line 607, in save 
    5657 mgr.discovery(self._state_containers) 
    5658 File
    5659 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5660 packages/chimerax/core/session.py", line 262, in discovery 
    5661 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    5662 ValueError: error processing: 'tools' ->  -> : Error while saving session data for 'tools' ->
    5663  ->   
    5664  
    5665 ValueError: error processing: 'tools' -> -> : Error while saving session data
    5666 for 'tools' -> -> 
    5667  
    5668 File
    5669 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5670 packages/chimerax/core/session.py", line 262, in discovery 
    5671 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    5672  
    5673 See log for complete Python traceback. 
    5674  
    5675 
    5676 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    5677 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_ac.cxs"
    5678 
    5679 Traceback (most recent call last): 
    5680 File
    5681 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5682 packages/chimerax/core/session.py", line 281, in process 
    5683 data = sm.take_snapshot(obj, session, self.state_flags) 
    5684 File
    5685 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5686 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    5687 'region browser': self.region_browser.state(), 
    5688 File
    5689 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5690 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    5691 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5692 File
    5693 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5694 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5695 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5696 File
    5697 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5698 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5699 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5700 ValueError:
    5701 is not in list 
    5702  
    5703 The above exception was the direct cause of the following exception: 
    5704  
    5705 Traceback (most recent call last): 
    5706 File
    5707 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5708 packages/chimerax/core/session.py", line 260, in discovery 
    5709 self.processed[key] = self.process(obj, parents) 
    5710 File
    5711 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5712 packages/chimerax/core/session.py", line 284, in process 
    5713 raise RuntimeError(msg) from e 
    5714 RuntimeError: Error while saving session data for 'tools' ->
    5715  ->   
    5716  
    5717 During handling of the above exception, another exception occurred: 
    5718  
    5719 Traceback (most recent call last): 
    5720 File
    5721 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5722 packages/chimerax/core/session.py", line 877, in save 
    5723 session.save(output, version=version, include_maps=include_maps) 
    5724 File
    5725 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5726 packages/chimerax/core/session.py", line 607, in save 
    5727 mgr.discovery(self._state_containers) 
    5728 File
    5729 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5730 packages/chimerax/core/session.py", line 262, in discovery 
    5731 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    5732 ValueError: error processing: 'tools' ->  -> : Error while saving session data for 'tools' ->
    5733  ->   
    5734  
    5735 ValueError: error processing: 'tools' -> -> : Error while saving session data
    5736 for 'tools' -> -> 
    5737  
    5738 File
    5739 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5740 packages/chimerax/core/session.py", line 262, in discovery 
    5741 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    5742  
    5743 See log for complete Python traceback. 
    5744  
    5745 Traceback (most recent call last): 
    5746 File
    5747 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5748 packages/chimerax/core/session.py", line 281, in process 
    5749 data = sm.take_snapshot(obj, session, self.state_flags) 
    5750 File
    5751 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5752 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    5753 'region browser': self.region_browser.state(), 
    5754 File
    5755 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5756 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    5757 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5758 File
    5759 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5760 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5761 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5762 File
    5763 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5764 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5765 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5766 ValueError:
    5767 is not in list 
    5768  
    5769 The above exception was the direct cause of the following exception: 
    5770  
    5771 Traceback (most recent call last): 
    5772 File
    5773 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5774 packages/chimerax/core/session.py", line 260, in discovery 
    5775 self.processed[key] = self.process(obj, parents) 
    5776 File
    5777 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5778 packages/chimerax/core/session.py", line 284, in process 
    5779 raise RuntimeError(msg) from e 
    5780 RuntimeError: Error while saving session data for 'tools' ->
    5781  ->   
    5782  
    5783 During handling of the above exception, another exception occurred: 
    5784  
    5785 Traceback (most recent call last): 
    5786 File
    5787 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5788 packages/chimerax/save_command/dialog.py", line 116, in   
    5789 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    5790 file", 
    5791 File
    5792 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5793 packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog 
    5794 _dlg.display(session, **kw) 
    5795 File
    5796 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5797 packages/chimerax/save_command/dialog.py", line 51, in display 
    5798 run(session, cmd) 
    5799 File
    5800 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5801 packages/chimerax/core/commands/run.py", line 36, in run 
    5802 results = command.run(text, log=log, return_json=return_json) 
    5803 File
    5804 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5805 packages/chimerax/core/commands/cli.py", line 2852, in run 
    5806 result = ci.function(session, **kw_args) 
    5807 File
    5808 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5809 packages/chimerax/save_command/cmd.py", line 75, in cmd_save 
    5810 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    5811 File
    5812 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5813 packages/chimerax/core/commands/cli.py", line 2852, in run 
    5814 result = ci.function(session, **kw_args) 
    5815 File
    5816 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5817 packages/chimerax/save_command/cmd.py", line 87, in provider_save 
    5818 provider_info.bundle_info.run_provider(session, provider_info.format_name, 
    5819 File
    5820 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5821 packages/chimerax/core_formats/__init__.py", line 79, in save 
    5822 return cxs_save(session, path, **kw) 
    5823 File
    5824 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5825 packages/chimerax/core/session.py", line 877, in save 
    5826 session.save(output, version=version, include_maps=include_maps) 
    5827 File
    5828 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5829 packages/chimerax/core/session.py", line 607, in save 
    5830 mgr.discovery(self._state_containers) 
    5831 File
    5832 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5833 packages/chimerax/core/session.py", line 262, in discovery 
    5834 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    5835 ValueError: error processing: 'tools' ->  -> : Error while saving session data for 'tools' ->
    5836  ->   
    5837  
    5838 ValueError: error processing: 'tools' -> -> : Error while saving session data
    5839 for 'tools' -> -> 
    5840  
    5841 File
    5842 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5843 packages/chimerax/core/session.py", line 262, in discovery 
    5844 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    5845  
    5846 See log for complete Python traceback. 
    5847  
    5848 
    5849 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    5850 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    5851 > includeMaps true
    5852 
    5853 Traceback (most recent call last): 
    5854 File
    5855 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5856 packages/chimerax/core/session.py", line 281, in process 
    5857 data = sm.take_snapshot(obj, session, self.state_flags) 
    5858 File
    5859 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5860 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    5861 'region browser': self.region_browser.state(), 
    5862 File
    5863 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5864 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    5865 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5866 File
    5867 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5868 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5869 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5870 File
    5871 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5872 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5873 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5874 ValueError:
    5875 is not in list 
    5876  
    5877 The above exception was the direct cause of the following exception: 
    5878  
    5879 Traceback (most recent call last): 
    5880 File
    5881 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5882 packages/chimerax/core/session.py", line 260, in discovery 
    5883 self.processed[key] = self.process(obj, parents) 
    5884 File
    5885 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5886 packages/chimerax/core/session.py", line 284, in process 
    5887 raise RuntimeError(msg) from e 
    5888 RuntimeError: Error while saving session data for 'tools' ->
    5889  ->   
    5890  
    5891 During handling of the above exception, another exception occurred: 
    5892  
    5893 Traceback (most recent call last): 
    5894 File
    5895 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5896 packages/chimerax/core/session.py", line 877, in save 
    5897 session.save(output, version=version, include_maps=include_maps) 
    5898 File
    5899 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5900 packages/chimerax/core/session.py", line 607, in save 
    5901 mgr.discovery(self._state_containers) 
    5902 File
    5903 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5904 packages/chimerax/core/session.py", line 262, in discovery 
    5905 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    5906 ValueError: error processing: 'tools' ->  -> : Error while saving session data for 'tools' ->
    5907  ->   
    5908  
    5909 ValueError: error processing: 'tools' -> -> : Error while saving session data
    5910 for 'tools' -> -> 
    5911  
    5912 File
    5913 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5914 packages/chimerax/core/session.py", line 262, in discovery 
    5915 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    5916  
    5917 See log for complete Python traceback. 
    5918  
    5919 Traceback (most recent call last): 
    5920 File
    5921 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5922 packages/chimerax/core/session.py", line 281, in process 
    5923 data = sm.take_snapshot(obj, session, self.state_flags) 
    5924 File
    5925 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5926 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    5927 'region browser': self.region_browser.state(), 
    5928 File
    5929 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5930 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    5931 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5932 File
    5933 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5934 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5935 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5936 File
    5937 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5938 packages/chimerax/seq-view/region_browser.py", line 1106, in   
    5939 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    5940 ValueError:
    5941 is not in list 
    5942  
    5943 The above exception was the direct cause of the following exception: 
    5944  
    5945 Traceback (most recent call last): 
    5946 File
    5947 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5948 packages/chimerax/core/session.py", line 260, in discovery 
    5949 self.processed[key] = self.process(obj, parents) 
    5950 File
    5951 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5952 packages/chimerax/core/session.py", line 284, in process 
    5953 raise RuntimeError(msg) from e 
    5954 RuntimeError: Error while saving session data for 'tools' ->
    5955  ->   
    5956  
    5957 During handling of the above exception, another exception occurred: 
    5958  
    5959 Traceback (most recent call last): 
    5960 File
    5961 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5962 packages/chimerax/save_command/dialog.py", line 116, in   
    5963 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    5964 file", 
    5965 File
    5966 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5967 packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog 
    5968 _dlg.display(session, **kw) 
    5969 File
    5970 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5971 packages/chimerax/save_command/dialog.py", line 51, in display 
    5972 run(session, cmd) 
    5973 File
    5974 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5975 packages/chimerax/core/commands/run.py", line 36, in run 
    5976 results = command.run(text, log=log, return_json=return_json) 
    5977 File
    5978 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5979 packages/chimerax/core/commands/cli.py", line 2852, in run 
    5980 result = ci.function(session, **kw_args) 
    5981 File
    5982 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5983 packages/chimerax/save_command/cmd.py", line 75, in cmd_save 
    5984 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    5985 File
    5986 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5987 packages/chimerax/core/commands/cli.py", line 2852, in run 
    5988 result = ci.function(session, **kw_args) 
    5989 File
    5990 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5991 packages/chimerax/save_command/cmd.py", line 87, in provider_save 
    5992 provider_info.bundle_info.run_provider(session, provider_info.format_name, 
    5993 File
    5994 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5995 packages/chimerax/core_formats/__init__.py", line 79, in save 
    5996 return cxs_save(session, path, **kw) 
    5997 File
    5998 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    5999 packages/chimerax/core/session.py", line 877, in save 
    6000 session.save(output, version=version, include_maps=include_maps) 
    6001 File
    6002 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    6003 packages/chimerax/core/session.py", line 607, in save 
    6004 mgr.discovery(self._state_containers) 
    6005 File
    6006 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    6007 packages/chimerax/core/session.py", line 262, in discovery 
    6008 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    6009 ValueError: error processing: 'tools' ->  -> : Error while saving session data for 'tools' ->
    6010  ->   
    6011  
    6012 ValueError: error processing: 'tools' -> -> : Error while saving session data
    6013 for 'tools' -> -> 
    6014  
    6015 File
    6016 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    6017 packages/chimerax/core/session.py", line 262, in discovery 
    6018 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    6019  
    6020 See log for complete Python traceback. 
    6021  
    6022 
    6023 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    6024 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    6025 > includeMaps true
    6026 
    6027 ——— End of log from Thu Mar 3 19:50:19 2022 ———
    6028 
    6029 opened ChimeraX session 
    6030 
    6031 > show #9 models
    6032 
    6033 > hide #!7 models
    6034 
    6035 > show #3 models
    6036 
    6037 > show #!7 models
    6038 
    6039 > volume #7 level 0.1304
    6040 
    6041 > hide #9 models
    6042 
    6043 > hide #!2 models
    6044 
    6045 > select #7
    6046 
    6047 2 models selected 
    6048 
    6049 > select #3
    6050 
    6051 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    6052 
    6053 > ui mousemode right "rotate selected models"
    6054 
    6055 > view matrix models
    6056 > #3,0.047588,-0.1037,-0.99347,365.91,0.86244,-0.4975,0.093243,89.677,-0.50392,-0.86124,0.065763,412.54
    6057 
    6058 > view matrix models
    6059 > #3,0.06743,-0.16738,-0.98358,371.36,0.85706,-0.49497,0.14299,81.335,-0.51078,-0.85264,0.11008,404.4
    6060 
    6061 > view matrix models
    6062 > #3,0.096228,-0.19565,-0.97594,369.69,0.85361,-0.48807,0.18201,73.83,-0.51194,-0.85059,0.12005,402.49
    6063 
    6064 > view matrix models
    6065 > #3,0.12326,-0.1737,-0.97705,361.44,0.80994,-0.55129,0.20019,88.903,-0.57341,-0.81603,0.072729,415.92
    6066 
    6067 > view matrix models
    6068 > #3,0.16662,-0.22348,-0.96036,359.21,0.80001,-0.5387,0.26416,77.136,-0.57639,-0.81231,0.089027,412.91
    6069 
    6070 > view matrix models
    6071 > #3,0.16293,-0.22083,-0.96161,359.64,0.8006,-0.54002,0.25966,78.055,-0.57663,-0.81217,0.088811,412.97
    6072 
    6073 > ui mousemode right "translate selected models"
    6074 
    6075 > view matrix models
    6076 > #3,0.16293,-0.22083,-0.96161,359.93,0.8006,-0.54002,0.25966,80.609,-0.57663,-0.81217,0.088811,411.39
    6077 
    6078 > view matrix models
    6079 > #3,0.16293,-0.22083,-0.96161,360.07,0.8006,-0.54002,0.25966,81.287,-0.57663,-0.81217,0.088811,412.29
    6080 
    6081 > ui mousemode right "rotate selected models"
    6082 
    6083 > view matrix models
    6084 > #3,0.17153,-0.1861,-0.96744,353.75,0.81713,-0.52169,0.24523,77.868,-0.55034,-0.83259,0.062584,415.78
    6085 
    6086 > view matrix models
    6087 > #3,0.18128,-0.16143,-0.97009,348.36,0.82389,-0.51369,0.23944,76.368,-0.53698,-0.84265,0.03988,419.16
    6088 
    6089 > view matrix models
    6090 > #3,0.15753,-0.14621,-0.97663,351.15,0.82063,-0.53075,0.21182,84.727,-0.54931,-0.83482,0.03638,420.64
    6091 
    6092 > view matrix models
    6093 > #3,0.14559,-0.14302,-0.97895,353.12,0.82526,-0.52818,0.1999,85.606,-0.54566,-0.837,0.04113,419.52
    6094 
    6095 > view matrix models
    6096 > #3,0.10891,-0.20392,-0.97291,368.74,0.80086,-0.56179,0.20739,94.212,-0.58886,-0.80175,0.10213,410.32
    6097 
    6098 > view matrix models
    6099 > #3,7.5917e-05,-0.38124,-0.92448,409.06,0.76186,-0.5988,0.247,100.24,-0.64774,-0.70434,0.29041,370.76
    6100 
    6101 > view matrix models
    6102 > #3,0.020851,-0.42125,-0.9067,408.97,0.8145,-0.51877,0.25975,75.255,-0.57979,-0.74392,0.33229,358
    6103 
    6104 > view matrix models
    6105 > #3,0.0058992,-0.41587,-0.90941,411.17,0.80554,-0.53687,0.25074,81.477,-0.59251,-0.73405,0.33183,358.66
    6106 
    6107 > view matrix models
    6108 > #3,0.010117,-0.39918,-0.91682,408.95,0.78121,-0.56916,0.25643,90.171,-0.62418,-0.71883,0.30608,366.25
    6109 
    6110 > show #!2 models
    6111 
    6112 > show #4 models
    6113 
    6114 > hide #!2 models
    6115 
    6116 > hide #4 models
    6117 
    6118 > hide #!7 models
    6119 
    6120 > show #!2 models
    6121 
    6122 > volume #2 level 0.1739
    6123 
    6124 > volume #2 level 0.2952
    6125 
    6126 > ui tool show "Show Sequence Viewer"
    6127 
    6128 > sequence chain #9/B #9/C
    6129 
    6130 Alignment identifier is 1 
    6131 
    6132 > select #3/B:2,7,40,94,101,112-114,116,120,122,233
    6133 
    6134 96 atoms, 87 bonds, 12 residues, 1 model selected 
    6135 
    6136 > color sel red
    6137 
    6138 > color sel red
    6139 
    6140 > volume #2 level 0.275
    6141 
    6142 > volume #2 level 0.2628
    6143 
    6144 > show #!7 models
    6145 
    6146 > show #9 models
    6147 
    6148 > hide #!7 models
    6149 
    6150 > hide #!2 models
    6151 
    6152 > select #9
    6153 
    6154 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    6155 
    6156 > view matrix models
    6157 > #9,0.38721,-0.79412,0.46845,171.91,0.90831,0.41577,-0.04598,200.21,-0.15825,0.4433,0.88229,215.35
    6158 
    6159 > view matrix models
    6160 > #9,-0.087483,-0.4123,0.90684,172.91,0.99343,0.031343,0.11009,201.89,-0.073812,0.91051,0.40685,212.01
    6161 
    6162 > view matrix models
    6163 > #9,-0.28915,-0.67075,0.68299,173.05,0.95728,-0.20238,0.20652,203.01,-0.00030104,0.71353,0.70062,213.67
    6164 
    6165 > view matrix models
    6166 > #9,-0.26136,-0.69506,0.66977,173.04,0.95462,-0.083484,0.28588,202.96,-0.14278,0.71409,0.68534,213.75
    6167 
    6168 > view matrix models
    6169 > #9,-0.24903,-0.6779,0.69169,173.06,0.94836,-0.025801,0.31615,202.9,-0.19647,0.7347,0.64932,213.61
    6170 
    6171 > view matrix models
    6172 > #9,-0.29521,-0.62627,0.72155,173.07,0.95342,-0.14413,0.26498,203.06,-0.061948,0.76617,0.63965,213.33
    6173 
    6174 > view matrix models
    6175 > #9,-0.20952,-0.51342,0.83217,173.06,0.97542,-0.05031,0.21455,202.56,-0.068285,0.85666,0.51134,212.57
    6176 
    6177 > view matrix models
    6178 > #9,0.10294,-0.34459,0.93309,172.61,0.93996,0.34057,0.022073,200.66,-0.32539,0.8748,0.35896,212.2
    6179 
    6180 > view matrix models
    6181 > #9,-0.16022,-0.18462,0.96966,172.53,0.98145,0.074958,0.17644,202.03,-0.10526,0.97995,0.16919,210.92
    6182 
    6183 > show #!2 models
    6184 
    6185 > view matrix models
    6186 > #9,-0.15367,-0.25507,0.95464,172.68,0.9497,-0.30492,0.0714,202.82,0.27288,0.91759,0.28909,211.18
    6187 
    6188 > view matrix models
    6189 > #9,-0.5038,0.50581,0.70024,169.74,0.53017,-0.45894,0.71295,206.18,0.68199,0.73043,-0.036959,210.08
    6190 
    6191 > view matrix models
    6192 > #9,-0.57338,0.5803,0.57834,169.11,0.40927,-0.40864,0.81579,206.54,0.70974,0.70446,-0.0031917,210.27
    6193 
    6194 > ui mousemode right "move picked models"
    6195 
    6196 > view matrix models
    6197 > #9,-0.57338,0.5803,0.57834,169.15,0.40927,-0.40864,0.81579,203.59,0.70974,0.70446,-0.0031917,212
    6198 
    6199 > view matrix models
    6200 > #3,0.010117,-0.39918,-0.91682,409.31,0.78121,-0.56916,0.25643,90.718,-0.62418,-0.71883,0.30608,366.04
    6201 
    6202 > view matrix models
    6203 > #3,0.010117,-0.39918,-0.91682,409.6,0.78121,-0.56916,0.25643,90.515,-0.62418,-0.71883,0.30608,366.16
    6204 
    6205 > view matrix models
    6206 > #2,-0.25925,0.42088,0.86928,32.265,0.23342,0.90067,-0.36647,74.017,-0.93718,0.1079,-0.33174,370.87
    6207 
    6208 > ui mousemode right "translate selected models"
    6209 
    6210 > ui mousemode right "rotate selected models"
    6211 
    6212 > view matrix models
    6213 > #9,-0.61844,0.56215,0.54911,169.14,0.3784,-0.39939,0.83505,203.67,0.68873,0.72421,0.034284,212.11
    6214 
    6215 > ui mousemode right "translate selected models"
    6216 
    6217 > view matrix models
    6218 > #9,-0.61844,0.56215,0.54911,177.9,0.3784,-0.39939,0.83505,199.13,0.68873,0.72421,0.034284,214.65
    6219 
    6220 > view matrix models
    6221 > #9,-0.61844,0.56215,0.54911,178.4,0.3784,-0.39939,0.83505,196.45,0.68873,0.72421,0.034284,215.17
    6222 
    6223 > view matrix models
    6224 > #9,-0.61844,0.56215,0.54911,178.59,0.3784,-0.39939,0.83505,195.92,0.68873,0.72421,0.034284,215.89
    6225 
    6226 > ui tool show "Fit in Map"
    6227 
    6228 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    6229 (#2) using 5602 atoms 
    6230 average map value = 0.1891, steps = 236 
    6231 shifted from previous position = 3.82 
    6232 rotated from previous position = 35.5 degrees 
    6233 atoms outside contour = 3840, contour level = 0.26284 
    6234  
    6235 Position of D2NS1.pdb (#3) relative to
    6236 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    6237 Matrix rotation and translation 
    6238 0.97831960 0.09903901 0.18188469 -62.54218727 
    6239 0.12885075 -0.97864261 -0.16017526 308.84298175 
    6240 0.16213651 0.18013858 -0.97018650 260.99607581 
    6241 Axis 0.99452465 0.05771160 0.08712110 
    6242 Axis point 0.00000000 144.84592078 146.67317576 
    6243 Rotation angle (degrees) 170.14858369 
    6244 Shift along axis -21.63765850 
    6245  
    6246 
    6247 > view matrix models
    6248 > #9,-0.61844,0.56215,0.54911,178.56,0.3784,-0.39939,0.83505,195.48,0.68873,0.72421,0.034284,215.15
    6249 
    6250 > ui mousemode right "rotate selected models"
    6251 
    6252 > view matrix models
    6253 > #9,-0.6283,0.53153,0.56808,178.73,0.62001,-0.098962,0.77833,194.1,0.46993,0.84124,-0.26738,213.86
    6254 
    6255 > view matrix models
    6256 > #9,-0.75088,0.39219,0.53138,179.14,0.55722,-0.055683,0.82849,194.22,0.35452,0.9182,-0.17673,214.09
    6257 
    6258 > view matrix models
    6259 > #9,-0.71529,0.36967,0.59305,179.41,0.62601,-0.03822,0.77888,193.91,0.31059,0.92838,-0.20408,214
    6260 
    6261 > ui mousemode right "translate selected models"
    6262 
    6263 > view matrix models
    6264 > #9,-0.71529,0.36967,0.59305,179.34,0.62601,-0.03822,0.77888,198.53,0.31059,0.92838,-0.20408,211.04
    6265 
    6266 > view matrix models
    6267 > #9,-0.71529,0.36967,0.59305,179.34,0.62601,-0.03822,0.77888,198.99,0.31059,0.92838,-0.20408,210.24
    6268 
    6269 > ui mousemode right "rotate selected models"
    6270 
    6271 > view matrix models
    6272 > #9,-0.63893,0.03031,0.76867,180.97,0.76527,0.12677,0.63111,197.77,-0.078317,0.99147,-0.10419,210.83
    6273 
    6274 > select #3/C:2,7,40,94,101,112-114,116,120,122,233
    6275 
    6276 96 atoms, 87 bonds, 12 residues, 1 model selected 
    6277 
    6278 > color sel red
    6279 
    6280 > show #4 models
    6281 
    6282 Average map value = 0.2376 for 3401 atoms, 1878 outside contour 
    6283 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    6284 (#2) using 3401 atoms 
    6285 average map value = 0.2415, steps = 72 
    6286 shifted from previous position = 1.54 
    6287 rotated from previous position = 3.06 degrees 
    6288 atoms outside contour = 1864, contour level = 0.26284 
    6289  
    6290 Position of F562a.pdb (#4) relative to
    6291 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    6292 Matrix rotation and translation 
    6293 0.23699392 -0.97040420 -0.04636322 286.30117001 
    6294 0.14025454 0.08139807 -0.98676390 234.10565599 
    6295 0.96133372 0.22735440 0.15539445 -33.95669350 
    6296 Axis 0.62922896 -0.52224902 0.57561001 
    6297 Axis point 0.00000000 269.86990420 6.31008896 
    6298 Rotation angle (degrees) 105.25448782 
    6299 Shift along axis 38.34172327 
    6300  
    6301 Fit map cryosparc_P47_J128_002_volume_map_sharp.mrc resampled in map
    6302 cryosparc_P47_J20_004_volume_map_sharp.mrc using 81674 points 
    6303 correlation = 0.9169, correlation about mean = 0.5151, overlap = 5213 
    6304 steps = 48, shift = 1.14, angle = 0.0547 degrees 
    6305  
    6306 Position of cryosparc_P47_J128_002_volume_map_sharp.mrc resampled (#7)
    6307 relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    6308 Matrix rotation and translation 
    6309 0.95972235 0.09553744 -0.26420752 39.07093414 
    6310 -0.07396939 0.99315174 0.09043310 -7.28703314 
    6311 0.27103791 -0.06724740 0.96021677 -23.53165945 
    6312 Axis -0.27038667 -0.91782581 -0.29066618 
    6313 Axis point 103.47778140 0.00000000 135.13797870 
    6314 Rotation angle (degrees) 16.95277212 
    6315 Shift along axis 2.96382485 
    6316  
    6317 
    6318 > close #7
    6319 
    6320 > volume #1 level 0.127
    6321 
    6322 > hide #!1 models
    6323 
    6324 > volume #2 level 0.2119
    6325 
    6326 > select #3
    6327 
    6328 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    6329 
    6330 > view matrix models
    6331 > #3,-0.067254,-0.26525,-0.96183,404.94,0.33444,-0.91423,0.22874,235.99,-0.94001,-0.30629,0.1502,378.5
    6332 
    6333 > view matrix models
    6334 > #3,-0.062041,-0.27434,-0.95963,405.16,0.30586,-0.92045,0.24337,239.46,-0.95005,-0.27841,0.14102,377.22
    6335 
    6336 > view matrix models
    6337 > #3,-0.080997,-0.27474,-0.9581,408.29,0.28653,-0.9271,0.24163,244.29,-0.95464,-0.25496,0.15382,371.8
    6338 
    6339 > view matrix models
    6340 > #3,-0.097933,-0.27408,-0.95671,410.91,0.27959,-0.93019,0.23786,246.7,-0.95511,-0.24419,0.16773,367.59
    6341 
    6342 > undo
    6343 
    6344 > view matrix models
    6345 > #3,-0.093936,-0.28928,-0.95262,412.03,0.28743,-0.92399,0.25224,241.72,-0.95318,-0.25012,0.16994,367.86
    6346 
    6347 > view matrix models
    6348 > #3,-0.099224,-0.30095,-0.94846,414.19,0.28616,-0.92153,0.26247,239.7,-0.95303,-0.24537,0.17756,365.67
    6349 
    6350 > select #9
    6351 
    6352 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    6353 
    6354 > ui mousemode right "translate selected models"
    6355 
    6356 > view matrix models
    6357 > #9,-0.63893,0.03031,0.76867,180.02,0.76527,0.12677,0.63111,198.98,-0.078317,0.99147,-0.10419,210.72
    6358 
    6359 > view matrix models
    6360 > #9,-0.63893,0.03031,0.76867,179.9,0.76527,0.12677,0.63111,199.21,-0.078317,0.99147,-0.10419,210.64
    6361 
    6362 > view matrix models
    6363 > #9,-0.63893,0.03031,0.76867,179.76,0.76527,0.12677,0.63111,199.9,-0.078317,0.99147,-0.10419,210.02
    6364 
    6365 > view matrix models
    6366 > #9,-0.63893,0.03031,0.76867,180,0.76527,0.12677,0.63111,200.37,-0.078317,0.99147,-0.10419,210.39
    6367 
    6368 > view matrix models
    6369 > #9,-0.63893,0.03031,0.76867,180.28,0.76527,0.12677,0.63111,200.62,-0.078317,0.99147,-0.10419,210.66
    6370 
    6371 > ui mousemode right "rotate selected models"
    6372 
    6373 > view matrix models
    6374 > #9,-0.6138,0.057604,0.78735,180.24,0.78755,0.11393,0.60562,200.54,-0.054817,0.99182,-0.1153,210.59
    6375 
    6376 > hide #!2 models
    6377 
    6378 > view matrix models
    6379 > #9,-0.57468,0.068825,0.81548,180.27,0.81757,0.092677,0.56833,200.43,-0.036461,0.99331,-0.10953,210.59
    6380 
    6381 > view matrix models
    6382 > #9,-0.55308,0.076775,0.82958,180.28,0.83069,0.12691,0.54207,200.21,-0.063663,0.98894,-0.13397,210.54
    6383 
    6384 > view matrix models
    6385 > #9,-0.59939,0.13134,0.78961,180.01,0.79964,0.14277,0.58326,200.35,-0.036127,0.981,-0.1906,210.32
    6386 
    6387 > view matrix models
    6388 > #9,-0.6287,0.16179,0.76063,179.83,0.77763,0.13788,0.61342,200.5,-0.0056352,0.97715,-0.2125,210.21
    6389 
    6390 > view matrix models
    6391 > #9,-0.66075,0.22875,0.7149,179.49,0.74952,0.14988,0.64479,200.62,0.040346,0.96188,-0.27049,209.99
    6392 
    6393 > view matrix models
    6394 > #9,-0.67709,0.24845,0.69269,179.36,0.73306,0.14512,0.6645,200.72,0.064571,0.95771,-0.28039,209.94
    6395 
    6396 > show #!2 models
    6397 
    6398 > show #!1 models
    6399 
    6400 > hide #!1 models
    6401 
    6402 > ~select #9
    6403 
    6404 Nothing selected 
    6405 
    6406 > volume #2 level 0.1883
    6407 
    6408 > ui mousemode right "translate selected models"
    6409 
    6410 > select #9
    6411 
    6412 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    6413 
    6414 > view matrix models
    6415 > #9,-0.67709,0.24845,0.69269,178.01,0.73306,0.14512,0.6645,202.1,0.064571,0.95771,-0.28039,210.69
    6416 
    6417 > view matrix models
    6418 > #9,-0.67709,0.24845,0.69269,178.34,0.73306,0.14512,0.6645,203.46,0.064571,0.95771,-0.28039,208.74
    6419 
    6420 > ~select #9
    6421 
    6422 Nothing selected 
    6423 
    6424 > hide #!2 models
    6425 
    6426 > show #!2 models
    6427 
    6428 Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
    6429 map cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 3334 atoms 
    6430 average map value = 0.1762, steps = 284 
    6431 shifted from previous position = 2.13 
    6432 rotated from previous position = 46.6 degrees 
    6433 atoms outside contour = 1895, contour level = 0.18834 
    6434  
    6435 Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
    6436 relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    6437 Matrix rotation and translation 
    6438 0.67425254 -0.64675933 -0.35649092 139.61136773 
    6439 0.63282394 0.25716285 0.73034312 159.63361093 
    6440 -0.38068004 -0.71803171 0.58267751 133.55311546 
    6441 Axis -0.74936689 0.01251508 0.66203673 
    6442 Axis point 0.00000000 205.05562824 -10.25332907 
    6443 Rotation angle (degrees) 75.10511823 
    6444 Shift along axis -14.20524073 
    6445  
    6446 
    6447 > undo
    6448 
    6449 > undo
    6450 
    6451 > undo
    6452 
    6453 > ~select #9
    6454 
    6455 Nothing selected 
    6456 
    6457 > volume #2 level 0.2324
    6458 
    6459 Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
    6460 map cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 3334 atoms 
    6461 average map value = 0.1762, steps = 284 
    6462 shifted from previous position = 2.13 
    6463 rotated from previous position = 46.6 degrees 
    6464 atoms outside contour = 2433, contour level = 0.23244 
    6465  
    6466 Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
    6467 relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    6468 Matrix rotation and translation 
    6469 0.67425254 -0.64675933 -0.35649092 139.61136773 
    6470 0.63282394 0.25716285 0.73034312 159.63361093 
    6471 -0.38068004 -0.71803171 0.58267751 133.55311546 
    6472 Axis -0.74936689 0.01251508 0.66203673 
    6473 Axis point 0.00000000 205.05562824 -10.25332907 
    6474 Rotation angle (degrees) 75.10511823 
    6475 Shift along axis -14.20524073 
    6476  
    6477 
    6478 > ui mousemode right "rotate selected models"
    6479 
    6480 > select #9
    6481 
    6482 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    6483 
    6484 > view matrix models
    6485 > #9,-0.51095,-0.017684,0.85943,178.44,0.84026,0.20068,0.50368,202.45,-0.18138,0.9795,-0.087678,211.18
    6486 
    6487 > view matrix models
    6488 > #9,-0.56127,0.054587,0.82583,178.14,0.82479,0.1196,0.55265,202.9,-0.068599,0.99132,-0.11215,210.93
    6489 
    6490 > hide #!2 models
    6491 
    6492 > show #!2 models
    6493 
    6494 > volume #2 level 0.1785
    6495 
    6496 > hide #!2 models
    6497 
    6498 > view matrix models
    6499 > #9,-0.55438,-0.0074968,0.83223,178.35,0.81959,0.16891,0.54748,202.74,-0.14467,0.9856,-0.087495,211.12
    6500 
    6501 > show #!2 models
    6502 
    6503 > hide #!2 models
    6504 
    6505 > view matrix models
    6506 > #9,-0.6081,0.00065434,0.79386,178.23,0.7807,0.18184,0.59786,202.93,-0.14397,0.98333,-0.11109,211.04
    6507 
    6508 > view matrix models
    6509 > #9,-0.60898,-0.00026107,0.79319,178.23,0.7797,0.18341,0.59869,202.93,-0.14563,0.98304,-0.11149,211.04
    6510 
    6511 > view matrix models
    6512 > #9,-0.56366,0.059523,0.82386,178.12,0.81918,0.1683,0.54829,202.74,-0.10602,0.98394,-0.14362,210.87
    6513 
    6514 > view matrix models
    6515 > #9,-0.61089,0.11381,0.78349,177.85,0.79055,0.14142,0.59585,203.04,-0.042985,0.98339,-0.17637,210.68
    6516 
    6517 > show #!2 models
    6518 
    6519 > volume #2 level 0.1908
    6520 
    6521 > view matrix models
    6522 > #9,-0.59527,0.088593,0.79863,177.97,0.80315,0.095932,0.588,203.13,-0.024521,0.99144,-0.12826,210.82
    6523 
    6524 > ui mousemode right "rotate selected models"
    6525 
    6526 > ui mousemode right "translate selected models"
    6527 
    6528 > view matrix models
    6529 > #9,-0.59527,0.088593,0.79863,180.49,0.80315,0.095932,0.588,202.55,-0.024521,0.99144,-0.12826,210.1
    6530 
    6531 > ui mousemode right "rotate selected models"
    6532 
    6533 > view matrix models
    6534 > #9,-0.54746,0.12014,0.82816,180.46,0.83671,0.062088,0.54411,202.45,0.013951,0.99081,-0.13451,210.04
    6535 
    6536 > view matrix models
    6537 > #9,-0.61653,0.1277,0.77691,180.31,0.78731,0.092096,0.60964,202.66,0.0063037,0.98753,-0.15732,209.97
    6538 
    6539 > view matrix models
    6540 > #9,-0.62782,0.073433,0.77489,180.48,0.77517,-0.030986,0.63099,203.13,0.070346,0.99682,-0.03747,210.34
    6541 
    6542 > view matrix models
    6543 > #9,-0.62087,0.053369,0.7821,180.56,0.78091,-0.045216,0.62301,203.14,0.068612,0.99755,-0.013603,210.43
    6544 
    6545 > view matrix models
    6546 > #9,-0.5736,-0.023782,0.81879,180.89,0.81885,0.0096521,0.57392,202.74,-0.021552,0.99967,0.013938,210.62
    6547 
    6548 > ui mousemode right "translate selected models"
    6549 
    6550 > view matrix models
    6551 > #9,-0.5736,-0.023782,0.81879,180.02,0.81885,0.0096521,0.57392,202.98,-0.021552,0.99967,0.013938,210.7
    6552 
    6553 > ui mousemode right "rotate selected models"
    6554 
    6555 > view matrix models
    6556 > #9,-0.57847,0.031132,0.81511,179.85,0.81555,0.041881,0.57717,202.9,-0.01617,0.99864,-0.049616,210.46
    6557 
    6558 > view matrix models
    6559 > #9,-0.56603,-0.015391,0.82424,180.01,0.82431,0.0025727,0.56613,202.97,-0.010834,0.99988,0.011231,210.68
    6560 
    6561 > view matrix models
    6562 > #9,-0.71029,0.24008,0.6617,178.75,0.68817,0.039154,0.72449,203.6,0.14803,0.96996,-0.19303,209.83
    6563 
    6564 > view matrix models
    6565 > #9,-0.68393,0.22919,0.69261,178.88,0.71976,0.056987,0.69188,203.39,0.1191,0.97171,-0.20393,209.81
    6566 
    6567 > ui mousemode right "translate selected models"
    6568 
    6569 > view matrix models
    6570 > #9,-0.68393,0.22919,0.69261,177.76,0.71976,0.056987,0.69188,203.72,0.1191,0.97171,-0.20393,209.9
    6571 
    6572 > view matrix models
    6573 > #9,-0.68393,0.22919,0.69261,177.24,0.71976,0.056987,0.69188,203.81,0.1191,0.97171,-0.20393,210.17
    6574 
    6575 > view matrix models
    6576 > #9,-0.68393,0.22919,0.69261,176.83,0.71976,0.056987,0.69188,203.91,0.1191,0.97171,-0.20393,210.29
    6577 
    6578 > view matrix models
    6579 > #9,-0.68393,0.22919,0.69261,176.71,0.71976,0.056987,0.69188,203.93,0.1191,0.97171,-0.20393,210.32
    6580 
    6581 > view matrix models
    6582 > #9,-0.68393,0.22919,0.69261,177.17,0.71976,0.056987,0.69188,203.92,0.1191,0.97171,-0.20393,210.31
    6583 
    6584 > view matrix models
    6585 > #9,-0.68393,0.22919,0.69261,177.48,0.71976,0.056987,0.69188,203.79,0.1191,0.97171,-0.20393,210.28
    6586 
    6587 > view matrix models
    6588 > #9,-0.68393,0.22919,0.69261,177.92,0.71976,0.056987,0.69188,203.73,0.1191,0.97171,-0.20393,210.27
    6589 
    6590 > view matrix models
    6591 > #9,-0.68393,0.22919,0.69261,177.96,0.71976,0.056987,0.69188,203.75,0.1191,0.97171,-0.20393,210.29
    6592 
    6593 > view matrix models
    6594 > #9,-0.68393,0.22919,0.69261,177.7,0.71976,0.056987,0.69188,203.84,0.1191,0.97171,-0.20393,210.22
    6595 
    6596 > ui mousemode right "rotate selected models"
    6597 
    6598 > view matrix models
    6599 > #9,-0.64555,0.14914,0.74902,178.12,0.76365,0.11273,0.63571,203.41,0.010372,0.98237,-0.18667,210.37
    6600 
    6601 > ~select #9
    6602 
    6603 Nothing selected 
    6604 
    6605 > hide #!2 models
    6606 
    6607 > show #!2 models
    6608 
    6609 > select #9
    6610 
    6611 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    6612 
    6613 > view matrix models
    6614 > #9,-0.39517,0.13421,0.90875,178.52,0.91486,0.1468,0.37614,202.16,-0.082923,0.98002,-0.18079,210.49
    6615 
    6616 > ui mousemode right "translate selected models"
    6617 
    6618 > view matrix models
    6619 > #9,-0.39517,0.13421,0.90875,178.76,0.91486,0.1468,0.37614,202.52,-0.082923,0.98002,-0.18079,210.02
    6620 
    6621 > view matrix models
    6622 > #9,-0.39517,0.13421,0.90875,178.91,0.91486,0.1468,0.37614,202.6,-0.082923,0.98002,-0.18079,209.94
    6623 
    6624 > view matrix models
    6625 > #9,-0.39517,0.13421,0.90875,178.84,0.91486,0.1468,0.37614,202.6,-0.082923,0.98002,-0.18079,209.69
    6626 
    6627 > view matrix models
    6628 > #9,-0.39517,0.13421,0.90875,178.58,0.91486,0.1468,0.37614,202.13,-0.082923,0.98002,-0.18079,210.55
    6629 
    6630 > view matrix models
    6631 > #9,-0.39517,0.13421,0.90875,178.72,0.91486,0.1468,0.37614,203.01,-0.082923,0.98002,-0.18079,210.68
    6632 
    6633 > ui mousemode right "rotate selected models"
    6634 
    6635 > view matrix models
    6636 > #9,-0.44867,0.076406,0.89043,178.88,0.88471,0.17889,0.43044,203.15,-0.1264,0.9809,-0.14786,210.85
    6637 
    6638 > ~select #9
    6639 
    6640 Nothing selected 
    6641 
    6642 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    6643 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    6644 
    6645 ——— End of log from Thu Mar 3 21:24:07 2022 ———
    6646 
    6647 opened ChimeraX session 
    6648 
    6649 > ui tool show ViewDockX
    6650 
    6651 No suitable models found for ViewDockX 
    6652 
    6653 > ui tool show "Show Sequence Viewer"
    6654 
    6655 > sequence chain #3/B #3/C
    6656 
    6657 Alignment identifier is 1 
    6658 
    6659 > select #3/B-C:1
    6660 
    6661 16 atoms, 14 bonds, 2 residues, 1 model selected 
    6662 
    6663 > select #3/B-C:1-36
    6664 
    6665 582 atoms, 598 bonds, 72 residues, 1 model selected 
    6666 
    6667 > hide #!2 models
    6668 
    6669 > hide #9 models
    6670 
    6671 > select #3/B-C:1
    6672 
    6673 16 atoms, 14 bonds, 2 residues, 1 model selected 
    6674 
    6675 > select #3/B-C:1-31
    6676 
    6677 486 atoms, 496 bonds, 62 residues, 1 model selected 
    6678 
    6679 > select #3/B-C:1-2
    6680 
    6681 28 atoms, 26 bonds, 4 residues, 1 model selected 
    6682 
    6683 > select #3/B-C:1-28
    6684 
    6685 436 atoms, 446 bonds, 56 residues, 1 model selected 
    6686 
    6687 > select #3/B-C:25
    6688 
    6689 14 atoms, 12 bonds, 2 residues, 1 model selected 
    6690 
    6691 > select #3/B-C:1-25
    6692 
    6693 374 atoms, 378 bonds, 50 residues, 1 model selected 
    6694 
    6695 > color sel orange
    6696 
    6697 > select #3/B-C:32-33
    6698 
    6699 42 atoms, 42 bonds, 4 residues, 1 model selected 
    6700 
    6701 > select #3/B-C:32-139
    6702 
    6703 1726 atoms, 1764 bonds, 216 residues, 1 model selected 
    6704 
    6705 > select #3/B-C:32
    6706 
    6707 24 atoms, 24 bonds, 2 residues, 1 model selected 
    6708 
    6709 > select #3/B-C:32-144
    6710 
    6711 1794 atoms, 1834 bonds, 226 residues, 1 model selected 
    6712 
    6713 > select #3/B-C:32
    6714 
    6715 24 atoms, 24 bonds, 2 residues, 1 model selected 
    6716 
    6717 > select #3/B-C:32-150
    6718 
    6719 1900 atoms, 1944 bonds, 238 residues, 1 model selected 
    6720 
    6721 > select #3/B-C:32
    6722 
    6723 24 atoms, 24 bonds, 2 residues, 1 model selected 
    6724 
    6725 > select #3/B-C:32-159
    6726 
    6727 2042 atoms, 2088 bonds, 256 residues, 1 model selected 
    6728 
    6729 > select #3/B-C:32
    6730 
    6731 24 atoms, 24 bonds, 2 residues, 1 model selected 
    6732 
    6733 > select #3/B-C:32-171
    6734 
    6735 2246 atoms, 2300 bonds, 280 residues, 1 model selected 
    6736 
    6737 > select #3/B-C:23
    6738 
    6739 16 atoms, 14 bonds, 2 residues, 1 model selected 
    6740 
    6741 > select #3/B-C:23-171
    6742 
    6743 2404 atoms, 2464 bonds, 298 residues, 1 model selected 
    6744 
    6745 > select #3/B-C:26
    6746 
    6747 20 atoms, 20 bonds, 2 residues, 1 model selected 
    6748 
    6749 > select #3/B-C:26-171
    6750 
    6751 2358 atoms, 2418 bonds, 292 residues, 1 model selected 
    6752 
    6753 > select #3/B-C:172
    6754 
    6755 18 atoms, 16 bonds, 2 residues, 1 model selected 
    6756 
    6757 > select #3/B-C:26-172
    6758 
    6759 2376 atoms, 2436 bonds, 294 residues, 1 model selected 
    6760 
    6761 > select #3/B-C:174
    6762 
    6763 22 atoms, 20 bonds, 2 residues, 1 model selected 
    6764 
    6765 > select #3/B-C:26-174
    6766 
    6767 2416 atoms, 2476 bonds, 298 residues, 1 model selected 
    6768 
    6769 > color sel medium blue
    6770 
    6771 > color sel blue
    6772 
    6773 > select #3
    6774 
    6775 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    6776 
    6777 > ~select #3
    6778 
    6779 Nothing selected 
    6780 
    6781 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    6782 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    6783 > includeMaps true
    6784 
    6785 > show #!1 models
    6786 
    6787 > show #!2 models
    6788 
    6789 > hide #!1 models
    6790 
    6791 > volume #2 level 0.2959
    6792 
    6793 > volume #2 level 0.3364
    6794 
    6795 > volume #2 level 0.1382
    6796 
    6797 > ui mousemode right "map eraser"
    6798 
    6799 > volume erase #2 center 237.19,212.38,256.03 radius 33.098
    6800 
    6801 > volume #2 level 0.1382
    6802 
    6803 > volume erase #2 center 169.45,251.87,161.34 radius 16.218
    6804 
    6805 > volume erase #2 center 169.29,250.35,162.17 radius 16.218
    6806 
    6807 > volume erase #2 center 178.55,248.01,162.61 radius 16.218
    6808 
    6809 > volume erase #2 center 193.98,241.53,160.53 radius 16.218
    6810 
    6811 > volume erase #2 center 199.47,236.96,159.26 radius 16.218
    6812 
    6813 > volume erase #2 center 162.44,240.05,168.47 radius 10.426
    6814 
    6815 > volume erase #2 center 192.43,185.48,150.8 radius 10.426
    6816 
    6817 > volume erase #2 center 222.56,163.1,224.04 radius 10.426
    6818 
    6819 > volume erase #2 center 210.8,157.36,204.71 radius 4.3027
    6820 
    6821 > volume erase #2 center 213.21,164.78,209.75 radius 4.3027
    6822 
    6823 > volume erase #2 center 213.74,163.67,210.79 radius 4.3027
    6824 
    6825 > volume erase #2 center 140.42,146.88,222.98 radius 7.2815
    6826 
    6827 > volume erase #2 center 143.97,147.47,221.25 radius 7.2815
    6828 
    6829 > volume erase #2 center 148.25,145.4,219.55 radius 7.2815
    6830 
    6831 > volume erase #2 center 152.8,142.67,217.68 radius 7.2815
    6832 
    6833 > volume erase #2 center 152.46,140.9,223.5 radius 7.2815
    6834 
    6835 > volume erase #2 center 139.51,151.13,215.18 radius 7.2815
    6836 
    6837 > volume erase #2 center 146.44,146.78,211.4 radius 7.2815
    6838 
    6839 > volume erase #2 center 152.32,144.56,208.69 radius 7.2815
    6840 
    6841 > volume erase #2 center 146.84,150.8,208.72 radius 7.2815
    6842 
    6843 > volume erase #2 center 152.17,153.98,201.44 radius 7.2815
    6844 
    6845 > hide #!2 models
    6846 
    6847 > show #!2 models
    6848 
    6849 > volume #2 level 0.3838
    6850 
    6851 > volume #2 level 0.2253
    6852 
    6853 > volume #2 level 0.0986
    6854 
    6855 > volume #2 level 0.01
    6856 
    6857 > volume #2 level 0.001
    6858 
    6859 > volume #2 level 0.1
    6860 
    6861 > volume #2 level 0.1475
    6862 
    6863 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    6864 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    6865 
    6866 > color #3-4 bypolymer
    6867 
    6868 > undo
    6869 
    6870 > lighting flat
    6871 
    6872 > lighting shadows true intensity 0.5
    6873 
    6874 > graphics silhouettes false
    6875 
    6876 > graphics silhouettes true
    6877 
    6878 > lighting shadows false
    6879 
    6880 > lighting shadows true
    6881 
    6882 > lighting shadows false
    6883 
    6884 > ui tool show "Fit in Map"
    6885 
    6886 > hide #3 models
    6887 
    6888 > show #3 models
    6889 
    6890 > show #5 models
    6891 
    6892 > hide #5 models
    6893 
    6894 > select #3
    6895 
    6896 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    6897 
    6898 > ui mousemode right "translate selected models"
    6899 
    6900 > view matrix models
    6901 > #3,-0.099224,-0.30095,-0.94846,413.97,0.28616,-0.92153,0.26247,239.58,-0.95303,-0.24537,0.17756,365.68
    6902 
    6903 > view matrix models
    6904 > #3,-0.099224,-0.30095,-0.94846,414.09,0.28616,-0.92153,0.26247,239.88,-0.95303,-0.24537,0.17756,365.5
    6905 
    6906 > view matrix models
    6907 > #3,-0.099224,-0.30095,-0.94846,414.1,0.28616,-0.92153,0.26247,239.98,-0.95303,-0.24537,0.17756,365.39
    6908 
    6909 > ui mousemode right "rotate selected models"
    6910 
    6911 > view matrix models
    6912 > #3,-0.098121,-0.30274,-0.94801,414.12,0.28638,-0.9209,0.26444,239.49,-0.95308,-0.24554,0.17706,365.52
    6913 
    6914 > view matrix models
    6915 > #3,-0.10399,-0.29321,-0.95038,413.98,0.28519,-0.92422,0.25393,242.13,-0.95281,-0.24463,0.17973,364.84
    6916 
    6917 > view matrix models
    6918 > #3,-0.10804,-0.25387,-0.96119,410,0.28731,-0.93356,0.21428,250.39,-0.95173,-0.25301,0.1738,367.12
    6919 
    6920 > view matrix models
    6921 > #3,-0.089326,-0.26965,-0.95881,408.94,0.27746,-0.93128,0.23606,247.86,-0.95658,-0.24494,0.15801,369.43
    6922 
    6923 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    6924 (#1) using 5602 atoms 
    6925 average map value = 0.07054, steps = 76 
    6926 shifted from previous position = 1.56 
    6927 rotated from previous position = 7.95 degrees 
    6928 atoms outside contour = 4416, contour level = 0.12697 
    6929  
    6930 Position of D2NS1.pdb (#3) relative to
    6931 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    6932 Matrix rotation and translation 
    6933 0.01853403 0.20523285 0.97853769 -30.97334856 
    6934 0.00646830 0.97866071 -0.20538117 45.38206352 
    6935 -0.99980733 0.01013602 0.01681102 356.85899567 
    6936 Axis 0.10776124 0.98919674 -0.09938471 
    6937 Axis point 163.99516504 0.00000000 196.80902229 
    6938 Rotation angle (degrees) 89.59876110 
    6939 Shift along axis 6.08773536 
    6940  
    6941 
    6942 > select #4
    6943 
    6944 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    6945 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    6946 (#1) using 3401 atoms 
    6947 average map value = 0.1044, steps = 92 
    6948 shifted from previous position = 1.81 
    6949 rotated from previous position = 8.09 degrees 
    6950 atoms outside contour = 2312, contour level = 0.12697 
    6951  
    6952 Position of F562a.pdb (#4) relative to
    6953 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    6954 Matrix rotation and translation 
    6955 -0.87188277 -0.47824853 0.10535086 355.37302112 
    6956 0.20869056 -0.16823549 0.96340288 57.21596158 
    6957 -0.44302225 0.86196009 0.24648757 74.93473678 
    6958 Axis -0.11464921 0.61976358 0.77636889 
    6959 Axis point 179.54922209 52.98960138 0.00000000 
    6960 Rotation angle (degrees) 153.74256446 
    6961 Shift along axis 52.89413028 
    6962  
    6963 
    6964 > view matrix models
    6965 > #4,0.86605,0.44369,-0.23043,24.081,-0.15116,-0.20695,-0.9666,357.32,-0.47656,0.87196,-0.11216,122.76
    6966 
    6967 > view matrix models
    6968 > #4,0.24178,-0.10097,-0.96506,327.04,0.9586,-0.12931,0.25369,-9.1181,-0.15041,-0.98645,0.065523,378.67
    6969 
    6970 > view matrix models
    6971 > #4,0.29714,-0.29814,-0.9071,345.67,0.95329,0.14663,0.26408,-59.546,0.054273,-0.94319,0.32778,301.43
    6972 
    6973 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    6974 (#1) using 3401 atoms 
    6975 average map value = 0.1127, steps = 320 
    6976 shifted from previous position = 4.37 
    6977 rotated from previous position = 11.4 degrees 
    6978 atoms outside contour = 2213, contour level = 0.12697 
    6979  
    6980 Position of F562a.pdb (#4) relative to
    6981 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    6982 Matrix rotation and translation 
    6983 -0.22359030 0.19234587 0.95551582 13.46864170 
    6984 -0.96386692 0.10200874 -0.24607887 369.19247060 
    6985 -0.14480322 -0.97601092 0.16258766 360.07001914 
    6986 Axis -0.41589505 0.62693129 -0.65877801 
    6987 Axis point 62.48187352 351.98959539 0.00000000 
    6988 Rotation angle (degrees) 118.65255170 
    6989 Shift along axis -11.34943811 
    6990  
    6991 
    6992 > hide #!2 models
    6993 
    6994 > show #!2 models
    6995 
    6996 > hide #!2 models
    6997 
    6998 > show #5 models
    6999 
    7000 > hide #5 models
    7001 
    7002 > show #!2 models
    7003 
    7004 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    7005 (#1) using 3401 atoms 
    7006 average map value = 0.1127, steps = 44 
    7007 shifted from previous position = 0.0117 
    7008 rotated from previous position = 0.0621 degrees 
    7009 atoms outside contour = 2215, contour level = 0.12697 
    7010  
    7011 Position of F562a.pdb (#4) relative to
    7012 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    7013 Matrix rotation and translation 
    7014 -0.22386136 0.19222999 0.95547567 13.54489824 
    7015 -0.96395914 0.10094242 -0.24615736 369.41500556 
    7016 -0.14376685 -0.97614461 0.16270474 359.89902128 
    7017 Axis -0.41608471 0.62655616 -0.65901510 
    7018 Axis point 62.46779097 351.82779571 0.00000000 
    7019 Rotation angle (degrees) 118.69239674 
    7020 Shift along axis -11.35546781 
    7021  
    7022 
    7023 > ui mousemode right "translate selected models"
    7024 
    7025 > view matrix models
    7026 > #4,0.25124,-0.17542,-0.9519,335.64,0.9404,0.27709,0.19714,-70.324,0.22917,-0.9447,0.23458,277.59
    7027 
    7028 > view matrix models
    7029 > #4,0.25124,-0.17542,-0.9519,335.72,0.9404,0.27709,0.19714,-70.489,0.22917,-0.9447,0.23458,277.37
    7030 
    7031 > view matrix models
    7032 > #4,0.25124,-0.17542,-0.9519,336.84,0.9404,0.27709,0.19714,-70.794,0.22917,-0.9447,0.23458,276.49
    7033 
    7034 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    7035 (#1) using 3401 atoms 
    7036 average map value = 0.1127, steps = 60 
    7037 shifted from previous position = 2.03 
    7038 rotated from previous position = 0.0879 degrees 
    7039 atoms outside contour = 2217, contour level = 0.12697 
    7040  
    7041 Position of F562a.pdb (#4) relative to
    7042 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    7043 Matrix rotation and translation 
    7044 -0.22340595 0.19254318 0.95551920 13.40638758 
    7045 -0.96384599 0.10241826 -0.24599073 369.10197141 
    7046 -0.14522645 -0.97592912 0.16270112 360.10914844 
    7047 Axis -0.41580714 0.62703635 -0.65873351 
    7048 Axis point 62.50395161 352.02889088 0.00000000 
    7049 Rotation angle (degrees) 118.62946316 
    7050 Shift along axis -11.35008346 
    7051  
    7052 
    7053 > ui tool show "Show Sequence Viewer"
    7054 
    7055 > sequence chain #4/C
    7056 
    7057 Alignment identifier is 4/C 
    7058 
    7059 > ui tool show "Show Sequence Viewer"
    7060 
    7061 > sequence chain #4/B
    7062 
    7063 Alignment identifier is 4/B 
    7064 
    7065 > select #4/B:1
    7066 
    7067 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7068 
    7069 > select #4/B:1-228
    7070 
    7071 1769 atoms, 1825 bonds, 228 residues, 1 model selected 
    7072 
    7073 > color sel forest green
    7074 
    7075 > hide #!2 models
    7076 
    7077 > ui tool show "Color Actions"
    7078 
    7079 > color sel forest green
    7080 
    7081 > color sel #e0fff2ff
    7082 
    7083 > color sel #defff1ff
    7084 
    7085 > color sel #c2ffcdff
    7086 
    7087 > color sel #79ff7dff
    7088 
    7089 > color sel #00ff05ff
    7090 
    7091 > color sel #00ff07ff
    7092 
    7093 > color sel #00ff09ff
    7094 
    7095 > color sel #00ff07ff
    7096 
    7097 [Repeated 1 time(s)]
    7098 
    7099 > color sel #00f707ff
    7100 
    7101 > color sel #00f507ff
    7102 
    7103 > color sel #00f407ff
    7104 
    7105 > color sel #00f307ff
    7106 
    7107 > color sel #00f107ff
    7108 
    7109 > color sel #00eb07ff
    7110 
    7111 > color sel #00e907ff
    7112 
    7113 > color sel #00e707ff
    7114 
    7115 > color sel #00e106ff
    7116 
    7117 > color sel #00dd06ff
    7118 
    7119 > color sel #00db06ff
    7120 
    7121 > color sel #00d906ff
    7122 
    7123 > color sel #00d806ff
    7124 
    7125 [Repeated 1 time(s)]
    7126 
    7127 > color sel #00d606ff
    7128 
    7129 > color sel #00d006ff
    7130 
    7131 > color sel #00c706ff
    7132 
    7133 > color sel #00c205ff
    7134 
    7135 > color sel #00b905ff
    7136 
    7137 > color sel #00b305ff
    7138 
    7139 > color sel #00ab05ff
    7140 
    7141 > color sel #00a605ff
    7142 
    7143 > color sel #009d04ff
    7144 
    7145 > color sel #009a04ff
    7146 
    7147 > color sel #009604ff
    7148 
    7149 > color sel #009404ff
    7150 
    7151 > color sel #009204ff
    7152 
    7153 > color sel #009104ff
    7154 
    7155 > color sel #008f04ff
    7156 
    7157 > color sel #008e04ff
    7158 
    7159 [Repeated 1 time(s)]
    7160 
    7161 > color sel #008d04ff
    7162 
    7163 > color sel #008a04ff
    7164 
    7165 [Repeated 1 time(s)]
    7166 
    7167 > color sel #008804ff
    7168 
    7169 > color sel #008704ff
    7170 
    7171 > color sel #008604ff
    7172 
    7173 > color sel #008504ff
    7174 
    7175 [Repeated 1 time(s)]
    7176 
    7177 > color sel #008304ff
    7178 
    7179 > color sel #008204ff
    7180 
    7181 > color sel #007f04ff
    7182 
    7183 > color sel #007903ff
    7184 
    7185 > color sel #007303ff
    7186 
    7187 > color sel #006f03ff
    7188 
    7189 > color sel #006e03ff
    7190 
    7191 > color sel #006d03ff
    7192 
    7193 > color sel #006c03ff
    7194 
    7195 > color sel #006803ff
    7196 
    7197 > color sel #005f03ff
    7198 
    7199 > color sel #005c03ff
    7200 
    7201 [Repeated 1 time(s)]
    7202 
    7203 > color sel #005d03ff
    7204 
    7205 > color sel #005e03ff
    7206 
    7207 [Repeated 1 time(s)]
    7208 
    7209 > color sel #005f03ff
    7210 
    7211 > color sel #006003ff
    7212 
    7213 [Repeated 2 time(s)]
    7214 
    7215 > color sel #006103ff
    7216 
    7217 [Repeated 2 time(s)]
    7218 
    7219 > color sel #006203ff
    7220 
    7221 [Repeated 3 time(s)]
    7222 
    7223 > color sel #006103ff
    7224 
    7225 [Repeated 2 time(s)]
    7226 
    7227 > color sel #006003ff
    7228 
    7229 [Repeated 1 time(s)]
    7230 
    7231 > color sel #005f03ff
    7232 
    7233 [Repeated 1 time(s)]
    7234 
    7235 > color sel #005e03ff
    7236 
    7237 [Repeated 1 time(s)]
    7238 
    7239 > color sel #005d03ff
    7240 
    7241 [Repeated 1 time(s)]
    7242 
    7243 > color sel #005b03ff
    7244 
    7245 [Repeated 1 time(s)]
    7246 
    7247 > color sel #005a03ff
    7248 
    7249 [Repeated 1 time(s)]
    7250 
    7251 > color sel #005c03ff
    7252 
    7253 > select #4
    7254 
    7255 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    7256 
    7257 > ~select #4
    7258 
    7259 Nothing selected 
    7260 
    7261 > show #!2 models
    7262 
    7263 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    7264 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    7265 > includeMaps true
    7266 
    7267 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    7268 > (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C1.png"
    7269 > width 854 height 684 supersample 3 transparentBackground true
    7270 
    7271 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    7272 > (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C2.png"
    7273 > width 1167 height 801 supersample 3
    7274 
    7275 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    7276 > (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C2.png"
    7277 > width 1167 height 801 supersample 3 transparentBackground true
    7278 
    7279 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    7280 > (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C3.png"
    7281 > width 1167 height 801 supersample 3 transparentBackground true
    7282 
    7283 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    7284 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    7285 > includeMaps true
    7286 
    7287 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    7288 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    7289 > sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J90_005_volume_map_sharp.mrc
    7290 
    7291 Opened cryosparc_P35_J90_005_volume_map_sharp.mrc as #6, grid size
    7292 416,416,416, pixel 0.858, shown at level 0.0366, step 2, values float32 
    7293 
    7294 > hide #4 models
    7295 
    7296 > hide #3 models
    7297 
    7298 > volume #6 step 1
    7299 
    7300 > volume #6 level 0.05781
    7301 
    7302 > lighting flat
    7303 
    7304 > lighting shadows true intensity 0.5
    7305 
    7306 > lighting shadows false
    7307 
    7308 > graphics silhouettes false
    7309 
    7310 > lighting simple
    7311 
    7312 > volume #6 level 0.08608
    7313 
    7314 > volume #6 level 0.1744
    7315 
    7316 > volume #6 level 0.07548
    7317 
    7318 > volume #6 level 0.06841
    7319 
    7320 > volume #6 level 0.08255
    7321 
    7322 > color #6 #bfb700 models transparency 0
    7323 
    7324 > color #6 #bfb70039 models
    7325 
    7326 > color #6 #bfb70028 models
    7327 
    7328 > color #6 #fff40028 models
    7329 
    7330 > color #6 #33300028 models
    7331 
    7332 > color #6 #b4ac0028 models
    7333 
    7334 > color #6 #b4ac00 models transparency 0
    7335 
    7336 > color #6 #fff400 models transparency 0
    7337 
    7338 > color #6 #f0e500 models transparency 0
    7339 
    7340 > color #6 #f0e65a models transparency 0
    7341 
    7342 > color #6 #c3bb49 models transparency 0
    7343 
    7344 > color #6 #c3bb499a models
    7345 
    7346 > color #6 #c3bb4941 models
    7347 
    7348 > color #6 #c3bb4942 models
    7349 
    7350 > color #6 #fffb00 models transparency 0
    7351 
    7352 > color #6 #fffb0044 models
    7353 
    7354 > color #6 #fffb0016 models
    7355 
    7356 > color #6 #fffb0033 models
    7357 
    7358 > color #6 #fffc79 models transparency 0
    7359 
    7360 > color #6 #fffc7932 models
    7361 
    7362 > color #6 #fffc7943 models
    7363 
    7364 > color #6 #fffc794c models
    7365 
    7366 > color #6 #fffc794d models
    7367 
    7368 > select #6
    7369 
    7370 2 models selected 
    7371 
    7372 > ui mousemode right "rotate selected models"
    7373 
    7374 > view matrix models
    7375 > #6,0.022009,-0.94973,0.31229,283.41,-0.71721,-0.23262,-0.65689,470,0.69651,-0.20952,-0.68628,231.36
    7376 
    7377 > view matrix models
    7378 > #6,0.48413,-0.86475,0.13353,218.33,-0.43491,-0.37024,-0.82084,473.48,0.75926,0.33932,-0.55533,99.971
    7379 
    7380 > view matrix models
    7381 > #6,-0.32751,-0.77901,0.53468,275.33,-0.92972,0.16487,-0.32929,377.53,0.16837,-0.60495,-0.77826,413.98
    7382 
    7383 > view matrix models
    7384 > #6,-0.2755,-0.92018,0.27814,339.29,-0.85315,0.10072,-0.51185,409.53,0.44298,-0.37831,-0.8128,331.15
    7385 
    7386 > view matrix models
    7387 > #6,0.69873,-0.70402,0.127,152.52,0.37445,0.20866,-0.90346,241.09,0.60956,0.67883,0.40942,-115.9
    7388 
    7389 > view matrix models
    7390 > #6,0.45295,-0.31947,0.83233,-3.9083,0.64601,-0.52579,-0.55337,251.33,0.61441,0.78834,-0.031778,-51.296
    7391 
    7392 > ui mousemode right "translate selected models"
    7393 
    7394 > view matrix models
    7395 > #6,0.45295,-0.31947,0.83233,16.369,0.64601,-0.52579,-0.55337,269.43,0.61441,0.78834,-0.031778,-42.833
    7396 
    7397 > view matrix models
    7398 > #6,0.45295,-0.31947,0.83233,16.57,0.64601,-0.52579,-0.55337,267.55,0.61441,0.78834,-0.031778,-43.336
    7399 
    7400 > view matrix models
    7401 > #6,0.45295,-0.31947,0.83233,17.018,0.64601,-0.52579,-0.55337,268.42,0.61441,0.78834,-0.031778,-43.438
    7402 
    7403 > view matrix models
    7404 > #6,0.45295,-0.31947,0.83233,13.457,0.64601,-0.52579,-0.55337,265.98,0.61441,0.78834,-0.031778,-43.237
    7405 
    7406 > view matrix models
    7407 > #6,0.45295,-0.31947,0.83233,13.708,0.64601,-0.52579,-0.55337,267.25,0.61441,0.78834,-0.031778,-43.377
    7408 
    7409 > view matrix models
    7410 > #6,0.45295,-0.31947,0.83233,13.833,0.64601,-0.52579,-0.55337,266.18,0.61441,0.78834,-0.031778,-42.937
    7411 
    7412 > view matrix models
    7413 > #6,0.45295,-0.31947,0.83233,14.199,0.64601,-0.52579,-0.55337,266.61,0.61441,0.78834,-0.031778,-44.947
    7414 
    7415 > volume #2 color #b8b5af4b
    7416 
    7417 > volume #2 color #b8b5af4d
    7418 
    7419 > show #3 models
    7420 
    7421 > hide #!2 models
    7422 
    7423 > volume #6 level 0.2239
    7424 
    7425 > ui mousemode right "rotate selected models"
    7426 
    7427 > view matrix models
    7428 > #6,-0.29246,-0.71165,0.63876,258.29,-0.85627,-0.10251,-0.50625,462.3,0.42576,-0.69501,-0.57939,354.66
    7429 
    7430 > view matrix models
    7431 > #6,-0.47549,-0.59046,0.65212,268.57,-0.79255,-0.034193,-0.60885,458.81,0.3818,-0.80634,-0.45171,357.01
    7432 
    7433 > view matrix models
    7434 > #6,-0.34414,-0.36794,0.86382,164.08,-0.77861,-0.40232,-0.48157,495.02,0.52473,-0.8383,-0.14803,276.41
    7435 
    7436 > ui mousemode right "translate selected models"
    7437 
    7438 > view matrix models
    7439 > #6,-0.34414,-0.36794,0.86382,151.79,-0.77861,-0.40232,-0.48157,494.89,0.52473,-0.8383,-0.14803,279.06
    7440 
    7441 > view matrix models
    7442 > #6,-0.34414,-0.36794,0.86382,151.48,-0.77861,-0.40232,-0.48157,494.87,0.52473,-0.8383,-0.14803,277.43
    7443 
    7444 > volume #6 level 0.1673
    7445 
    7446 > view matrix models
    7447 > #6,-0.34414,-0.36794,0.86382,149.97,-0.77861,-0.40232,-0.48157,494.85,0.52473,-0.8383,-0.14803,278.57
    7448 
    7449 > view matrix models
    7450 > #6,-0.34414,-0.36794,0.86382,150.29,-0.77861,-0.40232,-0.48157,492.94,0.52473,-0.8383,-0.14803,277.18
    7451 
    7452 > ui mousemode right "rotate selected models"
    7453 
    7454 > view matrix models
    7455 > #6,-0.34656,-0.40224,0.84741,159.86,-0.77344,-0.38862,-0.50077,493.34,0.53075,-0.82896,-0.17642,279.97
    7456 
    7457 > view matrix models
    7458 > #6,-0.31668,-0.43946,0.84059,162.15,-0.77551,-0.39032,-0.49622,493.13,0.54617,-0.80903,-0.2172,281.6
    7459 
    7460 > view matrix models
    7461 > #6,-0.32094,-0.45467,0.83083,167.46,-0.7722,-0.38228,-0.5075,493.32,0.54836,-0.80445,-0.22841,282.58
    7462 
    7463 > view matrix models
    7464 > #6,-0.20123,-0.51264,0.83469,154.78,0.96454,0.044877,0.2601,-48.467,-0.1708,0.85743,0.48543,-11.902
    7465 
    7466 > view matrix models
    7467 > #6,-0.19126,-0.46003,0.86706,137.55,0.78245,0.46189,0.41766,-117.87,-0.59262,0.75831,0.27161,124.2
    7468 
    7469 > view matrix models
    7470 > #6,-0.16309,-0.47088,0.86699,134.27,0.77568,0.48185,0.40761,-118.14,-0.6097,0.73898,0.28667,127.76
    7471 
    7472 > ui mousemode right "move picked models"
    7473 
    7474 > view matrix models
    7475 > #6,-0.16309,-0.47088,0.86699,134.42,0.77568,0.48185,0.40761,-149.14,-0.6097,0.73898,0.28667,101.11
    7476 
    7477 > view matrix models
    7478 > #3,0.001066,-0.23035,-0.97311,385.86,0.36811,-0.90469,0.21456,228.51,-0.92978,-0.35844,0.08383,403.03
    7479 
    7480 > ui mousemode right "rotate selected models"
    7481 
    7482 > view matrix models
    7483 > #6,-0.043523,-0.55853,0.82834,135.17,0.777,0.50225,0.37948,-147.46,-0.62799,0.66014,0.41212,93.77
    7484 
    7485 > view matrix models
    7486 > #6,-0.13478,-0.49296,0.85955,134.49,0.77638,0.48647,0.40073,-148.74,-0.61569,0.72134,0.31716,99.344
    7487 
    7488 > view matrix models
    7489 > #6,0.96181,-0.16288,-0.21999,85.595,0.2594,0.79899,0.54252,-135.51,0.087404,-0.57887,0.81072,99.737
    7490 
    7491 > show #4 models
    7492 
    7493 > view matrix models
    7494 > #6,0.67607,-0.69317,-0.24988,235.71,0.28695,0.56004,-0.77719,157.01,0.67866,0.45373,0.57753,-142.42
    7495 
    7496 > view matrix models
    7497 > #6,0.24716,-0.80723,0.536,181.65,0.88374,0.41465,0.21697,-120.33,-0.39739,0.42006,0.81586,14.664
    7498 
    7499 > view matrix models
    7500 > #6,-0.091274,-0.52365,0.84703,134.26,0.8991,0.32235,0.29617,-122.53,-0.42813,0.7886,0.44139,29.149
    7501 
    7502 > view matrix models
    7503 > #6,-0.11554,-0.4685,0.87587,123.56,0.69127,0.59529,0.40961,-153.69,-0.7133,0.65279,0.25508,141.19
    7504 
    7505 > view matrix models
    7506 > #6,-0.046411,-0.35281,0.93454,79.438,0.59316,0.74302,0.30997,-141.93,-0.80374,0.56872,0.17479,187.94
    7507 
    7508 > view matrix models
    7509 > #6,-0.069072,-0.35388,0.93274,84.134,0.6004,0.73194,0.32216,-143.71,-0.79671,0.58226,0.16191,186.8
    7510 
    7511 > view matrix models
    7512 > #6,-0.057044,-0.36632,0.92874,84.856,0.64945,0.69291,0.31319,-144.21,-0.75826,0.62103,0.19838,165.95
    7513 
    7514 > view matrix models
    7515 > #6,-0.079957,-0.35928,0.9298,87.636,0.65299,0.68589,0.32118,-145.19,-0.75313,0.63283,0.17976,166.58
    7516 
    7517 > view matrix models
    7518 > #6,-0.1341,-0.37541,0.91711,102.83,0.65851,0.65782,0.36557,-149.96,-0.74053,0.65295,0.159,164.81
    7519 
    7520 > view matrix models
    7521 > #6,-0.12427,-0.37199,0.91988,99.899,0.65174,0.66844,0.35836,-149.16,-0.74819,0.64406,0.15938,167.68
    7522 
    7523 > view matrix models
    7524 > #6,-0.11498,-0.39854,0.90992,104.73,0.64766,0.66446,0.37287,-150.54,-0.7532,0.63219,0.18172,166.32
    7525 
    7526 > view matrix models
    7527 > #6,0.0002274,-0.40749,0.91321,84.492,0.63579,0.70493,0.3144,-144.02,-0.77186,0.58054,0.25924,163.65
    7528 
    7529 > volume #6 level 0.1497
    7530 
    7531 > view matrix models
    7532 > #6,0.0046913,-0.41214,0.91111,84.898,0.66603,0.68091,0.30458,-143.4,-0.74591,0.60539,0.27769,151.16
    7533 
    7534 > view matrix models
    7535 > #6,-0.048323,-0.43445,0.8994,100.5,0.7189,0.61,0.33328,-146.09,-0.69343,0.66268,0.28285,130.85
    7536 
    7537 > view matrix models
    7538 > #6,-0.10978,-0.42931,0.89646,111.19,0.68648,0.6195,0.38074,-151.02,-0.71881,0.6572,0.22671,147.1
    7539 
    7540 > view matrix models
    7541 > #6,-0.12181,-0.41902,0.89977,110.93,0.69056,0.61537,0.38006,-150.91,-0.71294,0.66764,0.2144,146.6
    7542 
    7543 > ui mousemode right "translate selected models"
    7544 
    7545 > view matrix models
    7546 > #6,-0.12181,-0.41902,0.89977,108.89,0.69056,0.61537,0.38006,-148.49,-0.71294,0.66764,0.2144,143.63
    7547 
    7548 > view matrix models
    7549 > #6,-0.12181,-0.41902,0.89977,110.07,0.69056,0.61537,0.38006,-147.38,-0.71294,0.66764,0.2144,145.3
    7550 
    7551 > ui mousemode right "rotate selected models"
    7552 
    7553 > view matrix models
    7554 > #6,-0.59223,-0.7712,-0.2335,472.46,-0.072251,0.33944,-0.93785,289.57,0.80252,-0.53855,-0.25675,172.86
    7555 
    7556 > ui mousemode right "move picked models"
    7557 
    7558 > ui mousemode right "translate selected models"
    7559 
    7560 > view matrix models
    7561 > #6,-0.59223,-0.7712,-0.2335,487.54,-0.072251,0.33944,-0.93785,305.54,0.80252,-0.53855,-0.25675,191.57
    7562 
    7563 > view matrix models
    7564 > #6,-0.59223,-0.7712,-0.2335,493,-0.072251,0.33944,-0.93785,306.92,0.80252,-0.53855,-0.25675,188.04
    7565 
    7566 > view matrix models
    7567 > #6,-0.59223,-0.7712,-0.2335,502.5,-0.072251,0.33944,-0.93785,311.18,0.80252,-0.53855,-0.25675,188.67
    7568 
    7569 > view matrix models
    7570 > #6,-0.59223,-0.7712,-0.2335,499.52,-0.072251,0.33944,-0.93785,313.18,0.80252,-0.53855,-0.25675,187.29
    7571 
    7572 > ui mousemode right "rotate selected models"
    7573 
    7574 > view matrix models
    7575 > #6,-0.82421,-0.553,0.12194,435.21,-0.037209,-0.16199,-0.98609,402.96,0.56506,-0.81729,0.11294,207.26
    7576 
    7577 > view matrix models
    7578 > #6,-0.44543,-0.86122,0.24473,397.17,-0.26729,-0.13296,-0.9544,433.08,0.85449,-0.49053,-0.17097,153.23
    7579 
    7580 > view matrix models
    7581 > #6,-0.36539,-0.89648,0.25061,387.81,-0.30567,-0.13874,-0.94198,438.58,0.87924,-0.4208,-0.22333,146.76
    7582 
    7583 > volume #6 level 0.2451
    7584 
    7585 > view matrix models
    7586 > #6,-0.26247,-0.55243,0.79116,201.13,-0.8293,-0.29003,-0.47764,470,0.49332,-0.78148,-0.382,313.01
    7587 
    7588 > view matrix models
    7589 > #6,-0.28569,-0.52355,0.80267,198.17,-0.82429,-0.29297,-0.48448,470.94,0.48881,-0.80004,-0.34786,310.26
    7590 
    7591 > ui mousemode right "move picked models"
    7592 
    7593 > ui mousemode right "translate selected models"
    7594 
    7595 > view matrix models
    7596 > #6,-0.28569,-0.52355,0.80267,180.48,-0.82429,-0.29297,-0.48448,474.67,0.48881,-0.80004,-0.34786,307.45
    7597 
    7598 > volume #6 level 0.1673
    7599 
    7600 > view matrix models
    7601 > #6,-0.28569,-0.52355,0.80267,178.35,-0.82429,-0.29297,-0.48448,476.02,0.48881,-0.80004,-0.34786,306.81
    7602 
    7603 > ui mousemode right "rotate selected models"
    7604 
    7605 > view matrix models
    7606 > #6,-0.14718,-0.54954,0.8224,153.6,-0.85753,-0.34346,-0.38298,471.17,0.49292,-0.7616,-0.4207,313.54
    7607 
    7608 > view matrix models
    7609 > #6,-0.14519,-0.57785,0.80312,161.88,-0.8523,-0.33921,-0.39815,472.41,0.5025,-0.74231,-0.44325,312.81
    7610 
    7611 > view matrix models
    7612 > #6,-0.14171,-0.61705,0.77406,173.68,-0.84479,-0.3322,-0.41948,473.96,0.51599,-0.71336,-0.47421,311.33
    7613 
    7614 > view matrix models
    7615 > #6,-0.123,-0.64321,0.75574,178.33,-0.8848,-0.2738,-0.37704,462.95,0.44944,-0.71506,-0.53544,335.73
    7616 
    7617 > view matrix models
    7618 > #6,0.10222,-0.64957,0.7534,138.55,-0.86358,-0.43386,-0.2569,463.46,0.49374,-0.62436,-0.6053,325.44
    7619 
    7620 > view matrix models
    7621 > #6,0.10839,-0.64998,0.75218,137.72,-0.86646,-0.4327,-0.24905,462.27,0.48734,-0.62473,-0.61008,327.61
    7622 
    7623 > view matrix models
    7624 > #6,-0.17656,-0.48355,0.85733,140.78,-0.84554,-0.37137,-0.38359,473.92,0.50387,-0.79263,-0.34329,301.87
    7625 
    7626 > view matrix models
    7627 > #6,-0.23478,-0.43523,0.86917,140.8,-0.85004,-0.34178,-0.40076,472.95,0.47149,-0.83292,-0.28972,304.4
    7628 
    7629 > view matrix models
    7630 > #6,-0.22867,-0.43704,0.86989,139.85,-0.85367,-0.33948,-0.39497,472.09,0.46792,-0.83292,-0.29546,306.17
    7631 
    7632 > ui mousemode right "translate selected models"
    7633 
    7634 > view matrix models
    7635 > #6,-0.22867,-0.43704,0.86989,137.64,-0.85367,-0.33948,-0.39497,471.42,0.46792,-0.83292,-0.29546,310.38
    7636 
    7637 > view matrix models
    7638 > #6,-0.22867,-0.43704,0.86989,137.55,-0.85367,-0.33948,-0.39497,472.47,0.46792,-0.83292,-0.29546,308.95
    7639 
    7640 > ui mousemode right "rotate selected models"
    7641 
    7642 > view matrix models
    7643 > #6,-0.25766,-0.4215,0.86945,140.27,-0.85126,-0.32669,-0.41064,472.85,0.45712,-0.84594,-0.27463,309.15
    7644 
    7645 > view matrix models
    7646 > #6,-0.24131,-0.47116,0.8484,149.96,-0.84523,-0.32751,-0.42229,474.15,0.47682,-0.81899,-0.3192,309.52
    7647 
    7648 > view matrix models
    7649 > #6,-0.22049,-0.52796,0.82015,161.46,-0.83815,-0.32752,-0.43617,475.54,0.4989,-0.78357,-0.37029,309.25
    7650 
    7651 > view matrix models
    7652 > #6,-0.16435,-0.57156,0.80393,161.86,-0.87529,-0.29128,-0.38603,466.35,0.45481,-0.76712,-0.45241,330.43
    7653 
    7654 > view matrix models
    7655 > #6,-0.18555,-0.55494,0.81094,161.51,-0.86165,-0.30484,-0.40575,470.03,0.47237,-0.77403,-0.4216,322.42
    7656 
    7657 > view matrix models
    7658 > #6,-0.2448,-0.5224,0.8168,165.61,-0.85708,-0.27726,-0.4342,469.93,0.4533,-0.80636,-0.37987,323.42
    7659 
    7660 > view matrix models
    7661 > #6,-0.1668,-0.4734,0.86491,133.46,-0.84447,-0.38422,-0.37316,474.3,0.50897,-0.79263,-0.33568,302.25
    7662 
    7663 > ui mousemode right "translate selected models"
    7664 
    7665 > view matrix models
    7666 > #6,-0.1668,-0.4734,0.86491,132.36,-0.84447,-0.38422,-0.37316,474.18,0.50897,-0.79263,-0.33568,304.38
    7667 
    7668 > view matrix models
    7669 > #6,-0.1668,-0.4734,0.86491,132.99,-0.84447,-0.38422,-0.37316,474.25,0.50897,-0.79263,-0.33568,304.17
    7670 
    7671 > view matrix models
    7672 > #6,-0.1668,-0.4734,0.86491,133.6,-0.84447,-0.38422,-0.37316,474.33,0.50897,-0.79263,-0.33568,303.95
    7673 
    7674 > ui mousemode right "rotate selected models"
    7675 
    7676 > view matrix models
    7677 > #6,-0.32695,-0.44627,0.83303,164.48,-0.82463,-0.29585,-0.48214,476.54,0.46162,-0.84458,-0.27128,309.14
    7678 
    7679 > ui mousemode right "translate selected models"
    7680 
    7681 > view matrix models
    7682 > #6,-0.32695,-0.44627,0.83303,165.99,-0.82463,-0.29585,-0.48214,476.36,0.46162,-0.84458,-0.27128,308.97
    7683 
    7684 > view matrix models
    7685 > #6,-0.32695,-0.44627,0.83303,166.94,-0.82463,-0.29585,-0.48214,479.3,0.46162,-0.84458,-0.27128,310.62
    7686 
    7687 > view matrix models
    7688 > #6,-0.32695,-0.44627,0.83303,166.99,-0.82463,-0.29585,-0.48214,477.92,0.46162,-0.84458,-0.27128,311.73
    7689 
    7690 > view matrix models
    7691 > #6,-0.32695,-0.44627,0.83303,166.29,-0.82463,-0.29585,-0.48214,478.59,0.46162,-0.84458,-0.27128,310.92
    7692 
    7693 > volume #6 level 0.1249
    7694 
    7695 > view matrix models
    7696 > #6,-0.32695,-0.44627,0.83303,165.96,-0.82463,-0.29585,-0.48214,479.04,0.46162,-0.84458,-0.27128,311.24
    7697 
    7698 > show #!1 models
    7699 
    7700 > hide #3 models
    7701 
    7702 > hide #4 models
    7703 
    7704 > select #1
    7705 
    7706 2 models selected 
    7707 
    7708 > view matrix models
    7709 > #1,-0.99948,-0.025572,-0.01976,364.95,0.031105,-0.92707,-0.3736,414.45,-0.0087649,-0.37402,0.92738,76.793
    7710 
    7711 > ui mousemode right "rotate selected models"
    7712 
    7713 > view matrix models
    7714 > #1,-0.93251,0.32395,-0.15963,316.09,0.35214,0.71758,-0.6009,105.04,-0.080113,-0.61656,-0.78322,444.34
    7715 
    7716 > view matrix models
    7717 > #1,-0.92079,0.38867,0.032827,267.4,0.38993,0.91934,0.052624,-56.723,-0.009726,0.061257,-0.99807,349.94
    7718 
    7719 > view matrix models
    7720 > #1,-0.87777,0.3565,0.32005,213.16,0.3764,0.92646,0.00035867,-46.06,-0.29638,0.12078,-0.9474,381.24
    7721 
    7722 > view matrix models
    7723 > #1,-0.89237,0.44968,0.038176,250.47,0.16187,0.3979,-0.90304,251.08,-0.42127,-0.79967,-0.42786,473.18
    7724 
    7725 > ui mousemode right "translate selected models"
    7726 
    7727 > view matrix models
    7728 > #1,-0.89237,0.44968,0.038176,252.64,0.16187,0.3979,-0.90304,250.64,-0.42127,-0.79967,-0.42786,471.5
    7729 
    7730 > ui mousemode right "rotate selected models"
    7731 
    7732 > view matrix models
    7733 > #1,-0.91313,0.40742,0.014419,268.22,0.16668,0.40537,-0.89883,247.68,-0.37205,-0.81834,-0.43806,467.9
    7734 
    7735 > view matrix models
    7736 > #1,-0.86639,0.4978,-0.039456,253.56,0.25363,0.37062,-0.89348,237.39,-0.43015,-0.78411,-0.44736,473.86
    7737 
    7738 > ui mousemode right "translate selected models"
    7739 
    7740 > view matrix models
    7741 > #1,-0.86639,0.4978,-0.039456,247.82,0.25363,0.37062,-0.89348,237.47,-0.43015,-0.78411,-0.44736,473.22
    7742 
    7743 > ui mousemode right "rotate selected models"
    7744 
    7745 > view matrix models
    7746 > #1,-0.87597,0.47955,-0.052144,255.09,0.30604,0.46893,-0.82852,198.74,-0.37286,-0.74171,-0.55753,475.49
    7747 
    7748 > view matrix models
    7749 > #1,-0.88553,0.45898,0.071919,237.88,0.23094,0.5692,-0.7891,187.07,-0.40311,-0.68216,-0.61004,479.83
    7750 
    7751 > ui mousemode right "translate selected models"
    7752 
    7753 > view matrix models
    7754 > #1,-0.88553,0.45898,0.071919,232.83,0.23094,0.5692,-0.7891,186.52,-0.40311,-0.68216,-0.61004,479.89
    7755 
    7756 > ui mousemode right "rotate selected models"
    7757 
    7758 > view matrix models
    7759 > #1,-0.93268,0.36026,0.017859,268.7,0.20808,0.57784,-0.78918,189.07,-0.29463,-0.73234,-0.6139,470.19
    7760 
    7761 > view matrix models
    7762 > #1,-0.9521,0.2987,0.065475,274.48,0.12858,0.58532,-0.80054,204,-0.27744,-0.75378,-0.59569,467.63
    7763 
    7764 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    7765 cryosparc_P35_J90_005_volume_map_sharp.mrc using 125084 points 
    7766 correlation = 0.7737, correlation about mean = 0.5148, overlap = 4611 
    7767 steps = 324, shift = 10.7, angle = 12.5 degrees 
    7768  
    7769 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    7770 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    7771 Matrix rotation and translation 
    7772 -0.00018548 -0.96024693 0.27915190 304.64819825 
    7773 0.47329448 0.24582180 0.84591014 -90.95034872 
    7774 -0.88090425 0.13227795 0.45443398 232.87270604 
    7775 Axis -0.36089737 0.58666245 0.72496915 
    7776 Axis point 266.13823335 42.12806522 0.00000000 
    7777 Rotation angle (degrees) 98.62488972 
    7778 Shift along axis 5.52163959 
    7779  
    7780 
    7781 > show #!2 models
    7782 
    7783 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    7784 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
    7785 > NS1ts.cxs"
    7786 
    7787 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    7788 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
    7789 > NS1ts.cxs" includeMaps true
    7790 
    7791 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    7792 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    7793 > sNS1-Fab56-2/NS1ts-HDL/cryosparc_P35_J88_003_volume_map_sharp.mrc
    7794 
    7795 Opened cryosparc_P35_J88_003_volume_map_sharp.mrc as #7, grid size
    7796 416,416,416, pixel 0.858, shown at level 0.0322, step 2, values float32 
    7797 
    7798 > hide #!6 models
    7799 
    7800 > hide #!1 models
    7801 
    7802 > hide #!2 models
    7803 
    7804 > volume #7 level 0.08768
    7805 
    7806 > volume #7 level 0.03374
    7807 
    7808 > volume #7 level 0.01342
    7809 
    7810 > volume #7 level 0.05407
    7811 
    7812 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    7813 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    7814 > sNS1-Fab56-2/NS1ts-HDL/cryosparc_P35_J87_003_volume_map_sharp.mrc
    7815 
    7816 Opened cryosparc_P35_J87_003_volume_map_sharp.mrc as #8, grid size
    7817 416,416,416, pixel 0.858, shown at level 0.0329, step 2, values float32 
    7818 
    7819 > close #7
    7820 
    7821 > volume #8 level 0.07979
    7822 
    7823 > volume #8 level 0.05868
    7824 
    7825 > volume #8 level 0.0493
    7826 
    7827 > volume #8 color #b2ffff76
    7828 
    7829 > volume #8 color #b2ffff75
    7830 
    7831 > show #3 models
    7832 
    7833 > select #8
    7834 
    7835 2 models selected 
    7836 
    7837 > ui mousemode right "translate selected models"
    7838 
    7839 > view matrix models #8,1,0,0,-5.0701,0,1,0,25.403,0,0,1,13.725
    7840 
    7841 > view matrix models #8,1,0,0,-2.4128,0,1,0,22.261,0,0,1,17.693
    7842 
    7843 > view matrix models #8,1,0,0,13.637,0,1,0,15.538,0,0,1,17.629
    7844 
    7845 > view matrix models #8,1,0,0,17.759,0,1,0,21.107,0,0,1,15.457
    7846 
    7847 > ui mousemode right "rotate selected models"
    7848 
    7849 > view matrix models
    7850 > #8,0.9437,0.30533,-0.12727,-1.7134,-0.30648,0.95181,0.01092,77.369,0.12448,0.028702,0.99181,-8.2592
    7851 
    7852 > view matrix models
    7853 > #8,0.93379,0.13868,-0.32987,64.541,0.05145,0.86023,0.5073,-55.026,0.35412,-0.49068,0.79614,77.197
    7854 
    7855 > view matrix models
    7856 > #8,0.93056,0.16968,-0.32446,58.857,0.023869,0.85614,0.5162,-51.428,0.36537,-0.48809,0.79263,75.552
    7857 
    7858 > view matrix models
    7859 > #8,0.92836,0.172,-0.32949,59.73,0.0092364,0.87553,0.48308,-46.35,0.37157,-0.45151,0.81122,65.012
    7860 
    7861 > view matrix models
    7862 > #8,0.90406,0.053265,-0.42407,100.79,0.15019,0.88934,0.43188,-62.499,0.40015,-0.45413,0.79602,63.521
    7863 
    7864 > view matrix models
    7865 > #8,0.90236,0.062663,-0.42639,99.9,0.13798,0.8953,0.42357,-60.014,0.40829,-0.44104,0.79924,59.399
    7866 
    7867 > view matrix models
    7868 > #8,0.95884,0.13052,-0.25215,47.832,0.14193,0.54884,0.82379,-74.184,0.24591,-0.82568,0.50772,203.41
    7869 
    7870 > view matrix models
    7871 > #8,0.8439,0.43609,-0.31252,25.859,0.15414,0.36088,0.91979,-61.706,0.51389,-0.82438,0.23733,208.08
    7872 
    7873 > view matrix models
    7874 > #8,0.72071,0.42588,-0.547,89.933,0.3615,0.44239,0.82074,-91.531,0.59152,-0.78925,0.16489,202.5
    7875 
    7876 > view matrix models
    7877 > #8,0.88841,0.1882,-0.4187,79.584,0.16981,0.71266,0.68065,-80.646,0.42648,-0.6758,0.60117,131.75
    7878 
    7879 > view matrix models
    7880 > #8,0.81278,0.18222,-0.55333,117.19,0.28518,0.70377,0.65067,-92.602,0.50799,-0.68666,0.52005,134.87
    7881 
    7882 > ui mousemode right "translate selected models"
    7883 
    7884 > view matrix models
    7885 > #8,0.81278,0.18222,-0.55333,111.12,0.28518,0.70377,0.65067,-89.214,0.50799,-0.68666,0.52005,131.56
    7886 
    7887 > ui mousemode right "rotate selected models"
    7888 
    7889 > view matrix models
    7890 > #8,0.66641,0.31634,-0.67515,134.32,0.37078,0.645,0.6682,-96.429,0.64685,-0.69563,0.31254,147.74
    7891 
    7892 > view matrix models
    7893 > #8,0.64719,0.35366,-0.67533,131.19,0.38471,0.61328,0.68984,-97.242,0.65814,-0.70627,0.26085,157
    7894 
    7895 > view matrix models
    7896 > #8,0.58239,0.30728,-0.75259,163.52,0.46192,0.63672,0.61743,-100.78,0.66892,-0.70723,0.22888,161.16
    7897 
    7898 > view matrix models
    7899 > #8,0.7541,0.27199,-0.59778,113.55,0.30905,0.65618,0.68842,-91.868,0.5795,-0.70388,0.41077,142.46
    7900 
    7901 > view matrix models
    7902 > #8,0.61599,0.12295,-0.7781,193.77,0.49388,0.70924,0.50306,-97.665,0.61371,-0.69417,0.37616,141.46
    7903 
    7904 > view matrix models
    7905 > #8,0.73698,0.11525,-0.66601,155.12,0.40454,0.71417,0.57123,-96.173,0.54148,-0.69041,0.47971,133.98
    7906 
    7907 > ui mousemode right "translate selected models"
    7908 
    7909 > view matrix models
    7910 > #8,0.73698,0.11525,-0.66601,155.56,0.40454,0.71417,0.57123,-90.04,0.54148,-0.69041,0.47971,141.01
    7911 
    7912 > view matrix models
    7913 > #8,0.73698,0.11525,-0.66601,154.44,0.40454,0.71417,0.57123,-89.633,0.54148,-0.69041,0.47971,140.1
    7914 
    7915 > view matrix models
    7916 > #8,0.73698,0.11525,-0.66601,153.2,0.40454,0.71417,0.57123,-89.182,0.54148,-0.69041,0.47971,139.08
    7917 
    7918 > ui mousemode right "rotate selected models"
    7919 
    7920 > view matrix models
    7921 > #8,0.73974,0.19261,-0.64473,135.84,0.34001,0.71983,0.60517,-85.705,0.58066,-0.66689,0.467,130.99
    7922 
    7923 > close #8
    7924 
    7925 > volume #1 color #b2b2b280
    7926 
    7927 [Repeated 1 time(s)]
    7928 
    7929 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    7930 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/011762271936024191787_FoilHole_12249383_Data_12248537_12248539_20211012_184153-341492_patch_aligned.mrc
    7931 
    7932 Opened
    7933 011762271936024191787_FoilHole_12249383_Data_12248537_12248539_20211012_184153-341492_patch_aligned.mrc
    7934 as #7, grid size 3838,3710,1, pixel 0.85,0.85,0.85, shown at step 1, values
    7935 float32 
    7936 
    7937 > close #7
    7938 
    7939 > show #!2 models
    7940 
    7941 > hide #3 models
    7942 
    7943 > show #3 models
    7944 
    7945 > hide #3 models
    7946 
    7947 > show #3 models
    7948 
    7949 > show #4 models
    7950 
    7951 > show #9 models
    7952 
    7953 > hide #!2 models
    7954 
    7955 > hide #4 models
    7956 
    7957 > show #4 models
    7958 
    7959 > hide #4 models
    7960 
    7961 > ui tool show "Show Sequence Viewer"
    7962 
    7963 > sequence chain #9/B
    7964 
    7965 Alignment identifier is 9/B 
    7966 
    7967 > sequence chain #9/C
    7968 
    7969 Alignment identifier is 9/C 
    7970 
    7971 > select #9/B:2-3
    7972 
    7973 13 atoms, 12 bonds, 2 residues, 1 model selected 
    7974 
    7975 > select #9/B:2-19
    7976 
    7977 142 atoms, 143 bonds, 18 residues, 1 model selected 
    7978 
    7979 > select #9/B:1
    7980 
    7981 6 atoms, 5 bonds, 1 residue, 1 model selected 
    7982 
    7983 > select #9/B:1-27
    7984 
    7985 211 atoms, 212 bonds, 27 residues, 1 model selected 
    7986 
    7987 > select #9/B:1-27
    7988 
    7989 211 atoms, 212 bonds, 27 residues, 1 model selected 
    7990 
    7991 > select #9/B:30
    7992 
    7993 4 atoms, 3 bonds, 1 residue, 1 model selected 
    7994 
    7995 > select #9/B:1-30
    7996 
    7997 232 atoms, 233 bonds, 30 residues, 1 model selected 
    7998 
    7999 > ui mousemode right "color key"
    8000 
    8001 > key delete
    8002 
    8003 > ui mousemode right "rotate selected models"
    8004 
    8005 > color sel cornflower blue
    8006 
    8007 > color sel #7a81ffff
    8008 
    8009 > ui tool show "Show Sequence Viewer"
    8010 
    8011 > sequence chain #9/B #9/C
    8012 
    8013 Alignment identifier is 1 
    8014 
    8015 > select #9/B-C:1
    8016 
    8017 12 atoms, 10 bonds, 2 residues, 1 model selected 
    8018 
    8019 > select #9/B-C:1-30
    8020 
    8021 464 atoms, 466 bonds, 60 residues, 1 model selected 
    8022 
    8023 > color sel #0433ffff
    8024 
    8025 > color sel #7a81ffff
    8026 
    8027 > select #9/B-C:31-33
    8028 
    8029 42 atoms, 42 bonds, 6 residues, 1 model selected 
    8030 
    8031 > select #9/B-C:31-63
    8032 
    8033 562 atoms, 570 bonds, 66 residues, 1 model selected 
    8034 
    8035 > color sel dim gray
    8036 
    8037 > select #9/B-C:64-65
    8038 
    8039 38 atoms, 40 bonds, 4 residues, 1 model selected 
    8040 
    8041 > select #9/B-C:64-85
    8042 
    8043 402 atoms, 414 bonds, 44 residues, 1 model selected 
    8044 
    8045 > color sel #d783ffff
    8046 
    8047 > color sel #7a81ffff
    8048 
    8049 > select #9/B-C:86
    8050 
    8051 14 atoms, 14 bonds, 2 residues, 1 model selected 
    8052 
    8053 > select #9/B-C:86-107
    8054 
    8055 358 atoms, 360 bonds, 44 residues, 1 model selected 
    8056 
    8057 > color sel dim gray
    8058 
    8059 > select #9/B-C:108-109
    8060 
    8061 30 atoms, 30 bonds, 4 residues, 1 model selected 
    8062 
    8063 > select #9/B-C:108-129
    8064 
    8065 360 atoms, 362 bonds, 44 residues, 1 model selected 
    8066 
    8067 > color sel #d783ffff
    8068 
    8069 > color sel #7a81ffff
    8070 
    8071 > select #9/B-C:130
    8072 
    8073 14 atoms, 14 bonds, 2 residues, 1 model selected 
    8074 
    8075 > select #9/B-C:130-140
    8076 
    8077 190 atoms, 192 bonds, 22 residues, 1 model selected 
    8078 
    8079 > select #9/B-C:130-201
    8080 
    8081 1092 atoms, 1102 bonds, 144 residues, 1 model selected 
    8082 
    8083 > select #9/B-C:130-150
    8084 
    8085 334 atoms, 336 bonds, 42 residues, 1 model selected 
    8086 
    8087 > select #9/B-C:88-151
    8088 
    8089 1030 atoms, 1038 bonds, 128 residues, 1 model selected 
    8090 
    8091 > select #9/B-C:130-151
    8092 
    8093 342 atoms, 344 bonds, 44 residues, 1 model selected 
    8094 
    8095 > color sel dim gray
    8096 
    8097 > select #9/B-C:2-149,151-206
    8098 
    8099 3296 atoms, 3340 bonds, 408 residues, 1 model selected 
    8100 
    8101 > select #9/B-C:151
    8102 
    8103 8 atoms, 6 bonds, 2 residues, 1 model selected 
    8104 
    8105 > select #9/B-C:151-157
    8106 
    8107 108 atoms, 110 bonds, 14 residues, 1 model selected 
    8108 
    8109 > select #9/B-C:152-153
    8110 
    8111 28 atoms, 26 bonds, 4 residues, 1 model selected 
    8112 
    8113 > select #9/B-C:152-172
    8114 
    8115 318 atoms, 320 bonds, 42 residues, 1 model selected 
    8116 
    8117 > select #9/B-C:31-34
    8118 
    8119 60 atoms, 60 bonds, 8 residues, 1 model selected 
    8120 
    8121 > select #9/B-C:31-63
    8122 
    8123 562 atoms, 570 bonds, 66 residues, 1 model selected 
    8124 
    8125 > select #9/B-C:2-149,151-206
    8126 
    8127 3296 atoms, 3340 bonds, 408 residues, 1 model selected 
    8128 
    8129 > select #9/B-C:53
    8130 
    8131 18 atoms, 16 bonds, 2 residues, 1 model selected 
    8132 
    8133 > select #9/B-C:53-63
    8134 
    8135 186 atoms, 184 bonds, 22 residues, 1 model selected 
    8136 
    8137 > color sel #d783ffff
    8138 
    8139 > color sel #7a81ffff
    8140 
    8141 > select #9/B-C:64
    8142 
    8143 14 atoms, 14 bonds, 2 residues, 1 model selected 
    8144 
    8145 > select #9/B-C:64-85
    8146 
    8147 402 atoms, 414 bonds, 44 residues, 1 model selected 
    8148 
    8149 > color sel dim gray
    8150 
    8151 > select #9/B-C:86-87
    8152 
    8153 30 atoms, 30 bonds, 4 residues, 1 model selected 
    8154 
    8155 > select #9/B-C:86-107
    8156 
    8157 358 atoms, 360 bonds, 44 residues, 1 model selected 
    8158 
    8159 > color sel #d783ffff
    8160 
    8161 > color sel #7a81ffff
    8162 
    8163 > color sel dim gray
    8164 
    8165 > select #9/B-C:108
    8166 
    8167 14 atoms, 14 bonds, 2 residues, 1 model selected 
    8168 
    8169 > select #9/B-C:108-129
    8170 
    8171 360 atoms, 362 bonds, 44 residues, 1 model selected 
    8172 
    8173 > select #9/B-C:107
    8174 
    8175 12 atoms, 10 bonds, 2 residues, 1 model selected 
    8176 
    8177 > select #9/B-C:86-107
    8178 
    8179 358 atoms, 360 bonds, 44 residues, 1 model selected 
    8180 
    8181 > color sel #d783ffff
    8182 
    8183 > color sel #7a81ffff
    8184 
    8185 > select #9/B-C:108-109
    8186 
    8187 30 atoms, 30 bonds, 4 residues, 1 model selected 
    8188 
    8189 > select #9/B-C:108-129
    8190 
    8191 360 atoms, 362 bonds, 44 residues, 1 model selected 
    8192 
    8193 > color sel dim gray
    8194 
    8195 > select #9/B-C:130
    8196 
    8197 14 atoms, 14 bonds, 2 residues, 1 model selected 
    8198 
    8199 > select #9/B-C:130-149
    8200 
    8201 326 atoms, 328 bonds, 40 residues, 1 model selected 
    8202 
    8203 > select #9/B-C:130-131
    8204 
    8205 38 atoms, 40 bonds, 4 residues, 1 model selected 
    8206 
    8207 > select #9/B-C:130-150
    8208 
    8209 334 atoms, 336 bonds, 42 residues, 1 model selected 
    8210 
    8211 > select #9/B-C:130
    8212 
    8213 14 atoms, 14 bonds, 2 residues, 1 model selected 
    8214 
    8215 > select #9/B-C:130-151
    8216 
    8217 342 atoms, 344 bonds, 44 residues, 1 model selected 
    8218 
    8219 > color sel #d783ffff
    8220 
    8221 > color sel #7a81ffff
    8222 
    8223 > select #9/B-C:152-153
    8224 
    8225 28 atoms, 26 bonds, 4 residues, 1 model selected 
    8226 
    8227 > select #9/B-C:152-172
    8228 
    8229 318 atoms, 320 bonds, 42 residues, 1 model selected 
    8230 
    8231 > color sel dim gray
    8232 
    8233 > select #9/B-C:174
    8234 
    8235 14 atoms, 12 bonds, 2 residues, 1 model selected 
    8236 
    8237 > select #9/B-C:174-176
    8238 
    8239 48 atoms, 46 bonds, 6 residues, 1 model selected 
    8240 
    8241 > select #9/B-C:173
    8242 
    8243 14 atoms, 14 bonds, 2 residues, 1 model selected 
    8244 
    8245 > select #9/B-C:173-183
    8246 
    8247 174 atoms, 174 bonds, 22 residues, 1 model selected 
    8248 
    8249 > color sel #d783ffff
    8250 
    8251 > color sel #7a81ffff
    8252 
    8253 > select #9/B-C:184
    8254 
    8255 14 atoms, 14 bonds, 2 residues, 1 model selected 
    8256 
    8257 > select #9/B-C:184-207
    8258 
    8259 354 atoms, 354 bonds, 48 residues, 1 model selected 
    8260 
    8261 > color sel dim gray
    8262 
    8263 > select #9
    8264 
    8265 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    8266 
    8267 > ~select #9
    8268 
    8269 Nothing selected 
    8270 
    8271 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    8272 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    8273 > includeMaps true
    8274 
    8275 > show #!2 models
    8276 
    8277 > show #4 models
    8278 
    8279 > hide #4 models
    8280 
    8281 > volume #2 level 0.1179
    8282 
    8283 > show #4 models
    8284 
    8285 > volume #2 level 0.13
    8286 
    8287 > volume #2 level 0.14
    8288 
    8289 > volume #2 level 0.15
    8290 
    8291 > lighting flat
    8292 
    8293 > graphics silhouettes false
    8294 
    8295 > graphics silhouettes true
    8296 
    8297 > lighting shadows true intensity 0.5
    8298 
    8299 > lighting shadows false
    8300 
    8301 > lighting shadows true
    8302 
    8303 > lighting shadows false
    8304 
    8305 > lighting shadows true
    8306 
    8307 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    8308 > (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig4_D.png"
    8309 > width 1009 height 824 supersample 3 transparentBackground true
    8310 
    8311 > show #!6 models
    8312 
    8313 > hide #!2 models
    8314 
    8315 > show #!2 models
    8316 
    8317 Fit map cryosparc_P35_J90_005_volume_map_sharp.mrc in map
    8318 cryosparc_P47_J20_004_volume_map_sharp.mrc using 114729 points 
    8319 correlation = 0.672, correlation about mean = 0.08483, overlap = 3988 
    8320 steps = 212, shift = 5.69, angle = 24.1 degrees 
    8321  
    8322 Position of cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) relative to
    8323 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    8324 Matrix rotation and translation 
    8325 -0.48667344 0.82476587 0.28794127 36.88441365 
    8326 -0.86459172 -0.40757626 -0.29387534 426.86136408 
    8327 -0.12502033 -0.39197297 0.91144230 73.88929120 
    8328 Axis -0.05631763 0.23708030 -0.96985631 
    8329 Axis point 142.84730785 210.89177337 0.00000000 
    8330 Rotation angle (degrees) 119.43288522 
    8331 Shift along axis 27.46118471 
    8332  
    8333 
    8334 > hide #!2 models
    8335 
    8336 > show #!2 models
    8337 
    8338 > hide #!2 models
    8339 
    8340 > volume #6 level 0.12
    8341 
    8342 > select #3
    8343 
    8344 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    8345 
    8346 > ~select #3
    8347 
    8348 Nothing selected 
    8349 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
    8350 (#6) using 5602 atoms 
    8351 average map value = 0.08293, steps = 148 
    8352 shifted from previous position = 4.12 
    8353 rotated from previous position = 15.3 degrees 
    8354 atoms outside contour = 4112, contour level = 0.12 
    8355  
    8356 Position of D2NS1.pdb (#3) relative to
    8357 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    8358 Matrix rotation and translation 
    8359 -0.47334151 0.84962673 0.23255592 79.20387762 
    8360 0.74805308 0.24829808 0.61543861 -93.30922995 
    8361 0.46514990 0.46527681 -0.75309567 157.40236379 
    8362 Axis -0.50919647 -0.78872280 -0.34443477 
    8363 Axis point 62.66416490 -0.00000000 102.29599347 
    8364 Rotation angle (degrees) 171.52083443 
    8365 Shift along axis -20.95006494 
    8366  
    8367 
    8368 > undo
    8369 
    8370 [Repeated 2 time(s)]
    8371 
    8372 > hide #!2 models
    8373 
    8374 > log metadata #3
    8375 
    8376 The model has no metadata
    8377 
    8378 > log chains #3
    8379 
    8380 Chain information for D2NS1.pdb #3 
    8381 --- 
    8382 Chain | Description 
    8383 B C | No description available 
    8384  
    8385 
    8386 > ui mousemode right "rotate selected models"
    8387 
    8388 > select #3
    8389 
    8390 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    8391 
    8392 > view matrix models
    8393 > #3,-0.0085676,-0.30727,-0.95158,398.88,0.38479,-0.87936,0.28049,211.07,-0.92297,-0.36375,0.12577,388.55
    8394 
    8395 > view matrix models
    8396 > #3,-0.13489,-0.29223,-0.94679,417.71,0.36981,-0.90133,0.22551,227.19,-0.91926,-0.31971,0.22965,361.99
    8397 
    8398 > view matrix models
    8399 > #3,-0.071496,-0.30058,-0.95107,408.73,0.37829,-0.89045,0.25298,218.98,-0.92292,-0.34169,0.17737,375.64
    8400 
    8401 > view matrix models
    8402 > #3,-0.18267,-0.34044,-0.92235,429.87,0.39852,-0.88325,0.24708,215.26,-0.89878,-0.32244,0.29702,346.84
    8403 
    8404 > view matrix models
    8405 > #3,-0.40995,0.57223,-0.71028,278.61,-0.10972,-0.804,-0.58442,439.45,-0.90548,-0.16165,0.39238,304
    8406 
    8407 > view matrix models
    8408 > #3,-0.46987,0.63995,-0.60802,259.54,-0.55045,-0.75089,-0.36493,468.93,-0.69009,0.16321,0.70508,155.79
    8409 
    8410 > view matrix models
    8411 > #3,-0.65716,0.081263,-0.74936,411.59,-0.053676,-0.99669,-0.061013,368.75,-0.75184,0.0001281,0.65934,202.22
    8412 
    8413 > view matrix models
    8414 > #3,-0.62292,-0.22233,0.75003,189.5,-0.068144,-0.9397,-0.33515,410.55,0.77931,-0.25988,0.5702,-7.4739
    8415 
    8416 > view matrix models
    8417 > #3,0.31022,-0.41267,0.85643,38.43,-0.2398,-0.90571,-0.34955,437.59,0.91992,-0.096935,-0.37993,109.67
    8418 
    8419 > view matrix models
    8420 > #3,0.14284,-0.48882,0.86061,79.927,-0.73689,-0.63302,-0.23725,459.16,0.66075,-0.60029,-0.45063,252.47
    8421 
    8422 > view matrix models
    8423 > #3,0.069717,-0.45875,0.88582,83.239,-0.93425,-0.34135,-0.10325,420.96,0.34974,-0.82038,-0.45239,344.49
    8424 
    8425 > view matrix models
    8426 > #3,-0.24695,0.22628,0.94224,13.705,-0.87659,-0.46663,-0.11768,434.45,0.41304,-0.85502,0.31359,202.72
    8427 
    8428 > view matrix models
    8429 > #3,-0.099087,-0.011917,0.99501,18.348,-0.8839,-0.45823,-0.09351,430.02,0.45706,-0.88875,0.034872,250.31
    8430 
    8431 > view matrix models
    8432 > #3,0.0096812,0.032947,0.99941,-9.1088,-0.93353,-0.3579,0.020842,401.51,0.35838,-0.93318,0.027292,276.48
    8433 
    8434 > view matrix models
    8435 > #3,-0.060408,-0.021128,0.99795,12.57,-0.98054,-0.18582,-0.063289,395.83,0.18678,-0.98236,-0.0094914,321.48
    8436 
    8437 > view matrix models
    8438 > #3,-0.14852,-0.072188,0.98627,38.731,-0.98683,-0.053816,-0.15254,390.64,0.064089,-0.99594,-0.063245,354.92
    8439 
    8440 > view matrix models
    8441 > #3,-0.35842,-0.23162,0.90437,117.04,-0.92969,0.00036447,-0.36835,409.93,0.084987,-0.97281,-0.21546,374.47
    8442 
    8443 > view matrix models
    8444 > #3,-0.16442,-0.085208,0.9827,44.354,-0.94873,-0.25901,-0.1812,423.54,0.26997,-0.96211,-0.038251,308.57
    8445 
    8446 > view matrix models
    8447 > #3,-0.29929,0.026962,0.95378,54.365,-0.9175,-0.28257,-0.27991,439.6,0.26196,-0.95887,0.10931,283.15
    8448 
    8449 > view matrix models
    8450 > #3,0.21447,0.471,0.85566,-93.169,0.97669,-0.095031,-0.1925,59.362,-0.0093522,0.877,-0.4804,127.25
    8451 
    8452 > view matrix models
    8453 > #3,0.56515,0.56728,0.59899,-125.3,0.82406,-0.42253,-0.37735,174.2,0.03903,0.70687,-0.70627,187.59
    8454 
    8455 > view matrix models
    8456 > #3,0.2047,0.3956,0.89532,-85.837,0.92678,0.21596,-0.30731,36.306,-0.31492,0.89267,-0.32243,150.21
    8457 
    8458 > view matrix models
    8459 > #3,0.26975,0.34464,0.89914,-89.39,0.91144,0.20987,-0.35388,48.323,-0.31067,0.91497,-0.25751,134.15
    8460 
    8461 > view matrix models
    8462 > #3,0.15293,0.16968,0.97356,-52.687,0.98145,0.089212,-0.16972,23.489,-0.11565,0.98145,-0.15289,70.037
    8463 
    8464 > view matrix models
    8465 > #3,0.042216,0.087727,0.99525,-23.3,0.97412,0.21777,-0.060515,-16.293,-0.22204,0.97205,-0.076263,76.678
    8466 
    8467 > view matrix models
    8468 > #3,0.035376,0.093709,0.99497,-23.053,0.9291,0.36366,-0.067284,-31.697,-0.36814,0.92681,-0.0742,109.61
    8469 
    8470 > view matrix models
    8471 > #3,-0.74086,0.45839,0.49092,141.95,-0.6574,-0.34504,-0.66991,473.84,-0.13769,-0.81904,0.55697,250.17
    8472 
    8473 > view matrix models
    8474 > #3,-0.12274,0.85219,0.50863,-36.128,-0.96225,-0.22764,0.1492,361.79,0.24294,-0.47111,0.84796,72.892
    8475 
    8476 > view matrix models
    8477 > #3,-0.67677,0.0678,0.73307,153.21,-0.71984,-0.26966,-0.63962,466.75,0.15432,-0.96057,0.2313,280.63
    8478 
    8479 > view matrix models
    8480 > #3,-0.31096,-0.28409,0.90697,117.06,-0.89867,-0.2227,-0.37788,443.68,0.30934,-0.93258,-0.18605,323.01
    8481 
    8482 > view matrix models
    8483 > #3,-0.31328,-0.20485,0.9273,100.52,-0.94642,-0.013217,-0.32266,407.02,0.078354,-0.9787,-0.18974,372.05
    8484 
    8485 > view matrix models
    8486 > #3,0.084796,0.15045,0.98497,-39.503,-0.99107,-0.089391,0.098974,352.56,0.10294,-0.98457,0.14152,309.7
    8487 
    8488 > view matrix models
    8489 > #3,-0.17084,-0.018385,0.98513,33.815,-0.98351,0.06341,-0.16938,373.35,-0.059353,-0.99782,-0.028915,370.83
    8490 
    8491 > view matrix models
    8492 > #3,-0.3307,0.24426,0.91158,30.874,-0.94057,-0.0062546,-0.33954,407.82,-0.077235,-0.96969,0.23181,322.8
    8493 
    8494 > view matrix models
    8495 > #3,-0.4809,0.025548,0.8764,100.33,-0.81554,-0.38005,-0.43642,465.94,0.32193,-0.92461,0.2036,250.04
    8496 
    8497 > view matrix models
    8498 > #3,-0.53944,-0.043921,0.84088,128.63,-0.79768,-0.29313,-0.52705,464.33,0.26964,-0.95506,0.12309,278.7
    8499 
    8500 > view matrix models
    8501 > #3,-0.45493,0.037354,0.88974,91.401,-0.78489,-0.48882,-0.3808,468.93,0.4207,-0.87159,0.2517,215.19
    8502 
    8503 > view matrix models
    8504 > #3,-0.42074,0.12675,0.89828,68.835,-0.79214,-0.53394,-0.29568,462.63,0.44215,-0.83597,0.32506,192.35
    8505 
    8506 > view matrix models
    8507 > #3,-0.55645,0.18988,0.80889,98.012,-0.74741,-0.53968,-0.38746,472.08,0.36297,-0.82018,0.44222,182.75
    8508 
    8509 > view matrix models
    8510 > #3,-0.56077,0.17343,0.8096,101.41,-0.75525,-0.50786,-0.41434,472.89,0.3393,-0.8438,0.41578,195.6
    8511 
    8512 > ui mousemode right "rotate selected models"
    8513 
    8514 > ui mousemode right "translate selected models"
    8515 
    8516 > view matrix models
    8517 > #3,-0.56077,0.17343,0.8096,97.107,-0.75525,-0.50786,-0.41434,471.77,0.3393,-0.8438,0.41578,196.64
    8518 
    8519 > ui mousemode right "rotate selected models"
    8520 
    8521 > view matrix models
    8522 > #3,-0.31072,0.047476,0.94931,49.418,-0.82644,-0.50685,-0.24516,453.98,0.46952,-0.86073,0.19672,215.61
    8523 
    8524 > view matrix models
    8525 > #3,-0.10594,-0.13924,0.98458,38.514,-0.92405,-0.35194,-0.1492,428.01,0.36729,-0.92561,-0.091386,295.82
    8526 
    8527 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
    8528 (#6) using 5602 atoms 
    8529 average map value = 0.08181, steps = 140 
    8530 shifted from previous position = 5.91 
    8531 rotated from previous position = 5.33 degrees 
    8532 atoms outside contour = 4112, contour level = 0.12 
    8533  
    8534 Position of D2NS1.pdb (#3) relative to
    8535 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    8536 Matrix rotation and translation 
    8537 0.96127167 0.06226622 -0.26847668 48.62307340 
    8538 -0.22542895 0.73805618 -0.63596769 218.36928771 
    8539 0.15855157 0.67186013 0.72350910 -87.31437189 
    8540 Axis 0.93048244 -0.30381850 -0.20468696 
    8541 Axis point 0.00000000 232.24708974 246.16405973 
    8542 Rotation angle (degrees) 44.64955765 
    8543 Shift along axis -3.22959992 
    8544  
    8545 
    8546 > view matrix models
    8547 > #3,-0.2167,-0.046006,0.97515,46.998,-0.825,-0.52541,-0.20812,455.06,0.52193,-0.8496,0.075903,227.93
    8548 
    8549 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
    8550 (#6) using 5602 atoms 
    8551 average map value = 0.08275, steps = 232 
    8552 shifted from previous position = 0.39 
    8553 rotated from previous position = 10.7 degrees 
    8554 atoms outside contour = 4141, contour level = 0.12 
    8555  
    8556 Position of D2NS1.pdb (#3) relative to
    8557 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    8558 Matrix rotation and translation 
    8559 0.94687496 0.16521963 -0.27591724 34.87295901 
    8560 -0.32111058 0.53311437 -0.78273693 296.77138746 
    8561 0.01777194 0.82975393 0.55784641 -59.68855935 
    8562 Axis 0.94317112 -0.17178339 -0.28446215 
    8563 Axis point 0.00000000 208.08374987 254.78468856 
    8564 Rotation angle (degrees) 58.74030833 
    8565 Shift along axis -1.11009298 
    8566  
    8567 
    8568 > view matrix models
    8569 > #3,-0.29357,0.29509,0.90925,14.248,-0.93223,-0.29887,-0.20399,435.37,0.21155,-0.90752,0.36283,240.41
    8570 
    8571 > view matrix models
    8572 > #3,-0.024736,0.33337,0.94247,-45.387,-0.98041,-0.19235,0.042305,382.05,0.19538,-0.92297,0.3316,251.41
    8573 
    8574 > ui mousemode right "translate selected models"
    8575 
    8576 > view matrix models
    8577 > #3,-0.024736,0.33337,0.94247,-50.647,-0.98041,-0.19235,0.042305,380.65,0.19538,-0.92297,0.3316,252
    8578 
    8579 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
    8580 (#6) using 5602 atoms 
    8581 average map value = 0.07754, steps = 124 
    8582 shifted from previous position = 0.984 
    8583 rotated from previous position = 11.7 degrees 
    8584 atoms outside contour = 4222, contour level = 0.12 
    8585  
    8586 Position of D2NS1.pdb (#3) relative to
    8587 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    8588 Matrix rotation and translation 
    8589 0.97038128 -0.18348442 -0.15714223 69.99792136 
    8590 -0.04643502 0.49668363 -0.86668864 273.08312267 
    8591 0.23707384 0.84831532 0.47345239 -88.46523910 
    8592 Axis 0.97164206 -0.22334462 0.07764586 
    8593 Axis point 0.00000000 220.43718489 187.11160518 
    8594 Rotation angle (degrees) 61.94891347 
    8595 Shift along axis 0.15231786 
    8596  
    8597 
    8598 > view matrix models
    8599 > #3,-0.16161,0.20679,0.96495,-7.8987,-0.94599,-0.31092,-0.091808,418.86,0.28103,-0.92767,0.24587,240.27
    8600 
    8601 > view matrix models
    8602 > #3,-0.16161,0.20679,0.96495,-7.6794,-0.94599,-0.31092,-0.091808,419.8,0.28103,-0.92767,0.24587,239.05
    8603 
    8604 > ui mousemode right "rotate selected models"
    8605 
    8606 > view matrix models
    8607 > #3,-0.065282,0.14337,0.98751,-17.979,-0.96082,-0.2762,-0.023418,404.39,0.26939,-0.95035,0.15578,260.96
    8608 
    8609 > view matrix models
    8610 > #3,0.11914,-0.22697,0.96659,15.581,-0.91769,-0.3968,0.019938,409.35,0.37901,-0.8894,-0.25556,304.72
    8611 
    8612 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
    8613 (#6) using 5602 atoms 
    8614 average map value = 0.082, steps = 232 
    8615 shifted from previous position = 14.3 
    8616 rotated from previous position = 15.8 degrees 
    8617 atoms outside contour = 4100, contour level = 0.12 
    8618  
    8619 Position of D2NS1.pdb (#3) relative to
    8620 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    8621 Matrix rotation and translation 
    8622 0.93730079 0.13375954 -0.32183172 47.54908073 
    8623 -0.32984053 0.63871002 -0.69516528 263.49850116 
    8624 0.11257216 0.75773210 0.64278271 -75.44380421 
    8625 Axis 0.91623198 -0.27394552 -0.29235734 
    8626 Axis point -0.00000000 224.55289345 259.75440758 
    8627 Rotation angle (degrees) 52.45410370 
    8628 Shift along axis -6.56169478 
    8629  
    8630 
    8631 > ui mousemode right "translate selected models"
    8632 
    8633 > view matrix models
    8634 > #3,-0.018323,-0.060034,0.99803,13.026,-0.84305,-0.53571,-0.047702,432.04,0.53752,-0.84226,-0.040796,240.98
    8635 
    8636 > ui mousemode right "rotate selected models"
    8637 
    8638 > view matrix models
    8639 > #3,-0.036597,-0.098259,0.99449,23.297,-0.80637,-0.58491,-0.087465,440.94,0.59028,-0.80513,-0.057828,228.49
    8640 
    8641 > view matrix models
    8642 > #3,-0.027477,-0.10288,0.99431,22.501,-0.77374,-0.6276,-0.086317,442.18,0.63291,-0.77171,-0.062357,216.18
    8643 
    8644 > view matrix models
    8645 > #3,-0.10002,-0.07995,0.99177,31.858,-0.93297,-0.33885,-0.12141,427.89,0.34577,-0.93744,-0.040699,290.69
    8646 
    8647 > view matrix models
    8648 > #3,-0.10077,-0.089813,0.99085,33.811,-0.91689,-0.37822,-0.12753,432.77,0.38621,-0.92135,-0.044236,281.5
    8649 
    8650 > view matrix models
    8651 > #3,-0.032685,-0.1875,0.98172,39.889,-0.92726,-0.36087,-0.099796,426.73,0.37298,-0.91357,-0.16207,303.51
    8652 
    8653 > volume #2 level 0.1688
    8654 
    8655 > hide #!2 models
    8656 
    8657 [Repeated 1 time(s)]
    8658 
    8659 > volume #6 level 0.1932
    8660 
    8661 > view matrix models
    8662 > #3,-0.15943,5.3271e-05,0.98721,29.667,-0.88694,0.43911,-0.14326,292.88,-0.4335,-0.89843,-0.06996,426.39
    8663 
    8664 > view matrix models
    8665 > #3,-0.23062,0.17059,0.95797,18.724,-0.93077,-0.3257,-0.16608,433.25,0.28369,-0.92996,0.23389,251.43
    8666 
    8667 > view matrix models
    8668 > #3,-0.029625,-0.49902,0.86608,112.33,-0.48854,-0.74869,-0.44809,476.83,0.87204,-0.43639,-0.22161,146.12
    8669 
    8670 > view matrix models
    8671 > #3,0.26982,-0.40253,0.87474,41.898,-0.5711,-0.79831,-0.1912,453.92,0.77527,-0.44797,-0.44528,204.93
    8672 
    8673 > view matrix models
    8674 > #3,-0.10768,-0.15758,0.98162,48.065,-0.99351,0.053323,-0.10043,368.86,-0.036518,-0.98607,-0.1623,387.76
    8675 
    8676 > view matrix models
    8677 > #3,-0.059748,-0.20275,0.97741,47.98,-0.99636,0.071795,-0.046014,356.56,-0.060844,-0.9766,-0.2063,398.29
    8678 
    8679 > view matrix models
    8680 > #3,-0.2527,-0.028861,0.96711,54.512,-0.96729,-0.015262,-0.2532,403,0.022068,-0.99947,-0.02406,355.08
    8681 
    8682 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    8683 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/4o6b_DV2NS1.pdb
    8684 
    8685 4o6b_DV2NS1.pdb title: 
    8686 Dengue TYPE2 virus non-structural protein 1 (NS1) form 1 crystal [more
    8687 info...] 
    8688  
    8689 Chain information for 4o6b_DV2NS1.pdb #7 
    8690 --- 
    8691 Chain | Description | UniProt 
    8692 A | NS1 | POLG_DEN26 
    8693 B | NS1 | POLG_DEN26 
    8694  
    8695 Non-standard residues in 4o6b_DV2NS1.pdb #7 
    8696 --- 
    8697 NAG — 2-acetamido-2-deoxy-β-D-glucopyranose 
    8698  
    8699 
    8700 > select #7
    8701 
    8702 5126 atoms, 5257 bonds, 5 pseudobonds, 644 residues, 2 models selected 
    8703 
    8704 > ui mousemode right "translate selected models"
    8705 
    8706 > view matrix models #7,1,0,0,195.73,0,1,0,55.756,0,0,1,0.30073
    8707 
    8708 > view matrix models #7,1,0,0,24.836,0,1,0,111.9,0,0,1,93.148
    8709 
    8710 > view matrix models #7,1,0,0,184.13,0,1,0,225.28,0,0,1,192.15
    8711 
    8712 > view matrix models #7,1,0,0,151.84,0,1,0,239.37,0,0,1,213.11
    8713 
    8714 > view matrix models #7,1,0,0,191.69,0,1,0,227.02,0,0,1,208.55
    8715 
    8716 > ui mousemode right "rotate selected models"
    8717 
    8718 > view matrix models
    8719 > #7,0.98804,-0.14623,0.048956,188.26,0.13002,0.61931,-0.7743,195.13,0.082905,0.77141,0.63092,223.81
    8720 
    8721 > view matrix models
    8722 > #7,0.99657,-0.079109,0.024224,189.79,0.063222,0.5393,-0.83974,190.38,0.053367,0.83839,0.54245,223.38
    8723 
    8724 > view matrix models
    8725 > #7,0.94783,-0.3073,0.084745,183.81,0.25252,0.5616,-0.78793,193.76,0.19454,0.76823,0.6099,223.91
    8726 
    8727 > view matrix models
    8728 > #7,0.59074,0.041726,0.80578,211.73,0.76522,0.28771,-0.57591,194.2,-0.25586,0.95681,0.13803,214.25
    8729 
    8730 > ui mousemode right "translate selected models"
    8731 
    8732 > view matrix models
    8733 > #7,0.59074,0.041726,0.80578,206.56,0.76522,0.28771,-0.57591,184.3,-0.25586,0.95681,0.13803,224.47
    8734 
    8735 > ui mousemode right "rotate selected models"
    8736 
    8737 > view matrix models
    8738 > #7,0.69999,-0.017723,0.71393,202.96,0.67927,0.32512,-0.65794,182.71,-0.22045,0.94551,0.23962,227.06
    8739 
    8740 > view matrix models
    8741 > #7,0.84135,0.059716,0.53718,201.67,0.50634,0.26057,-0.82202,175.1,-0.18906,0.96361,0.18899,226.5
    8742 
    8743 > view matrix models
    8744 > #7,0.91878,0.00070031,0.39477,196.52,0.37034,0.34484,-0.86252,175.78,-0.13674,0.93866,0.31658,229.47
    8745 
    8746 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    8747 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    8748 > sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J141_class_00_final_volume.mrc
    8749 
    8750 Opened cryosparc_P35_J141_class_00_final_volume.mrc as #8, grid size
    8751 128,128,128, pixel 2.79, shown at level 0.235, step 1, values float32 
    8752 
    8753 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    8754 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    8755 > sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J141_class_01_final_volume.mrc
    8756 
    8757 Opened cryosparc_P35_J141_class_01_final_volume.mrc as #10, grid size
    8758 128,128,128, pixel 2.79, shown at level 0.281, step 1, values float32 
    8759 
    8760 > select #10
    8761 
    8762 2 models selected 
    8763 
    8764 > view matrix models
    8765 > #10,-0.079171,0.66364,0.74385,-61.635,-0.22432,-0.73892,0.63536,232.1,0.97129,-0.11656,0.20737,-7.2572
    8766 
    8767 > view matrix models
    8768 > #10,-0.28893,0.313,0.90474,9.1948,-0.47663,-0.86662,0.1476,393.94,0.83026,-0.38858,0.39958,30.91
    8769 
    8770 > ~select #10
    8771 
    8772 Nothing selected 
    8773 
    8774 > select #8
    8775 
    8776 2 models selected 
    8777 
    8778 > view matrix models
    8779 > #8,0.27556,0.9224,0.27065,-84.292,-0.27059,-0.19574,0.94258,80.02,0.92241,-0.33297,0.19565,46.409
    8780 
    8781 > view matrix models
    8782 > #8,0.63638,0.51065,0.57815,-136.4,0.085328,0.6983,-0.7107,175.68,-0.76664,0.50161,0.40081,166.71
    8783 
    8784 > view matrix models
    8785 > #8,-0.3692,-0.17702,0.91234,105.18,-0.32493,-0.89515,-0.30518,456,0.8707,-0.40912,0.27296,54.461
    8786 
    8787 > view matrix models
    8788 > #8,-0.21183,0.1782,0.96092,3.7465,-0.32373,-0.94052,0.10305,384.86,0.92213,-0.28925,0.25692,26.817
    8789 
    8790 > color #10 #ffb2b270 models
    8791 
    8792 [Repeated 1 time(s)]
    8793 
    8794 > color #8 #ffb2ff56 models
    8795 
    8796 > color #8 #ffb2ff57 models
    8797 
    8798 > hide #4 models
    8799 
    8800 > hide #3 models
    8801 
    8802 > hide #!8 models
    8803 
    8804 > hide #9 models
    8805 
    8806 > show #9 models
    8807 
    8808 > hide #9 models
    8809 
    8810 > hide #!10 models
    8811 
    8812 > show #!8 models
    8813 
    8814 > view matrix models
    8815 > #8,0.27556,0.39667,0.87562,-107.73,0.79978,-0.59996,0.020098,134.95,0.53331,0.69477,-0.48257,65.706
    8816 
    8817 > view matrix models
    8818 > #8,0.27366,0.52314,0.80712,-116.65,0.91914,-0.38945,-0.059223,90.987,0.28335,0.75806,-0.58742,120.4
    8819 
    8820 > view matrix models
    8821 > #8,0.33758,0.53414,0.77507,-124.09,0.9382,-0.25771,-0.23103,97.287,0.076338,0.80516,-0.58813,149.98
    8822 
    8823 > view matrix models
    8824 > #8,0.45264,0.48026,0.75131,-130.92,0.89015,-0.19384,-0.41237,129.79,-0.052411,0.85544,-0.51524,150.44
    8825 
    8826 > view matrix models
    8827 > #8,0.65699,0.41807,0.62736,-133.2,0.73578,-0.1742,-0.65443,201.34,-0.16431,0.89156,-0.42206,146.43
    8828 
    8829 > ui mousemode right "translate selected models"
    8830 
    8831 > view matrix models
    8832 > #8,0.65699,0.41807,0.62736,-126.9,0.73578,-0.1742,-0.65443,207.73,-0.16431,0.89156,-0.42206,145.93
    8833 
    8834 > view matrix models
    8835 > #8,0.65699,0.41807,0.62736,-126.22,0.73578,-0.1742,-0.65443,209.21,-0.16431,0.89156,-0.42206,144.54
    8836 
    8837 > view matrix models
    8838 > #8,0.65699,0.41807,0.62736,-124.37,0.73578,-0.1742,-0.65443,208.1,-0.16431,0.89156,-0.42206,144.61
    8839 
    8840 > ui mousemode right "rotate selected models"
    8841 
    8842 > view matrix models
    8843 > #8,0.53344,-0.037486,0.84501,-62.766,0.5106,-0.78219,-0.35703,299.99,0.67434,0.62191,-0.39811,34.754
    8844 
    8845 > volume #8 level 0.8045
    8846 
    8847 > view matrix models
    8848 > #8,0.52401,-0.054439,0.84997,-58.961,0.47038,-0.81345,-0.3421,310.02,0.71003,0.57907,-0.40065,36.512
    8849 
    8850 > volume #8 level 0.3577
    8851 
    8852 > show #!10 models
    8853 
    8854 > hide #!8 models
    8855 
    8856 > view matrix models
    8857 > #8,0.60764,0.020079,0.79396,-76.868,0.73022,-0.40725,-0.54857,228.31,0.31232,0.9131,-0.26212,18.911
    8858 
    8859 > show #!8 models
    8860 
    8861 > view matrix models
    8862 > #8,0.37572,0.11623,0.91941,-75.961,0.70308,-0.68208,-0.20109,215.44,0.60375,0.72198,-0.33799,14.583
    8863 
    8864 Fit map cryosparc_P35_J141_class_01_final_volume.mrc in map
    8865 cryosparc_P35_J141_class_00_final_volume.mrc using 20957 points 
    8866 correlation = 0.9488, correlation about mean = 0.6585, overlap = 4385 
    8867 steps = 288, shift = 15.4, angle = 91.5 degrees 
    8868  
    8869 Position of cryosparc_P35_J141_class_01_final_volume.mrc (#10) relative to
    8870 cryosparc_P35_J141_class_00_final_volume.mrc (#8) coordinates: 
    8871 Matrix rotation and translation 
    8872 0.99679931 0.07719696 -0.02077903 -9.05098271 
    8873 -0.07875179 0.99291028 -0.08903553 30.04476737 
    8874 0.01375844 0.09038694 0.99581168 -19.54599107 
    8875 Axis 0.74691139 -0.14377477 -0.64919349 
    8876 Axis point 0.00000000 219.63678499 322.55619772 
    8877 Rotation angle (degrees) 6.89842857 
    8878 Shift along axis 1.60916844 
    8879  
    8880 
    8881 > volume #6 level 0.1566
    8882 
    8883 > volume #6 level 0.1346
    8884 
    8885 Fit map cryosparc_P35_J141_class_01_final_volume.mrc in map
    8886 cryosparc_P35_J90_005_volume_map_sharp.mrc using 20957 points 
    8887 correlation = 0.7294, correlation about mean = 0.2901, overlap = 713.6 
    8888 steps = 312, shift = 14.7, angle = 29.6 degrees 
    8889  
    8890 Position of cryosparc_P35_J141_class_01_final_volume.mrc (#10) relative to
    8891 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    8892 Matrix rotation and translation 
    8893 -0.81655312 0.57639109 -0.03184812 223.81505889 
    8894 -0.57200743 -0.81530920 -0.08987989 441.91818039 
    8895 -0.07777204 -0.05517435 0.99544327 24.62573349 
    8896 Axis 0.03018293 0.03993939 -0.99874613 
    8897 Axis point 182.23608880 186.02084504 0.00000000 
    8898 Rotation angle (degrees) 144.90596060 
    8899 Shift along axis -0.18951992 
    8900  
    8901 Fit map cryosparc_P35_J141_class_00_final_volume.mrc in map
    8902 cryosparc_P35_J90_005_volume_map_sharp.mrc using 13326 points 
    8903 correlation = 0.7531, correlation about mean = 0.2446, overlap = 614.5 
    8904 steps = 200, shift = 14.7, angle = 20.2 degrees 
    8905  
    8906 Position of cryosparc_P35_J141_class_00_final_volume.mrc (#8) relative to
    8907 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    8908 Matrix rotation and translation 
    8909 -0.51114495 0.85836696 -0.04401141 122.12595771 
    8910 -0.83601173 -0.50841524 -0.20639360 453.44795134 
    8911 -0.19953752 -0.06870298 0.97747873 53.02558896 
    8912 Axis 0.08065933 0.09110739 -0.99256915 
    8913 Axis point 191.43391939 194.60207731 0.00000000 
    8914 Rotation angle (degrees) 121.40208746 
    8915 Shift along axis -1.46850799 
    8916  
    8917 
    8918 > volume #10 level 0.3562
    8919 
    8920 > volume #8 level 0.2852
    8921 
    8922 > volume #8 level 0.318
    8923 
    8924 > hide #!7 models
    8925 
    8926 > show #!7 models
    8927 
    8928 > select #7
    8929 
    8930 5126 atoms, 5257 bonds, 5 pseudobonds, 644 residues, 2 models selected 
    8931 
    8932 > ui mousemode right "translate selected models"
    8933 
    8934 > view matrix models
    8935 > #7,0.91878,0.00070031,0.39477,195.03,0.37034,0.34484,-0.86252,183.44,-0.13674,0.93866,0.31658,212.37
    8936 
    8937 > view matrix models
    8938 > #7,0.91878,0.00070031,0.39477,207.4,0.37034,0.34484,-0.86252,186.87,-0.13674,0.93866,0.31658,221.02
    8939 
    8940 > ui mousemode right "rotate selected models"
    8941 
    8942 > view matrix models
    8943 > #7,0.73404,-0.62761,0.2594,182.53,-0.25829,-0.61129,-0.74807,155.21,0.62806,0.48212,-0.61082,186.96
    8944 
    8945 > view matrix models
    8946 > #7,0.74989,-0.64446,0.14946,179.17,-0.33839,-0.56778,-0.75041,155.99,0.56846,0.51215,-0.64386,186.63
    8947 
    8948 > ui mousemode right "translate selected models"
    8949 
    8950 > view matrix models
    8951 > #7,0.74989,-0.64446,0.14946,177.57,-0.33839,-0.56778,-0.75041,160.17,0.56846,0.51215,-0.64386,189.52
    8952 
    8953 > view matrix models
    8954 > #7,0.74989,-0.64446,0.14946,178.16,-0.33839,-0.56778,-0.75041,160.58,0.56846,0.51215,-0.64386,182.7
    8955 
    8956 > view matrix models
    8957 > #7,0.74989,-0.64446,0.14946,177.56,-0.33839,-0.56778,-0.75041,162.27,0.56846,0.51215,-0.64386,183.32
    8958 
    8959 > view matrix models
    8960 > #7,0.74989,-0.64446,0.14946,179.58,-0.33839,-0.56778,-0.75041,162.74,0.56846,0.51215,-0.64386,180.3
    8961 
    8962 > ui mousemode right "rotate selected models"
    8963 
    8964 > view matrix models
    8965 > #7,0.69567,-0.70398,0.14302,177.14,-0.33345,-0.49279,-0.80372,163.74,0.63628,0.51144,-0.57756,182.51
    8966 
    8967 > view matrix models
    8968 > #7,0.76223,-0.64567,0.045974,176.86,-0.30995,-0.42641,-0.84977,164.78,0.56827,0.63347,-0.52515,187.33
    8969 
    8970 > view matrix models
    8971 > #7,0.78877,-0.61274,0.04891,178.17,-0.30035,-0.4536,-0.83907,164.27,0.53632,0.64714,-0.54182,187.1
    8972 
    8973 > view matrix models
    8974 > #7,0.6402,-0.76747,-0.033591,170.03,-0.27585,-0.18885,-0.94246,170.1,0.71697,0.61263,-0.33261,192.81
    8975 
    8976 > view matrix models
    8977 > #7,0.62699,-0.77647,0.063022,172.23,-0.19611,-0.23561,-0.95186,168.91,0.75394,0.58444,-0.3,193.04
    8978 
    8979 > view matrix models
    8980 > #7,0.75838,-0.62248,0.19333,181.51,-0.13362,-0.43878,-0.8886,164.56,0.63797,0.64807,-0.41594,191.18
    8981 
    8982 > view matrix models
    8983 > #7,0.70141,-0.70676,0.092259,175.74,-0.28093,-0.39309,-0.87553,165.35,0.65506,0.58819,-0.47427,187.83
    8984 
    8985 > view matrix models
    8986 > #7,0.69618,-0.71217,0.090246,175.48,-0.28016,-0.38529,-0.87924,165.51,0.66094,0.58683,-0.46775,188
    8987 
    8988 > view matrix models
    8989 > #7,0.68522,-0.72338,0.084779,174.9,-0.27616,-0.36576,-0.88879,165.9,0.67395,0.58561,-0.4504,188.52
    8990 
    8991 > view matrix models
    8992 > #7,0.74436,-0.66753,0.018223,175.3,-0.26396,-0.31919,-0.91019,166.9,0.61339,0.6727,-0.4138,191.85
    8993 
    8994 > view matrix models
    8995 > #7,0.77161,-0.63604,-0.0079224,175.8,-0.26676,-0.31226,-0.91177,167.06,0.57745,0.70565,-0.41062,192.74
    8996 
    8997 > view matrix models
    8998 > #7,0.73389,-0.66982,0.11293,177.69,-0.19652,-0.36852,-0.90861,165.83,0.65022,0.64462,-0.40208,191.52
    8999 
    9000 > ui mousemode right "translate selected models"
    9001 
    9002 > view matrix models
    9003 > #7,0.73389,-0.66982,0.11293,176.82,-0.19652,-0.36852,-0.90861,164.33,0.65022,0.64462,-0.40208,195.23
    9004 
    9005 > show #3 models
    9006 
    9007 > hide #3 models
    9008 
    9009 > show #!2 models
    9010 
    9011 > show #3 models
    9012 
    9013 > hide #!10 models
    9014 
    9015 > hide #!7 models
    9016 
    9017 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    9018 (#2) using 5602 atoms 
    9019 average map value = 0.1888, steps = 160 
    9020 shifted from previous position = 4.81 
    9021 rotated from previous position = 23.5 degrees 
    9022 atoms outside contour = 2712, contour level = 0.1688 
    9023  
    9024 Position of D2NS1.pdb (#3) relative to
    9025 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    9026 Matrix rotation and translation 
    9027 -0.55420887 0.78282865 -0.28289899 176.19297958 
    9028 -0.82333712 -0.46560234 0.32454654 303.63070097 
    9029 0.12234590 0.41278781 0.90257282 -106.76939213 
    9030 Axis 0.05319429 -0.24429289 -0.96824137 
    9031 Axis point 171.19224328 117.42998509 0.00000000 
    9032 Rotation angle (degrees) 123.96035927 
    9033 Shift along axis 38.57618189 
    9034  
    9035 
    9036 > close #10
    9037 
    9038 > show #9 models
    9039 
    9040 > hide #9 models
    9041 
    9042 > show #!7 models
    9043 
    9044 > view matrix models
    9045 > #7,0.73389,-0.66982,0.11293,170.79,-0.19652,-0.36852,-0.90861,155.22,0.65022,0.64462,-0.40208,205.07
    9046 
    9047 > ui mousemode right "rotate selected models"
    9048 
    9049 > view matrix models
    9050 > #7,0.90325,0.19269,0.38342,206.62,0.0001087,0.89341,-0.44925,208.99,-0.42912,0.40583,0.80695,222.37
    9051 
    9052 > view matrix models
    9053 > #7,0.91285,-0.26756,0.30841,190.03,0.40807,0.57317,-0.7106,194.6,0.013357,0.77453,0.6324,232.47
    9054 
    9055 > view matrix models
    9056 > #7,0.76546,-0.55709,0.32206,180.18,0.59967,0.43603,-0.67102,192.6,0.23339,0.70677,0.66784,232.76
    9057 
    9058 > view matrix models
    9059 > #7,0.49342,-0.33249,0.80373,198.32,0.86883,0.23191,-0.43745,194.17,-0.040945,0.91415,0.4033,230.43
    9060 
    9061 > view matrix models
    9062 > #7,0.61212,-0.26384,0.74546,199.76,0.7065,0.60592,-0.36567,206.88,-0.35521,0.7505,0.5573,227.19
    9063 
    9064 > ui mousemode right "translate selected models"
    9065 
    9066 > view matrix models
    9067 > #7,0.61212,-0.26384,0.74546,192.13,0.7065,0.60592,-0.36567,204.9,-0.35521,0.7505,0.5573,229.56
    9068 
    9069 Fit molecule 4o6b_DV2NS1.pdb (#7) to map
    9070 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 5126 atoms 
    9071 average map value = 0.1927, steps = 152 
    9072 shifted from previous position = 14.6 
    9073 rotated from previous position = 16.1 degrees 
    9074 atoms outside contour = 2452, contour level = 0.1688 
    9075  
    9076 Position of 4o6b_DV2NS1.pdb (#7) relative to
    9077 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    9078 Matrix rotation and translation 
    9079 0.34465485 -0.66063558 -0.66691350 125.14009286 
    9080 0.80909618 0.56930074 -0.14580812 154.59882031 
    9081 0.47600039 -0.48934370 0.73073000 156.62388255 
    9082 Axis -0.18145322 -0.60367956 0.77630260 
    9083 Axis point -61.23617800 251.69459436 0.00000000 
    9084 Rotation angle (degrees) 71.19533318 
    9085 Shift along axis 5.55230604 
    9086  
    9087 
    9088 > close #7
    9089 
    9090 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    9091 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    9092 > sNS1-Fab56-2/cryosparc_P35_J130_004_volume_map_sharp.mrc
    9093 
    9094 Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
    9095 416,416,416, pixel 0.858, shown at level 0.0371, step 2, values float32 
    9096 
    9097 > volume #7 level 0.09025
    9098 
    9099 > lighting simple
    9100 
    9101 > hide #3 models
    9102 
    9103 > hide #!7 models
    9104 
    9105 > hide #!6 models
    9106 
    9107 > show #!7 models
    9108 
    9109 > show #3 models
    9110 
    9111 > show #!1 models
    9112 
    9113 > hide #!2 models
    9114 
    9115 > hide #3 models
    9116 
    9117 > select #7
    9118 
    9119 2 models selected 
    9120 
    9121 > ui mousemode right "rotate selected models"
    9122 
    9123 > view matrix models
    9124 > #7,0.24103,-0.29696,-0.92397,349.21,-0.038945,-0.95423,0.29653,285.57,-0.96974,-0.035487,-0.24156,398.71
    9125 
    9126 > view matrix models
    9127 > #7,-0.24983,0.23805,-0.93857,346.61,-0.30202,0.90179,0.30911,13.804,0.91998,0.3607,-0.1534,-14.399
    9128 
    9129 > view matrix models
    9130 > #7,-0.10249,0.16037,-0.98172,341.85,0.025379,0.98702,0.15858,-30.757,0.99441,-0.0086622,-0.10523,26.713
    9131 
    9132 > ui mousemode right "translate selected models"
    9133 
    9134 > view matrix models
    9135 > #7,-0.10249,0.16037,-0.98172,336.3,0.025379,0.98702,0.15858,-28.758,0.99441,-0.0086622,-0.10523,26.913
    9136 
    9137 > view matrix models
    9138 > #7,-0.10249,0.16037,-0.98172,337.29,0.025379,0.98702,0.15858,-28.672,0.99441,-0.0086622,-0.10523,28.197
    9139 
    9140 > ui mousemode right "rotate selected models"
    9141 
    9142 > view matrix models
    9143 > #7,-0.22211,-0.1265,-0.96678,404.24,-0.24639,0.96665,-0.069873,63.34,0.94338,0.22268,-0.24587,23.093
    9144 
    9145 > view matrix models
    9146 > #7,-0.19183,0.047993,-0.98025,371.72,-0.43799,0.88964,0.12927,74.05,0.87827,0.45414,-0.14964,-22.192
    9147 
    9148 > view matrix models
    9149 > #7,-0.34489,-0.073759,-0.93574,411.13,-0.53139,0.83711,0.12987,99.175,0.77374,0.54204,-0.32791,13.194
    9150 
    9151 > view matrix models
    9152 > #7,-0.36324,0.1037,-0.92591,382.4,-0.38069,0.89052,0.24908,42.339,0.85037,0.44296,-0.284,8.7541
    9153 
    9154 > view matrix models
    9155 > #7,-0.36165,0.10266,-0.92664,382.44,-0.38188,0.8904,0.24768,42.819,0.85051,0.44344,-0.28281,8.4329
    9156 
    9157 > view matrix models
    9158 > #7,-0.35715,0.16036,-0.92018,370.68,-0.43075,0.84586,0.3146,46.881,0.82879,0.50872,-0.23302,-7.8271
    9159 
    9160 > view matrix models
    9161 > #7,-0.37647,0.070708,-0.92373,389.93,-0.48903,0.83168,0.26297,68.754,0.78684,0.55073,-0.27853,0.54545
    9162 
    9163 > view matrix models
    9164 > #7,-0.21108,0.96488,-0.15637,71.026,-0.41939,0.055099,0.90613,72.864,0.88292,0.25684,0.39304,-87.108
    9165 
    9166 > view matrix models
    9167 > #7,-0.19093,-0.093424,0.97715,43.432,-0.59513,-0.78062,-0.19092,442.95,0.78062,-0.61798,0.093448,133.33
    9168 
    9169 > view matrix models
    9170 > #7,-0.25485,0.0071755,0.96696,39.327,0.96698,0.0034538,0.25483,-43.217,-0.0015111,0.99997,-0.0078187,13.125
    9171 
    9172 > view matrix models
    9173 > #7,-0.017228,0.34616,0.93802,-54.562,0.65851,0.70988,-0.24988,-18.615,-0.75238,0.61338,-0.24018,251.72
    9174 
    9175 > view matrix models
    9176 > #7,0.28808,0.16888,0.9426,-78.558,0.64678,0.69156,-0.32157,-0.5571,-0.70617,0.7023,0.089997,169.14
    9177 
    9178 > view matrix models
    9179 > #7,0.16326,0.14447,0.97595,-58.619,0.66325,0.71625,-0.21698,-26.446,-0.73037,0.68273,0.021113,189.08
    9180 
    9181 Fit map cryosparc_P35_J130_004_volume_map_sharp.mrc in map
    9182 cryosparc_P35_J96_006_volume_map_sharp.mrc using 19964 points 
    9183 correlation = 0.8354, correlation about mean = 0.6739, overlap = 929.1 
    9184 steps = 276, shift = 3.71, angle = 23.7 degrees 
    9185  
    9186 Position of cryosparc_P35_J130_004_volume_map_sharp.mrc (#7) relative to
    9187 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    9188 Matrix rotation and translation 
    9189 0.08559775 -0.03414562 -0.99574450 347.85846819 
    9190 0.92968539 -0.35664221 0.09214889 59.72132131 
    9191 -0.35827099 -0.93361685 0.00121691 410.96755552 
    9192 Axis -0.66385471 -0.41255988 0.62377181 
    9193 Axis point 0.00000000 67.86622584 347.54047210 
    9194 Rotation angle (degrees) 129.41358899 
    9195 Shift along axis 0.78387399 
    9196  
    9197 
    9198 > volume #1 level 0.09
    9199 
    9200 > volume #7 level 0.09
    9201 
    9202 > ~select #7
    9203 
    9204 Nothing selected 
    9205 
    9206 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    9207 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
    9208 > NS1ts.cxs" includeMaps true
    9209 
    9210 ——— End of log from Fri Mar 11 18:14:28 2022 ———
    9211 
    9212 opened ChimeraX session 
    9213 
    9214 > show #!2 models
    9215 
    9216 > hide #!2 models
    9217 
    9218 > show #!2 models
    9219 
    9220 > hide #!1 models
    9221 
    9222 > hide #!7 models
    9223 
    9224 > show #3 models
    9225 
    9226 > show #4 models
    9227 
    9228 > show #!8 models
    9229 
    9230 > hide #!8 models
    9231 
    9232 > close #8
    9233 
    9234 > show #!6 models
    9235 
    9236 > hide #!6 models
    9237 
    9238 > show #!6 models
    9239 
    9240 > hide #!6 models
    9241 
    9242 > close #6
    9243 
    9244 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    9245 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    9246 > includeMaps true
    9247 
    9248 ——— End of log from Sat Mar 12 14:58:51 2022 ———
    9249 
    9250 opened ChimeraX session 
    9251 
    9252 > show #!1 models
    9253 
    9254 > hide #!1 models
    9255 
    9256 > open "/Users/alvinchew/Library/CloudStorage/OneDrive-
    9257 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P39_J166_002_volume_map_sharp
    9258 > (1).mrc"
    9259 
    9260 Opened cryosparc_P39_J166_002_volume_map_sharp (1).mrc as #6, grid size
    9261 416,416,416, pixel 0.85, shown at level 0.0339, step 2, values float32 
    9262 
    9263 > volume #6 level 0.05868
    9264 
    9265 > volume #6 step 1
    9266 
    9267 > ui mousemode right "translate selected models"
    9268 
    9269 > show #!7 models
    9270 
    9271 > hide #!7 models
    9272 
    9273 > show #9 models
    9274 
    9275 > hide #9 models
    9276 
    9277 > select #6
    9278 
    9279 2 models selected 
    9280 
    9281 > view matrix models #6,1,0,0,1.4767,0,1,0,-0.11126,0,0,1,17.894
    9282 
    9283 > view matrix models #6,1,0,0,2.5835,0,1,0,15.467,0,0,1,19.701
    9284 
    9285 > ui mousemode right "rotate selected models"
    9286 
    9287 > view matrix models
    9288 > #6,0.077918,0.99542,-0.055373,-3.5895,-0.96552,0.089183,0.24459,303.08,0.24841,0.034406,0.96804,-24.193
    9289 
    9290 > view matrix models
    9291 > #6,-0.62577,0.77732,-0.06471,158.15,-0.76968,-0.62881,-0.1104,452.92,-0.12651,-0.019279,0.99178,46.339
    9292 
    9293 > view matrix models
    9294 > #6,-0.49195,0.83765,-0.23731,152.38,-0.80175,-0.32963,0.49855,307.08,0.33939,0.43553,0.83375,-88.641
    9295 
    9296 > view matrix models
    9297 > #6,-0.43603,0.58765,-0.68157,258.71,-0.82618,0.03888,0.56206,236.26,0.3568,0.80818,0.46855,-97.873
    9298 
    9299 > view matrix models
    9300 > #6,0.17544,0.72595,-0.66499,125.79,-0.86837,0.43236,0.24289,226.23,0.46384,0.53485,0.70625,-106.96
    9301 
    9302 > view matrix models
    9303 > #6,-0.010663,0.39041,-0.92058,258.46,-0.28789,0.88046,0.37672,25.213,0.95761,0.26904,0.103,-47.908
    9304 
    9305 > ui mousemode right "translate selected models"
    9306 
    9307 > view matrix models
    9308 > #6,-0.010663,0.39041,-0.92058,281.12,-0.28789,0.88046,0.37672,26.602,0.95761,0.26904,0.103,-46.122
    9309 
    9310 > ui mousemode right "rotate selected models"
    9311 
    9312 > view matrix models
    9313 > #6,0.14635,0.34874,-0.92572,262.07,-0.39341,0.87913,0.26899,62.599,0.90764,0.32483,0.26586,-73.695
    9314 
    9315 > view matrix models
    9316 > #6,0.12836,0.25158,-0.95929,287.7,-0.38687,0.90336,0.18515,70.814,0.91316,0.34735,0.21329,-70.077
    9317 
    9318 > view matrix models
    9319 > #6,0.14119,0.15753,-0.97737,304.94,-0.41649,0.90509,0.085709,91.778,0.89811,0.39496,0.1934,-72.61
    9320 
    9321 > view matrix models
    9322 > #6,0.16148,0.39933,-0.90248,246.79,-0.45122,0.84317,0.29235,75.141,0.87768,0.36001,0.31634,-82.878
    9323 
    9324 > view matrix models
    9325 > #6,0.26156,0.1615,-0.95158,279.21,-0.12782,0.98301,0.1317,20.613,0.95669,0.087181,0.27776,-42.368
    9326 
    9327 > ui mousemode right "translate selected models"
    9328 
    9329 > view matrix models
    9330 > #6,0.26156,0.1615,-0.95158,282.66,-0.12782,0.98301,0.1317,9.0483,0.95669,0.087181,0.27776,-38.201
    9331 
    9332 > ui mousemode right "rotate selected models"
    9333 
    9334 > view matrix models
    9335 > #6,0.13471,0.17399,-0.97549,306.32,-0.19051,0.97064,0.14682,19.629,0.9724,0.16606,0.1639,-36.307
    9336 
    9337 > view matrix models
    9338 > #6,0.1878,0.10849,-0.9762,308.75,-0.44957,0.89315,0.012769,99.878,0.87328,0.43647,0.21651,-75.185
    9339 
    9340 > view matrix models
    9341 > #6,0.28328,0.3407,-0.89648,238.47,-0.3572,0.905,0.23106,46.37,0.89003,0.25476,0.37807,-72.377
    9342 
    9343 > volume #6 level 0.169
    9344 
    9345 > volume #6 level 0.05336
    9346 
    9347 > ui tool show "Fit in Map"
    9348 
    9349 Fit map cryosparc_P39_J166_002_volume_map_sharp (1).mrc in map
    9350 cryosparc_P47_J20_004_volume_map_sharp.mrc using 331401 points 
    9351 correlation = 0.898, correlation about mean = 0.6711, overlap = 6198 
    9352 steps = 152, shift = 5.34, angle = 16.7 degrees 
    9353  
    9354 Position of cryosparc_P39_J166_002_volume_map_sharp (1).mrc (#6) relative to
    9355 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    9356 Matrix rotation and translation 
    9357 -0.92297785 -0.38455624 0.01511101 379.01804384 
    9358 -0.38212566 0.91106400 -0.15473309 83.70405585 
    9359 0.04573648 -0.14858952 -0.98784072 344.43723548 
    9360 Axis 0.19609203 -0.97751177 0.07757998 
    9361 Axis point 196.53062877 0.00000000 177.04366349 
    9362 Rotation angle (degrees) 179.10242404 
    9363 Shift along axis 19.22215351 
    9364  
    9365 
    9366 > volume #6 level 0.05037
    9367 
    9368 > volume #6 level 0.03372
    9369 
    9370 > volume #6 level 0.02603
    9371 
    9372 > volume #2 level 0.1649
    9373 
    9374 > volume #2 level 0.1496
    9375 
    9376 > show #9 models
    9377 
    9378 > volume #6 color #bf9d9e
    9379 
    9380 > volume #6 color #bf9d9e57
    9381 
    9382 > volume #6 level 0.05379
    9383 
    9384 > volume #6 level 0.06874
    9385 
    9386 > volume #2 level 0.1649
    9387 
    9388 > volume #2 level 0.17
    9389 
    9390 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    9391 > University/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig4_E2.png"
    9392 > width 1326 height 850 supersample 3 transparentBackground true
    9393 
    9394 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    9395 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220125_NTU-K2_NS1-WT_Fab/cryosparc_P36_J32_002_volume_map_sharp.mrc
    9396 
    9397 Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
    9398 416,416,416, pixel 0.85, shown at level 0.0324, step 2, values float32 
    9399 
    9400 > select #8
    9401 
    9402 2 models selected 
    9403 
    9404 > view matrix models
    9405 > #8,0.93452,-0.21005,-0.2873,102.16,-0.33903,-0.27981,-0.8982,451.28,0.10828,0.93679,-0.3327,69.288
    9406 
    9407 > view matrix models
    9408 > #8,-0.43794,-0.41147,0.79931,176.41,-0.88911,0.32976,-0.31738,334,-0.13299,-0.84967,-0.51026,455.34
    9409 
    9410 > view matrix models
    9411 > #8,-0.13025,-0.70515,0.697,191.9,-0.98813,0.15007,-0.032822,329.17,-0.081457,-0.693,-0.71632,457.81
    9412 
    9413 > close #8
    9414 
    9415 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    9416 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220125_NTU-K2_NS1-WT_Fab/cryosparc_P36_J32_002_volume_map_sharp.mrc
    9417 
    9418 Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
    9419 416,416,416, pixel 0.85, shown at level 0.0324, step 2, values float32 
    9420 
    9421 > color #8 #fff5c5 models transparency 0
    9422 
    9423 > select #8
    9424 
    9425 2 models selected 
    9426 
    9427 > view matrix models
    9428 > #8,-0.37477,-0.5067,0.77641,186,-0.92653,0.23447,-0.29422,352.81,-0.032965,-0.82963,-0.55734,442.95
    9429 
    9430 > view matrix models
    9431 > #8,-0.40741,-0.58403,0.70209,219.21,-0.91262,0.28892,-0.28924,339.96,-0.033924,-0.75857,-0.6507,448.38
    9432 
    9433 > view matrix models
    9434 > #8,-0.26337,-0.46915,0.84293,147.17,-0.95679,0.23865,-0.16612,333.34,-0.12323,-0.85026,-0.51174,453.98
    9435 
    9436 > ui mousemode right zoom
    9437 
    9438 > ui mousemode right "translate selected models"
    9439 
    9440 > view matrix models
    9441 > #8,-0.26337,-0.46915,0.84293,164.19,-0.95679,0.23865,-0.16612,339.86,-0.12323,-0.85026,-0.51174,459.4
    9442 
    9443 > color #8 #fff5c592 models
    9444 
    9445 > color #8 #fff5c591 models
    9446 
    9447 > view matrix models
    9448 > #8,-0.26337,-0.46915,0.84293,164.75,-0.95679,0.23865,-0.16612,339.53,-0.12323,-0.85026,-0.51174,460.75
    9449 
    9450 > ui mousemode right "rotate selected models"
    9451 
    9452 > view matrix models
    9453 > #8,-0.30728,0.18959,0.93254,41.475,-0.40778,0.85919,-0.30905,161.27,-0.85982,-0.47524,-0.1867,465.45
    9454 
    9455 > view matrix models
    9456 > #8,-0.48566,0.40603,0.77413,65.486,-0.39669,0.68678,-0.60908,245.69,-0.77896,-0.60289,-0.17248,470.53
    9457 
    9458 > view matrix models
    9459 > #8,-0.49722,0.30467,0.81237,77.911,-0.61559,0.53594,-0.57777,304.85,-0.61141,-0.78737,-0.078928,455.12
    9460 
    9461 > view matrix models
    9462 > #8,0.06302,-0.34884,0.93506,68.532,-0.69818,-0.6849,-0.20846,461.65,0.71314,-0.63971,-0.28672,233.22
    9463 
    9464 > view matrix models
    9465 > #8,0.26213,-0.7558,0.60005,166.78,-0.96461,-0.18676,0.18614,348.34,-0.028616,-0.62761,-0.778,455.47
    9466 
    9467 > view matrix models
    9468 > #8,-0.37994,0.023033,0.92472,84.739,-0.51716,0.82356,-0.233,172.57,-0.76693,-0.56676,-0.301,486.33
    9469 
    9470 > view matrix models
    9471 > #8,0.19338,0.23275,0.95312,-58.871,-0.72187,0.69166,-0.022445,192.18,-0.66446,-0.68369,0.30177,374.89
    9472 
    9473 > view matrix models
    9474 > #8,-0.21084,0.47884,0.85221,-10.689,-0.12039,0.85245,-0.50876,148.96,-0.97008,-0.20987,-0.12208,426.87
    9475 
    9476 > view matrix models
    9477 > #8,-0.41196,0.43496,0.80069,42.367,-0.11525,0.84679,-0.51929,151.02,-0.90389,-0.30621,-0.29871,465.07
    9478 
    9479 > view matrix models
    9480 > #8,-0.47775,0.38326,0.79049,64.945,-0.089881,0.87377,-0.47796,134.05,-0.87389,-0.29939,-0.38299,474.43
    9481 
    9482 > ui mousemode right "translate selected models"
    9483 
    9484 > view matrix models
    9485 > #8,-0.47775,0.38326,0.79049,62.298,-0.089881,0.87377,-0.47796,139.19,-0.87389,-0.29939,-0.38299,469.27
    9486 
    9487 > ui mousemode right "rotate selected models"
    9488 
    9489 [Repeated 1 time(s)]
    9490 
    9491 > view matrix models
    9492 > #8,-0.62887,0.14228,0.76438,135.85,-0.3807,0.80086,-0.46227,200.57,-0.67794,-0.5817,-0.44947,495.91
    9493 
    9494 > view matrix models
    9495 > #8,-0.68532,0.11195,0.71959,159.58,-0.34754,0.81805,-0.45826,190.94,-0.63997,-0.56414,-0.52172,499.72
    9496 
    9497 > view matrix models
    9498 > #8,-0.62799,-0.10151,0.77157,176.61,-0.55751,0.75043,-0.35503,220.55,-0.54297,-0.65311,-0.52785,499.06
    9499 
    9500 > ui tool show "Fit in Map"
    9501 
    9502 Fit map cryosparc_P36_J32_002_volume_map_sharp.mrc in map
    9503 cryosparc_P47_J20_004_volume_map_sharp.mrc using 89910 points 
    9504 correlation = 0.5947, correlation about mean = 0.2353, overlap = 907.9 
    9505 steps = 260, shift = 8.79, angle = 25 degrees 
    9506  
    9507 Position of cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) relative to
    9508 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    9509 Matrix rotation and translation 
    9510 0.83017657 0.55542318 0.04808244 -106.08230735 
    9511 -0.55722739 0.82397862 0.10274640 83.33490981 
    9512 0.01744883 -0.11209051 0.99354477 -6.27353855 
    9513 Axis -0.18951476 0.02702292 -0.98150594 
    9514 Axis point 82.90354713 206.61275632 0.00000000 
    9515 Rotation angle (degrees) 34.52792807 
    9516 Shift along axis 28.51363138 
    9517  
    9518 
    9519 > volume #8 level 0.03877
    9520 
    9521 > volume #8 step 1
    9522 
    9523 > volume #8 level 0.05098
    9524 
    9525 > volume #8 level 0.08193
    9526 
    9527 > volume #8 level 0.07541
    9528 
    9529 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    9530 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-23_NS1wt-Ab-Fab-
    9531 > ApoAI_hdl.cxs" includeMaps true
    9532 
    9533 ——— End of log from Thu Mar 24 12:02:48 2022 ———
    9534 
    9535 opened ChimeraX session 
    9536 
    9537 > ui tool show "Volume Viewer"
    9538 
    9539 > show #!1 models
    9540 
    9541 > close #1
    9542 
    9543 > show #!2 models
    9544 
    9545 > hide #!8 models
    9546 
    9547 > show #!8 models
    9548 
    9549 > hide #!8 models
    9550 
    9551 > show #!8 models
    9552 
    9553 > hide #!2 models
    9554 
    9555 > show #!2 models
    9556 
    9557 > rename #2 sNS1wt-Ab562.mrc
    9558 
    9559 > show #!6 models
    9560 
    9561 > hide #!6 models
    9562 
    9563 > show #!6 models
    9564 
    9565 > hide #!6 models
    9566 
    9567 > hide #!2 models
    9568 
    9569 > hide #3 models
    9570 
    9571 > show #3 models
    9572 
    9573 > hide #4 models
    9574 
    9575 > show #4 models
    9576 
    9577 > show #5 models
    9578 
    9579 > hide #5 models
    9580 
    9581 > show #!6 models
    9582 
    9583 > hide #!6 models
    9584 
    9585 > show #!6 models
    9586 
    9587 > show #!2 models
    9588 
    9589 > hide #!2 models
    9590 
    9591 > show #!2 models
    9592 
    9593 > hide #!2 models
    9594 
    9595 > hide #!8 models
    9596 
    9597 > volume #6 level 0.0595
    9598 
    9599 > show #!2 models
    9600 
    9601 > hide #!6 models
    9602 
    9603 > show #!6 models
    9604 
    9605 > hide #!2 models
    9606 
    9607 > show #!2 models
    9608 
    9609 > close #6
    9610 
    9611 > show #!7 models
    9612 
    9613 > hide #!2 models
    9614 
    9615 > show #!2 models
    9616 
    9617 > close #7
    9618 
    9619 > show #5 models
    9620 
    9621 > show #!8 models
    9622 
    9623 > hide #9 models
    9624 
    9625 > show #9 models
    9626 
    9627 > hide #!2 models
    9628 
    9629 > show #!2 models
    9630 
    9631 > hide #!2 models
    9632 
    9633 > hide #3 models
    9634 
    9635 > show #3 models
    9636 
    9637 > hide #3 models
    9638 
    9639 > hide #4 models
    9640 
    9641 > show #4 models
    9642 
    9643 > hide #4 models
    9644 
    9645 > hide #5 models
    9646 
    9647 > show #5 models
    9648 
    9649 > hide #!8 models
    9650 
    9651 > show #!8 models
    9652 
    9653 > hide #9 models
    9654 
    9655 > select add #5
    9656 
    9657 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    9658 
    9659 > ui mousemode right select
    9660 
    9661 > ui mousemode right zoom
    9662 
    9663 > ui mousemode right "translate selected models"
    9664 
    9665 > view matrix models
    9666 > #5,0.911,-0.19028,-0.36588,158.81,-0.385,-0.71042,-0.58914,511.26,-0.14783,0.67757,-0.72045,241.26
    9667 
    9668 > ui mousemode right "rotate selected models"
    9669 
    9670 > view matrix models
    9671 > #5,0.033091,0.22459,0.97389,-84.329,0.17148,0.9587,-0.22691,18.38,-0.98463,0.17451,-0.006788,310.39
    9672 
    9673 > ui mousemode right "translate selected models"
    9674 
    9675 > view matrix models
    9676 > #5,0.033091,0.22459,0.97389,-41.613,0.17148,0.9587,-0.22691,17.858,-0.98463,0.17451,-0.006788,323.69
    9677 
    9678 > ui mousemode right "rotate selected models"
    9679 
    9680 > view matrix models
    9681 > #5,-0.027159,0.41704,0.90848,-51.291,0.63529,0.70888,-0.30642,2.4644,-0.77179,0.56883,-0.2842,279.48
    9682 
    9683 > view matrix models
    9684 > #5,-0.080191,0.31482,0.94576,-31.96,0.72243,0.67208,-0.16247,-40.126,-0.68678,0.67022,-0.28133,245.19
    9685 
    9686 > view matrix models
    9687 > #5,-0.13135,0.33964,0.93134,-24.234,0.71868,0.67973,-0.14652,-44.687,-0.68283,0.65008,-0.33337,260.62
    9688 
    9689 > view matrix models
    9690 > #5,-0.11889,0.37005,0.92137,-29.677,0.7114,0.6791,-0.18095,-35.108,-0.69266,0.63395,-0.34399,267.86
    9691 
    9692 > view matrix models
    9693 > #5,0.045939,0.59116,0.80525,-71.763,0.70283,0.55371,-0.44659,52.881,-0.70988,0.58646,-0.39004,290.63
    9694 
    9695 > view matrix models
    9696 > #5,0.084841,0.56745,0.81902,-77.41,0.67501,0.57189,-0.46615,59,-0.73291,0.5924,-0.33452,280.32
    9697 
    9698 > view matrix models
    9699 > #5,-0.13391,0.55975,0.81777,-37.622,0.55097,0.72796,-0.40805,37.78,-0.82371,0.39592,-0.40589,349.58
    9700 
    9701 > view matrix models
    9702 > #5,-0.09912,0.51183,0.85335,-43.247,0.59183,0.71973,-0.36294,21.462,-0.79994,0.46907,-0.37425,324.33
    9703 
    9704 > view matrix models
    9705 > #5,-0.11178,0.47533,0.87268,-38.868,0.59167,0.73739,-0.32585,9.3844,-0.79839,0.47992,-0.36367,319.53
    9706 
    9707 > view matrix models
    9708 > #5,-0.22153,0.44542,0.86748,-12.986,0.53956,0.79699,-0.27144,-5.5629,-0.81228,0.40793,-0.41688,347.98
    9709 
    9710 > ui mousemode right "translate selected models"
    9711 
    9712 > view matrix models
    9713 > #5,-0.22153,0.44542,0.86748,-14.111,0.53956,0.79699,-0.27144,-5.3645,-0.81228,0.40793,-0.41688,348.49
    9714 
    9715 > select add #8
    9716 
    9717 3401 atoms, 3493 bonds, 442 residues, 3 models selected 
    9718 
    9719 > fitmap #5 inMap #8
    9720 
    9721 Fit molecule F562b.pdb (#5) to map cryosparc_P36_J32_002_volume_map_sharp.mrc
    9722 (#8) using 3401 atoms 
    9723 average map value = 0.09851, steps = 108 
    9724 shifted from previous position = 1.67 
    9725 rotated from previous position = 17.3 degrees 
    9726 atoms outside contour = 1366, contour level = 0.075413 
    9727  
    9728 Position of F562b.pdb (#5) relative to
    9729 cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) coordinates: 
    9730 Matrix rotation and translation 
    9731 0.45238682 -0.88366144 -0.12036870 287.11798101 
    9732 0.88783684 0.43349946 0.15435016 -99.22400613 
    9733 -0.08421352 -0.17669374 0.98065662 40.64404116 
    9734 Axis -0.18365545 -0.02005805 0.98278601 
    9735 Axis point 227.81128239 181.49795933 0.00000000 
    9736 Rotation angle (degrees) 64.32464577 
    9737 Shift along axis -10.79614671 
    9738  
    9739 
    9740 > fitmap #5 inMap #8
    9741 
    9742 Fit molecule F562b.pdb (#5) to map cryosparc_P36_J32_002_volume_map_sharp.mrc
    9743 (#8) using 3401 atoms 
    9744 average map value = 0.09851, steps = 44 
    9745 shifted from previous position = 0.00416 
    9746 rotated from previous position = 0.0187 degrees 
    9747 atoms outside contour = 1367, contour level = 0.075413 
    9748  
    9749 Position of F562b.pdb (#5) relative to
    9750 cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) coordinates: 
    9751 Matrix rotation and translation 
    9752 0.45231009 -0.88373711 -0.12010123 287.08058767 
    9753 0.88785087 0.43341968 0.15449342 -99.24674165 
    9754 -0.08447733 -0.17651091 0.98066686 40.65823137 
    9755 Axis -0.18362633 -0.01976254 0.98279744 
    9756 Axis point 227.80088638 181.42728547 0.00000000 
    9757 Rotation angle (degrees) 64.32929481 
    9758 Shift along axis -10.79538196 
    9759  
    9760 
    9761 > show #3 models
    9762 
    9763 > hide #3 models
    9764 
    9765 > show #3 models
    9766 
    9767 > color #8 #d7fef991 models
    9768 
    9769 > color #8 #c5fef791 models
    9770 
    9771 > color #8 #c4fbfe91 models
    9772 
    9773 > color #8 #c3fef791 models
    9774 
    9775 > rename #8 sNS1wt-Fab562.mrc
    9776 
    9777 > select subtract #5
    9778 
    9779 2 models selected 
    9780 
    9781 > select subtract #8
    9782 
    9783 Nothing selected 
    9784 
    9785 > show #4 models
    9786 
    9787 > show #!2 models
    9788 
    9789 > rename #4 F562a-FL.pdb
    9790 
    9791 > show #9 models
    9792 
    9793 > color #2 #c4a1924d models
    9794 
    9795 [Repeated 1 time(s)]
    9796 
    9797 > hide #!2 models
    9798 
    9799 > hide #4 models
    9800 
    9801 > ui mousemode right zoom
    9802 
    9803 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    9804 > (1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM Maps_docked
    9805 > structures/EDEN2 sNS1wt-Fab562/20220323_NS1wt-Ab-Fab-ApoAI_hdl.cxs"
    9806 > includeMaps true
    9807 
    9808 ——— End of log from Sat Nov 19 10:30:44 2022 ———
    9809 
    9810 opened ChimeraX session 
    9811 
    9812 > volume #8 color #dbfdf891
    9813 
    9814 > volume #8 color #c5fdf891
    9815 
    9816 > volume #8 color #c5fdf849
    9817 
    9818 > volume #8 color #c5fdf84c
    9819 
    9820 > select add #3
    9821 
    9822 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    9823 
    9824 > select subtract #3
    9825 
    9826 Nothing selected 
    9827 
    9828 > rename #3 eden2ns1.pdb
    9829 
    9830 > ui tool show "Show Sequence Viewer"
    9831 
    9832 > sequence chain #3/B #3/C
    9833 
    9834 Alignment identifier is 1 
    9835 
    9836 > select #3/B-C:2
    9837 
    9838 12 atoms, 10 bonds, 2 residues, 1 model selected 
    9839 
    9840 > select #3/B-C:2-75
    9841 
    9842 1174 atoms, 1200 bonds, 148 residues, 1 model selected 
    9843 
    9844 > select #3/B-C:172
    9845 
    9846 18 atoms, 16 bonds, 2 residues, 1 model selected 
    9847 
    9848 > select #3/B-C:172-178
    9849 
    9850 118 atoms, 116 bonds, 14 residues, 1 model selected 
    9851 
    9852 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    9853 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    9854 
    9855 Line 8 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr is either
    9856 not of the form 'name: value' or is missing initial tab 
    9857 
    9858 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    9859 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    9860 
    9861 Data line 8 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr not of
    9862 the form:  atomspec  value 
    9863 
    9864 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    9865 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    9866 
    9867 Line 43 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr is either
    9868 not of the form 'name: value' or is missing initial tab 
    9869 
    9870 > color #3/A-B dimgray
    9871 
    9872 > hide #3 models
    9873 
    9874 > show #3 models
    9875 
    9876 > select add #3
    9877 
    9878 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    9879 
    9880 > select subtract #3
    9881 
    9882 Nothing selected 
    9883 
    9884 > select add #3
    9885 
    9886 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    9887 
    9888 > color #3 dimgray
    9889 
    9890 > ui tool show "Change Chain IDs"
    9891 
    9892 > changechains C A
    9893 
    9894 Proposed chain ID change would produce multiple residues with the samechain-
    9895 ID/number/insertion-code combo (A/1/) 
    9896 
    9897 > changechains C A
    9898 
    9899 Proposed chain ID change would produce multiple residues with the samechain-
    9900 ID/number/insertion-code combo (A/1/) 
    9901 
    9902 > changechains sel C A
    9903 
    9904 Chain IDs of 352 residues changed 
    9905 
    9906 > ui tool show "Show Sequence Viewer"
    9907 
    9908 > sequence chain #3/B #3/A
    9909 
    9910 Alignment identifier is 1 
    9911 
    9912 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    9913 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    9914 
    9915 Summary of feedback from opening
    9916 /Users/alvinchew/Library/CloudStorage/OneDrive-
    9917 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    9918 --- 
    9919 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 1097
    9920 residues using match mode: any 
    9921  
    9922 
    9923 > ui tool show "Show Sequence Viewer"
    9924 
    9925 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    9926 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    9927 
    9928 Summary of feedback from opening
    9929 /Users/alvinchew/Library/CloudStorage/OneDrive-
    9930 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    9931 --- 
    9932 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 1097
    9933 residues using match mode: any 
    9934  
    9935 
    9936 > byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key true
    9937 > bluered noValueColor gray
    9938 
    9939 Unknown command: byattribute relative_deuterium_uptake_NS1c_10min
    9940 #3/A-B:174-361 key true bluered noValueColor gray 
    9941 
    9942 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    9943 > true bluered noValueColor gray
    9944 
    9945 Expected a keyword 
    9946 
    9947 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    9948 > true palette bluered noValueColor gray
    9949 
    9950 > key blue-white-red :-0.98 :-0.47 :0.04 showTool true
    9951 
    9952 > ui mousemode right "color key"
    9953 
    9954 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    9955 -0.98 to 0.04 
    9956 
    9957 > key blue-white-red :-0.98 :-0.47 :1
    9958 
    9959 > key blue-white-red :-2 :-0.47 :1
    9960 
    9961 > key blue-white-red :-2 :0 :1
    9962 
    9963 > hide #5 models
    9964 
    9965 > hide #9 models
    9966 
    9967 > hide #!8 models
    9968 
    9969 > hide #8.1 models
    9970 
    9971 > key pos 0.636108,0.370379 size 0.0013699,0.146465
    9972 
    9973 > undo
    9974 
    9975 > key pos 0.479592,0.196551 size 0.329083,0.0401247
    9976 
    9977 > ui mousemode right zoom
    9978 
    9979 > select subtract #3
    9980 
    9981 Nothing selected 
    9982 
    9983 > ui mousemode right "translate selected models"
    9984 
    9985 > ui mousemode right zoom
    9986 
    9987 > select #3/B,A:212-213
    9988 
    9989 34 atoms, 32 bonds, 4 residues, 1 model selected 
    9990 
    9991 > select #3/B,A:212-217
    9992 
    9993 96 atoms, 96 bonds, 12 residues, 1 model selected 
    9994 
    9995 > select #3/B,A:216
    9996 
    9997 12 atoms, 10 bonds, 2 residues, 1 model selected 
    9998 
    9999 > select #3/B,A:212-216
    10000 
    10001 74 atoms, 72 bonds, 10 residues, 1 model selected 
    10002 
    10003 > select #3/B,A:211
    10004 
    10005 18 atoms, 16 bonds, 2 residues, 1 model selected 
    10006 
    10007 > select #3/B,A:211-216
    10008 
    10009 92 atoms, 90 bonds, 12 residues, 1 model selected 
    10010 
    10011 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    10012 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    10013 
    10014 Summary of feedback from opening
    10015 /Users/alvinchew/Library/CloudStorage/OneDrive-
    10016 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    10017 --- 
    10018 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 984
    10019 residues using match mode: any 
    10020  
    10021 
    10022 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10023 > true palette bluered noValueColor gray
    10024 
    10025 > key blue-white-red :-0.98 :-0.47 :0.04 showTool true
    10026 
    10027 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10028 -0.98 to 0.04 
    10029 
    10030 > undo
    10031 
    10032 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10033 > true palette bluered noValueColor gray
    10034 
    10035 > key blue-white-red :-0.98 :-0.47 :0.04 showTool true
    10036 
    10037 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10038 -0.98 to 0.04 
    10039 
    10040 > undo
    10041 
    10042 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10043 > true palette bluered noValueColor grey
    10044 
    10045 > key blue-white-red :-0.98 :-0.47 :0.04 showTool true
    10046 
    10047 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10048 -0.98 to 0.04 
    10049 
    10050 > ui tool show "Selection Inspector"
    10051 
    10052 > toolshed show
    10053 
    10054 > view sel
    10055 
    10056 > key blue-white-red :-0.98 :-0.47 :1
    10057 
    10058 > key blue-white-red :- :-0.47 :1
    10059 
    10060 > key blue-white-red :-2 :-0.47 :1
    10061 
    10062 > key colorTreatment distinct
    10063 
    10064 > key colorTreatment blended
    10065 
    10066 > attributes available
    10067 
    10068 Unknown command: attributes available 
    10069 
    10070 > info attributes
    10071 
    10072 Expected a models specifier or a keyword 
    10073 
    10074 > info resattr
    10075 
    10076 resattr alt_loc 
    10077 resattr alt_locs 
    10078 resattr atoms 
    10079 resattr atomspec 
    10080 resattr center 
    10081 resattr chain 
    10082 resattr chain_id 
    10083 resattr chi1 
    10084 resattr chi2 
    10085 resattr chi3 
    10086 resattr chi4 
    10087 resattr cpp_pointer 
    10088 resattr custom_attrs 
    10089 resattr deleted 
    10090 resattr description 
    10091 resattr has_custom_attrs 
    10092 resattr insertion_code 
    10093 resattr is_helix 
    10094 resattr is_strand 
    10095 resattr label_one_letter_code 
    10096 resattr label_specifier 
    10097 resattr mmcif_chain_id 
    10098 resattr name 
    10099 resattr neighbors 
    10100 resattr num_atoms 
    10101 resattr number 
    10102 resattr omega 
    10103 resattr one_letter_code 
    10104 resattr phi 
    10105 resattr polymer_type 
    10106 resattr principal_atom 
    10107 resattr psi 
    10108 resattr relative_deuterium_uptake_NS1c_10min 
    10109 resattr ribbon_adjust 
    10110 resattr ribbon_color 
    10111 resattr ribbon_display 
    10112 resattr ribbon_hide_backbone 
    10113 resattr ring_color 
    10114 resattr ring_display 
    10115 resattr selected 
    10116 resattr seq_conservation 
    10117 resattr session 
    10118 resattr ss_id 
    10119 resattr ss_type 
    10120 resattr standard_aa_name 
    10121 resattr structure 
    10122 resattr sym_chi1 
    10123 resattr sym_chi2 
    10124 resattr sym_chi3 
    10125 resattr sym_chi4 
    10126 resattr thin_rings 
    10127 
    10128 > select #3/B,A:181
    10129 
    10130 12 atoms, 10 bonds, 2 residues, 1 model selected 
    10131 
    10132 > select #3/B,A:181-198
    10133 
    10134 268 atoms, 268 bonds, 36 residues, 1 model selected 
    10135 
    10136 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    10137 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    10138 
    10139 Summary of feedback from opening
    10140 /Users/alvinchew/Library/CloudStorage/OneDrive-
    10141 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    10142 --- 
    10143 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
    10144 residues using match mode: any 
    10145  
    10146 
    10147 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10148 > true palette bluered noValueColor grey
    10149 
    10150 > key blue-white-red :-0.98 :-0.47 :0.04 showTool true
    10151 
    10152 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10153 -0.98 to 0.04 
    10154 
    10155 > select #3/B,A:299-300
    10156 
    10157 36 atoms, 34 bonds, 4 residues, 1 model selected 
    10158 
    10159 > select #3/B,A:299-301
    10160 
    10161 50 atoms, 48 bonds, 6 residues, 1 model selected 
    10162 
    10163 > key red-white-blue :0.04 :-0.47 :-0.98
    10164 
    10165 > key blue-white-red :-0.98 :-0.47 :0.04
    10166 
    10167 > key red-white-blue :0.04 :-0.47 :-0.98
    10168 
    10169 > key blue-white-red :-0.98 :-0.47 :0.04
    10170 
    10171 > key blue-white-red :- :-0.47 :0.04
    10172 
    10173 > key blue-white-red :-2 :-0.47 :0.04
    10174 
    10175 > key blue-white-red :-2 :-0.47 :1
    10176 
    10177 > key blue-white-red :-2 :0 :1
    10178 
    10179 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10180 > true palette bluered range -2:1 noValueColor grey
    10181 
    10182 Invalid "range" argument: Expected some numbers or 'full' 
    10183 
    10184 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10185 > true palette bluered range -2,1 noValueColor grey
    10186 
    10187 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10188 
    10189 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10190 -0.98 to 0.04 
    10191 
    10192 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    10193 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    10194 
    10195 Summary of feedback from opening
    10196 /Users/alvinchew/Library/CloudStorage/OneDrive-
    10197 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    10198 --- 
    10199 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
    10200 residues using match mode: any 
    10201  
    10202 
    10203 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10204 > true palette bluered range -2,1 noValueColor grey
    10205 
    10206 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10207 
    10208 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10209 -1.98 to 0.04 
    10210 
    10211 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    10212 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
    10213 
    10214 Summary of feedback from opening
    10215 /Users/alvinchew/Library/CloudStorage/OneDrive-
    10216 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr 
    10217 --- 
    10218 note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
    10219 residues using match mode: any 
    10220  
    10221 
    10222 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10223 > true palette bluered range -2,1 noValueColor grey
    10224 
    10225 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10226 
    10227 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10228 -1.98 to 0.04 
    10229 
    10230 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    10231 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
    10232 
    10233 Summary of feedback from opening
    10234 /Users/alvinchew/Library/CloudStorage/OneDrive-
    10235 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr 
    10236 --- 
    10237 note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
    10238 residues using match mode: any 
    10239  
    10240 
    10241 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10242 > true palette bluered range -2,1 noValueColor grey
    10243 
    10244 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10245 
    10246 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10247 -1.98 to 0.04 
    10248 
    10249 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    10250 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    10251 
    10252 Summary of feedback from opening
    10253 /Users/alvinchew/Library/CloudStorage/OneDrive-
    10254 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    10255 --- 
    10256 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
    10257 residues using match mode: any 
    10258  
    10259 
    10260 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10261 > true palette bluered range -2,1 noValueColor grey
    10262 
    10263 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10264 
    10265 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10266 -1.98 to 0.04 
    10267 
    10268 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    10269 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    10270 
    10271 Summary of feedback from opening
    10272 /Users/alvinchew/Library/CloudStorage/OneDrive-
    10273 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    10274 --- 
    10275 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 866
    10276 residues using match mode: any 
    10277  
    10278 
    10279 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10280 > true palette bluered range -2,1 noValueColor grey
    10281 
    10282 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10283 
    10284 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10285 -1.98 to 0.04 
    10286 
    10287 > undo
    10288 
    10289 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10290 > true palette bluered range -2,1 noValueColor grey
    10291 
    10292 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10293 
    10294 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10295 -1.98 to 0.04 
    10296 
    10297 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    10298 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
    10299 
    10300 Summary of feedback from opening
    10301 /Users/alvinchew/Library/CloudStorage/OneDrive-
    10302 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr 
    10303 --- 
    10304 note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
    10305 residues using match mode: any 
    10306  
    10307 
    10308 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10309 > true palette bluered range -2,1 noValueColor grey
    10310 
    10311 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10312 
    10313 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    10314 -1.98 to 0.04 
    10315 
    10316 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10317 > true palette bluered range -2,1 noValueColor grey
    10318 
    10319 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10320 
    10321 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    10322 -1.03 to 0 
    10323 
    10324 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10325 > true palette bluered range -2,1 noValueColor grey
    10326 
    10327 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10328 
    10329 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    10330 -1.03 to 0 
    10331 
    10332 > undo
    10333 
    10334 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10335 > true palette bluered range -2,1 noValueColor grey
    10336 
    10337 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10338 
    10339 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    10340 -1.03 to 0 
    10341 
    10342 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10343 > true palette bluered range -2,1 noValueColor grey
    10344 
    10345 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10346 
    10347 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    10348 -1.03 to 0 
    10349 
    10350 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10351 > true palette bluered range -2,1 noValueColor grey
    10352 
    10353 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10354 
    10355 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    10356 -1.03 to 0 
    10357 
    10358 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    10359 > true palette bluered range -2,1 noValueColor grey
    10360 
    10361 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    10362 
    10363 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    10364 -1.03 to 0 
    10365 
    10366 > select #3/B,A:175
    10367 
    10368 18 atoms, 16 bonds, 2 residues, 1 model selected 
    10369 
    10370 > select #3/B,A:175-178
    10371 
    10372 60 atoms, 58 bonds, 8 residues, 1 model selected 
    10373 
    10374 > ui mousemode right translate
    10375 
    10376 > ui mousemode right zoom
    10377 
    10378 > select #3/B,A:172
    10379 
    10380 18 atoms, 16 bonds, 2 residues, 1 model selected 
    10381 
    10382 > select #3/B,A:172-174
    10383 
    10384 58 atoms, 56 bonds, 6 residues, 1 model selected 
    10385 
    10386 > select #3/B,A:174-175
    10387 
    10388 40 atoms, 38 bonds, 4 residues, 1 model selected 
    10389 
    10390 > select #3/B,A:174-178
    10391 
    10392 82 atoms, 80 bonds, 10 residues, 1 model selected 
    10393 
    10394 > ui tool show "Color Actions"
    10395 
    10396 > color sel #cbdbffff
    10397 
    10398 > color sel #c1d2ffff
    10399 
    10400 > color sel #c1d1ffff
    10401 
    10402 > color sel #c2d2ffff
    10403 
    10404 [Repeated 1 time(s)]
    10405 
    10406 > color sel #c3d3ffff
    10407 
    10408 > color sel #c4d3ffff
    10409 
    10410 > color sel #c4d4ffff
    10411 
    10412 > color sel #c4d5ffff
    10413 
    10414 > color sel #c5d6ffff
    10415 
    10416 > color sel #c5d5ffff
    10417 
    10418 > color sel #c4d4ffff
    10419 
    10420 > color sel #c4d3ffff
    10421 
    10422 [Repeated 1 time(s)]
    10423 
    10424 > color sel #c3d2ffff
    10425 
    10426 > color sel #c3d1ffff
    10427 
    10428 > color sel #c2d0ffff
    10429 
    10430 [Repeated 1 time(s)]
    10431 
    10432 > color sel #c1cfffff
    10433 
    10434 > color sel #c1ceffff
    10435 
    10436 > color sel #c1cdffff
    10437 
    10438 > color sel #c0cdffff
    10439 
    10440 > color sel #c0ccffff
    10441 
    10442 > color sel #c1cdffff
    10443 
    10444 [Repeated 1 time(s)]
    10445 
    10446 > color sel #c1ceffff
    10447 
    10448 > color sel #c2cfffff
    10449 
    10450 > color sel #b8c2ffff
    10451 
    10452 > color sel #aebdffff
    10453 
    10454 > select #3/B,A:179
    10455 
    10456 12 atoms, 10 bonds, 2 residues, 1 model selected 
    10457 
    10458 > select #3/B,A:179-187
    10459 
    10460 122 atoms, 120 bonds, 18 residues, 1 model selected 
    10461 
    10462 > color sel #c4cfffff
    10463 
    10464 > select #3/B,A:188
    10465 
    10466 16 atoms, 14 bonds, 2 residues, 1 model selected 
    10467 
    10468 > select #3/B,A:188-198
    10469 
    10470 174 atoms, 174 bonds, 22 residues, 1 model selected 
    10471 
    10472 > color sel #b1bbffff
    10473 
    10474 > select #3/B,A:199
    10475 
    10476 8 atoms, 6 bonds, 2 residues, 1 model selected 
    10477 
    10478 > select #3/B,A:199-200
    10479 
    10480 32 atoms, 32 bonds, 4 residues, 1 model selected 
    10481 
    10482 > color sel #99b0ffff
    10483 
    10484 > color sel #96baffff
    10485 
    10486 > color sel #92b4ffff
    10487 
    10488 > color sel #6a97ffff
    10489 
    10490 > select #3/B,A:201-202
    10491 
    10492 44 atoms, 46 bonds, 4 residues, 1 model selected 
    10493 
    10494 > select #3/B,A:201-211
    10495 
    10496 192 atoms, 198 bonds, 22 residues, 1 model selected 
    10497 
    10498 > color sel #91acffff
    10499 
    10500 > select #3/B,A:212
    10501 
    10502 16 atoms, 14 bonds, 2 residues, 1 model selected 
    10503 
    10504 > select #3/B,A:212-217
    10505 
    10506 96 atoms, 96 bonds, 12 residues, 1 model selected 
    10507 
    10508 > color sel #aabeffff
    10509 
    10510 > color sel #bfcfffff
    10511 
    10512 [Repeated 1 time(s)]
    10513 
    10514 > color sel #bfceffff
    10515 
    10516 > color sel #beceffff
    10517 
    10518 > color sel #becdffff
    10519 
    10520 > color sel #bdcdffff
    10521 
    10522 > select #3/B,A:218
    10523 
    10524 16 atoms, 14 bonds, 2 residues, 1 model selected 
    10525 
    10526 > select #3/B,A:218-219
    10527 
    10528 34 atoms, 32 bonds, 4 residues, 1 model selected 
    10529 
    10530 > color sel #adc4ffff
    10531 
    10532 > select #3/B,A:220
    10533 
    10534 14 atoms, 12 bonds, 2 residues, 1 model selected 
    10535 
    10536 > select #3/B,A:220-231
    10537 
    10538 198 atoms, 206 bonds, 24 residues, 1 model selected 
    10539 
    10540 > color sel #88a5ffff
    10541 
    10542 > color sel #83a2ffff
    10543 
    10544 > color sel #7fa0ffff
    10545 
    10546 > select #3/B,A:232
    10547 
    10548 28 atoms, 30 bonds, 2 residues, 1 model selected 
    10549 
    10550 > select #3/B,A:232-240
    10551 
    10552 142 atoms, 144 bonds, 18 residues, 1 model selected 
    10553 
    10554 > color sel #98b0ffff
    10555 
    10556 > select #3/B,A:231
    10557 
    10558 16 atoms, 14 bonds, 2 residues, 1 model selected 
    10559 
    10560 > select #3/B,A:220-231
    10561 
    10562 198 atoms, 206 bonds, 24 residues, 1 model selected 
    10563 
    10564 > color sel #8da3edff
    10565 
    10566 > color sel #8da3ecff
    10567 
    10568 [Repeated 1 time(s)]
    10569 
    10570 > color sel #8ca2ecff
    10571 
    10572 > color sel #8ca2ebff
    10573 
    10574 > color sel #8ba1eaff
    10575 
    10576 > color sel #8ba0e9ff
    10577 
    10578 > color sel #889ee5ff
    10579 
    10580 > color sel #869be0ff
    10581 
    10582 > color sel #8397dcff
    10583 
    10584 > color sel #8195d9ff
    10585 
    10586 > color sel #8094d7ff
    10587 
    10588 > color sel #7f93d6ff
    10589 
    10590 > color sel #7f93d5ff
    10591 
    10592 > color sel #7e92d4ff
    10593 
    10594 > color sel #7d90d2ff
    10595 
    10596 > color sel #7b8eceff
    10597 
    10598 > color sel #798cccff
    10599 
    10600 > color sel #788bc9ff
    10601 
    10602 > color sel #778ac8ff
    10603 
    10604 [Repeated 1 time(s)]
    10605 
    10606 > color sel #7689c7ff
    10607 
    10608 > color sel #7688c6ff
    10609 
    10610 > color sel #7587c5ff
    10611 
    10612 > color sel #7587c4ff
    10613 
    10614 > color sel #7487c3ff
    10615 
    10616 > color sel #7486c3ff
    10617 
    10618 > color sel #7081bcff
    10619 
    10620 > color sel #6878afff
    10621 
    10622 > color sel #6272a5ff
    10623 
    10624 > color sel #576592ff
    10625 
    10626 > color sel #4c5880ff
    10627 
    10628 > color sel #444f73ff
    10629 
    10630 > color sel #414b6dff
    10631 
    10632 > color sel #404a6cff
    10633 
    10634 > color sel #404a6bff
    10635 
    10636 > color sel #3f4969ff
    10637 
    10638 > color sel #3d4666ff
    10639 
    10640 > color sel #3b4463ff
    10641 
    10642 > color sel #38415fff
    10643 
    10644 > color sel #343c57ff
    10645 
    10646 > color sel #2e364eff
    10647 
    10648 > color sel #2c3249ff
    10649 
    10650 > color sel #2b3148ff
    10651 
    10652 > color sel #2a3146ff
    10653 
    10654 [Repeated 1 time(s)]
    10655 
    10656 > color sel #2a3147ff
    10657 
    10658 > color sel #2c334bff
    10659 
    10660 > color sel #2f364fff
    10661 
    10662 > color sel #343c58ff
    10663 
    10664 > color sel #3a4361ff
    10665 
    10666 > color sel #404a6cff
    10667 
    10668 > color sel #475277ff
    10669 
    10670 > color sel #4d5981ff
    10671 
    10672 > color sel #55638fff
    10673 
    10674 > color sel #596796ff
    10675 
    10676 > color sel #5d6b9cff
    10677 
    10678 > color sel #606fa1ff
    10679 
    10680 > color sel #6272a5ff
    10681 
    10682 > color sel #6878afff
    10683 
    10684 > color sel #6b7bb3ff
    10685 
    10686 > color sel #7082bcff
    10687 
    10688 > color sel #7284c0ff
    10689 
    10690 > color sel #7486c3ff
    10691 
    10692 > color sel #7587c5ff
    10693 
    10694 > color sel #7688c6ff
    10695 
    10696 > color sel #7689c6ff
    10697 
    10698 > color sel #778ac8ff
    10699 
    10700 > color sel #788ac9ff
    10701 
    10702 > color sel #788bcaff
    10703 
    10704 > color sel #798cccff
    10705 
    10706 > color sel #7a8dcdff
    10707 
    10708 > color sel #7b8eceff
    10709 
    10710 > color sel #7c8fcfff
    10711 
    10712 > color sel #7c90d0ff
    10713 
    10714 > color sel #7d90d1ff
    10715 
    10716 > color sel #7d91d2ff
    10717 
    10718 > color sel #7e91d3ff
    10719 
    10720 > color sel #7e92d4ff
    10721 
    10722 > color sel #7f93d5ff
    10723 
    10724 [Repeated 1 time(s)]
    10725 
    10726 > color sel #7f93d6ff
    10727 
    10728 > color sel #8094d7ff
    10729 
    10730 > color sel #8296daff
    10731 
    10732 > color sel #859ae0ff
    10733 
    10734 > color sel #879ce2ff
    10735 
    10736 > color sel #899ee5ff
    10737 
    10738 > color sel #899ee6ff
    10739 
    10740 [Repeated 1 time(s)]
    10741 
    10742 > color sel #899fe6ff
    10743 
    10744 > color sel #899fe7ff
    10745 
    10746 > color sel #8aa0e8ff
    10747 
    10748 > color sel #8ca2ebff
    10749 
    10750 > color sel #8da3ecff
    10751 
    10752 > color sel #8da3edff
    10753 
    10754 > color sel #8da4edff
    10755 
    10756 > color sel #8ea5efff
    10757 
    10758 > color sel #90a6f1ff
    10759 
    10760 > color sel #91a7f3ff
    10761 
    10762 > color sel #92a9f5ff
    10763 
    10764 > color sel #92a9f6ff
    10765 
    10766 > color sel #94abf8ff
    10767 
    10768 > color sel #95acfaff
    10769 
    10770 [Repeated 1 time(s)]
    10771 
    10772 > color sel #95adfbff
    10773 
    10774 > color sel #96aefcff
    10775 
    10776 > color sel #97affeff
    10777 
    10778 > color sel #98b0ffff
    10779 
    10780 [Repeated 1 time(s)]
    10781 
    10782 > color sel #97affeff
    10783 
    10784 > color sel #94abf9ff
    10785 
    10786 > color sel #92a9f6ff
    10787 
    10788 > color sel #92a8f4ff
    10789 
    10790 > color sel #91a8f4ff
    10791 
    10792 > color sel #91a7f3ff
    10793 
    10794 > color sel #90a7f2ff
    10795 
    10796 > color sel #91a7f3ff
    10797 
    10798 > color sel #91a8f4ff
    10799 
    10800 > color sel #92a9f5ff
    10801 
    10802 > color sel #92a9f6ff
    10803 
    10804 > color sel #93aaf7ff
    10805 
    10806 > color sel #94abf8ff
    10807 
    10808 > color sel #94abf9ff
    10809 
    10810 > color sel #6492f9ff
    10811 
    10812 > color sel #4f5af9ff
    10813 
    10814 > color sel #505df9ff
    10815 
    10816 > color sel #505ef9ff
    10817 
    10818 > color sel #515ff9ff
    10819 
    10820 [Repeated 1 time(s)]
    10821 
    10822 > color sel #5260f9ff
    10823 
    10824 > color sel #5362f9ff
    10825 
    10826 > color sel #5363f9ff
    10827 
    10828 [Repeated 1 time(s)]
    10829 
    10830 > color sel #5465f9ff
    10831 
    10832 > color sel #5567f9ff
    10833 
    10834 > color sel #5667f9ff
    10835 
    10836 > color sel #5668f9ff
    10837 
    10838 > color sel #5568f9ff
    10839 
    10840 > color sel #5569f9ff
    10841 
    10842 [Repeated 1 time(s)]
    10843 
    10844 > color sel #5469f9ff
    10845 
    10846 [Repeated 2 time(s)]
    10847 
    10848 > color sel #5369f9ff
    10849 
    10850 > color sel #536af9ff
    10851 
    10852 > color sel #546bf9ff
    10853 
    10854 > color sel #546cf9ff
    10855 
    10856 [Repeated 1 time(s)]
    10857 
    10858 > color sel #556df9ff
    10859 
    10860 > color sel #556ef9ff
    10861 
    10862 > color sel #556ff9ff
    10863 
    10864 > color sel #5670f9ff
    10865 
    10866 [Repeated 2 time(s)]
    10867 
    10868 > color sel #5671f9ff
    10869 
    10870 > color sel #5772f9ff
    10871 
    10872 > color sel #5672f9ff
    10873 
    10874 > color sel #5671f9ff
    10875 
    10876 [Repeated 1 time(s)]
    10877 
    10878 > color sel #5570f9ff
    10879 
    10880 > color sel #556ff9ff
    10881 
    10882 > color sel #546ef9ff
    10883 
    10884 [Repeated 1 time(s)]
    10885 
    10886 > color sel #536df9ff
    10887 
    10888 [Repeated 1 time(s)]
    10889 
    10890 > color sel #526cf9ff
    10891 
    10892 [Repeated 1 time(s)]
    10893 
    10894 > color sel #526bf9ff
    10895 
    10896 > color sel #516af9ff
    10897 
    10898 > color sel #5169f9ff
    10899 
    10900 > color sel #5069f9ff
    10901 
    10902 > color sel #5068f9ff
    10903 
    10904 > color sel #4f67f9ff
    10905 
    10906 > color sel #4f66f9ff
    10907 
    10908 > color sel #4f65f9ff
    10909 
    10910 > color sel #5069f9ff
    10911 
    10912 > color sel #516af9ff
    10913 
    10914 [Repeated 1 time(s)]
    10915 
    10916 > color sel #516bf9ff
    10917 
    10918 > color sel #536cf9ff
    10919 
    10920 > color sel #536df9ff
    10921 
    10922 > color sel #546df9ff
    10923 
    10924 > color sel #546ef9ff
    10925 
    10926 > color sel #556ff9ff
    10927 
    10928 > color sel #5670f9ff
    10929 
    10930 [Repeated 1 time(s)]
    10931 
    10932 > color sel #5770f9ff
    10933 
    10934 > color sel #5771f9ff
    10935 
    10936 > color sel #5872f9ff
    10937 
    10938 [Repeated 2 time(s)]
    10939 
    10940 > color sel #5972f9ff
    10941 
    10942 > color sel #5973f9ff
    10943 
    10944 > color sel #5a73f9ff
    10945 
    10946 [Repeated 1 time(s)]
    10947 
    10948 > color sel #5a74f9ff
    10949 
    10950 > color sel #5b73f9ff
    10951 
    10952 [Repeated 1 time(s)]
    10953 
    10954 > color sel #5c74f9ff
    10955 
    10956 [Repeated 2 time(s)]
    10957 
    10958 > color sel #5d74f9ff
    10959 
    10960 [Repeated 1 time(s)]
    10961 
    10962 > color sel #5e73f9ff
    10963 
    10964 > color sel #5e74f9ff
    10965 
    10966 [Repeated 1 time(s)]
    10967 
    10968 > select #3/B,A:241
    10969 
    10970 16 atoms, 14 bonds, 2 residues, 1 model selected 
    10971 
    10972 > select #3/B,A:241
    10973 
    10974 16 atoms, 14 bonds, 2 residues, 1 model selected 
    10975 
    10976 > color sel #8897f9ff
    10977 
    10978 > color sel #b4bff9ff
    10979 
    10980 > color sel #becff9ff
    10981 
    10982 > color sel #bdcff9ff
    10983 
    10984 [Repeated 1 time(s)]
    10985 
    10986 > color sel #bccff9ff
    10987 
    10988 [Repeated 1 time(s)]
    10989 
    10990 > color sel #bbcff9ff
    10991 
    10992 [Repeated 2 time(s)]
    10993 
    10994 > color sel #bbd0f9ff
    10995 
    10996 > color sel #bbcff9ff
    10997 
    10998 > color sel #bacff9ff
    10999 
    11000 > color sel #bacef9ff
    11001 
    11002 > color sel #b9cdf9ff
    11003 
    11004 > color sel #b9ccf9ff
    11005 
    11006 [Repeated 1 time(s)]
    11007 
    11008 > color sel #b8cbf9ff
    11009 
    11010 [Repeated 1 time(s)]
    11011 
    11012 > color sel #b7caf9ff
    11013 
    11014 [Repeated 1 time(s)]
    11015 
    11016 > color sel #b7c9f9ff
    11017 
    11018 > color sel #b5c8f9ff
    11019 
    11020 > color sel #b5c7f9ff
    11021 
    11022 > color sel #b5c6f9ff
    11023 
    11024 > color sel #b4c6f9ff
    11025 
    11026 [Repeated 1 time(s)]
    11027 
    11028 > color sel #b3c5f9ff
    11029 
    11030 > color sel #b3c4f9ff
    11031 
    11032 > color sel #b2c4f9ff
    11033 
    11034 > color sel #b2c3f9ff
    11035 
    11036 > color sel #b1c2f9ff
    11037 
    11038 > color sel #b1c1f9ff
    11039 
    11040 > color sel #b0c1f9ff
    11041 
    11042 > color sel #b0c0f9ff
    11043 
    11044 > color sel #afbff9ff
    11045 
    11046 [Repeated 1 time(s)]
    11047 
    11048 > color sel #aebef9ff
    11049 
    11050 > color sel #aebdf9ff
    11051 
    11052 > select #3/B,A:242
    11053 
    11054 16 atoms, 14 bonds, 2 residues, 1 model selected 
    11055 
    11056 > select #3/B,A:242-247
    11057 
    11058 102 atoms, 104 bonds, 12 residues, 1 model selected 
    11059 
    11060 > color sel #909df9ff
    11061 
    11062 > select #3/B,A:248-249
    11063 
    11064 18 atoms, 16 bonds, 4 residues, 1 model selected 
    11065 
    11066 > select #3/B,A:248-253
    11067 
    11068 76 atoms, 76 bonds, 12 residues, 1 model selected 
    11069 
    11070 > color sel #9fabf9ff
    11071 
    11072 > select #3/B,A:254-255
    11073 
    11074 36 atoms, 36 bonds, 4 residues, 1 model selected 
    11075 
    11076 > select #3/B,A:254-262
    11077 
    11078 162 atoms, 170 bonds, 18 residues, 1 model selected 
    11079 
    11080 > color sel #92a1f9ff
    11081 
    11082 > select #3/B,A:263-264
    11083 
    11084 32 atoms, 30 bonds, 4 residues, 1 model selected 
    11085 
    11086 > select #3/B,A:263-265
    11087 
    11088 42 atoms, 40 bonds, 6 residues, 1 model selected 
    11089 
    11090 > color sel #acbbf9ff
    11091 
    11092 [Repeated 1 time(s)]
    11093 
    11094 > color sel #abbaf9ff
    11095 
    11096 > color sel #abb9f9ff
    11097 
    11098 > select #3/B,A:266-267
    11099 
    11100 22 atoms, 22 bonds, 4 residues, 1 model selected 
    11101 
    11102 > select #3/B,A:266-267
    11103 
    11104 22 atoms, 22 bonds, 4 residues, 1 model selected 
    11105 
    11106 > color sel #7a98f9ff
    11107 
    11108 > color sel #6689f9ff
    11109 
    11110 > color sel #698bf9ff
    11111 
    11112 > color sel #698cf9ff
    11113 
    11114 > color sel #6a8cf9ff
    11115 
    11116 > color sel #6b8cf9ff
    11117 
    11118 > color sel #6c8df9ff
    11119 
    11120 > color sel #6c8ef9ff
    11121 
    11122 > color sel #6d8ef9ff
    11123 
    11124 > color sel #6e8ef9ff
    11125 
    11126 > color sel #6e8ff9ff
    11127 
    11128 > color sel #6f90f9ff
    11129 
    11130 > color sel #6f8ff9ff
    11131 
    11132 > color sel #6284f9ff
    11133 
    11134 > select #3/B,A:268-269
    11135 
    11136 48 atoms, 52 bonds, 4 residues, 1 model selected 
    11137 
    11138 > select #3/B,A:268-273
    11139 
    11140 110 atoms, 114 bonds, 12 residues, 1 model selected 
    11141 
    11142 > color sel #86abf9ff
    11143 
    11144 > select #3/B,A:274-275
    11145 
    11146 34 atoms, 32 bonds, 4 residues, 1 model selected 
    11147 
    11148 > select #3/B,A:274-275
    11149 
    11150 34 atoms, 32 bonds, 4 residues, 1 model selected 
    11151 
    11152 > color sel #5584f9ff
    11153 
    11154 > color sel #5684f9ff
    11155 
    11156 > color sel #5785f9ff
    11157 
    11158 > color sel #5886f9ff
    11159 
    11160 > color sel #5986f9ff
    11161 
    11162 > color sel #5b87f9ff
    11163 
    11164 > color sel #5c88f9ff
    11165 
    11166 [Repeated 1 time(s)]
    11167 
    11168 > color sel #5c89f9ff
    11169 
    11170 > color sel #5d89f9ff
    11171 
    11172 > color sel #5e8af9ff
    11173 
    11174 > color sel #5e8bf9ff
    11175 
    11176 > color sel #5f8bf9ff
    11177 
    11178 > color sel #5f8cf9ff
    11179 
    11180 > color sel #608df9ff
    11181 
    11182 > color sel #618df9ff
    11183 
    11184 > color sel #618ef9ff
    11185 
    11186 [Repeated 1 time(s)]
    11187 
    11188 > color sel #628ff9ff
    11189 
    11190 > color sel #638ff9ff
    11191 
    11192 > color sel #6390f9ff
    11193 
    11194 > color sel #6592f9ff
    11195 
    11196 > color sel #6994f9ff
    11197 
    11198 > color sel #6a96f9ff
    11199 
    11200 > color sel #6b96f9ff
    11201 
    11202 > color sel #6c97f9ff
    11203 
    11204 [Repeated 1 time(s)]
    11205 
    11206 > select #3/B,A:276-277
    11207 
    11208 38 atoms, 38 bonds, 4 residues, 1 model selected 
    11209 
    11210 > select #3/B,A:276-277
    11211 
    11212 38 atoms, 38 bonds, 4 residues, 1 model selected 
    11213 
    11214 > color sel #89aef9ff
    11215 
    11216 > select #3/B,A:278
    11217 
    11218 16 atoms, 14 bonds, 2 residues, 1 model selected 
    11219 
    11220 > select #3/B,A:278-285
    11221 
    11222 118 atoms, 118 bonds, 16 residues, 1 model selected 
    11223 
    11224 > select #3/B,A:286-287
    11225 
    11226 28 atoms, 26 bonds, 4 residues, 1 model selected 
    11227 
    11228 > select #3/B,A:286-287
    11229 
    11230 28 atoms, 26 bonds, 4 residues, 1 model selected 
    11231 
    11232 > select #3/B,A:286
    11233 
    11234 14 atoms, 12 bonds, 2 residues, 1 model selected 
    11235 
    11236 > select #3/B,A:286-299
    11237 
    11238 206 atoms, 206 bonds, 28 residues, 1 model selected 
    11239 
    11240 > color sel #7c9df9ff
    11241 
    11242 > color sel #798df9ff
    11243 
    11244 > select #3/B,A:300
    11245 
    11246 14 atoms, 12 bonds, 2 residues, 1 model selected 
    11247 
    11248 > select #3/B,A:300-309
    11249 
    11250 136 atoms, 134 bonds, 20 residues, 1 model selected 
    11251 
    11252 > color sel #527af9ff
    11253 
    11254 > color sel #3a5af9ff
    11255 
    11256 > select #3/B,A:310
    11257 
    11258 18 atoms, 16 bonds, 2 residues, 1 model selected 
    11259 
    11260 > select #3/B,A:310
    11261 
    11262 18 atoms, 16 bonds, 2 residues, 1 model selected 
    11263 
    11264 > color sel #526af9ff
    11265 
    11266 > select #3/B,A:311
    11267 
    11268 28 atoms, 30 bonds, 2 residues, 1 model selected 
    11269 
    11270 > select #3/B,A:311-333
    11271 
    11272 378 atoms, 392 bonds, 46 residues, 1 model selected 
    11273 
    11274 > color sel #c6c6f3ff
    11275 
    11276 > color sel #b6b4f3ff
    11277 
    11278 > select #3/B,A:334-335
    11279 
    11280 34 atoms, 32 bonds, 4 residues, 1 model selected 
    11281 
    11282 > select #3/B,A:334-335
    11283 
    11284 34 atoms, 32 bonds, 4 residues, 1 model selected 
    11285 
    11286 > color sel #9c98f3ff
    11287 
    11288 > select #3/B,A:336-337
    11289 
    11290 36 atoms, 36 bonds, 4 residues, 1 model selected 
    11291 
    11292 > select #3/B,A:336-341
    11293 
    11294 106 atoms, 106 bonds, 12 residues, 1 model selected 
    11295 
    11296 > color sel #a7acf3ff
    11297 
    11298 > select #3/B,A:341-342
    11299 
    11300 36 atoms, 34 bonds, 4 residues, 1 model selected 
    11301 
    11302 > select #3/B,A:341-350
    11303 
    11304 158 atoms, 156 bonds, 20 residues, 1 model selected 
    11305 
    11306 > color sel #6b69f3ff
    11307 
    11308 > color sel #6b6af3ff
    11309 
    11310 > color sel #6b6bf3ff
    11311 
    11312 > color sel #6d6ef3ff
    11313 
    11314 > color sel #6f70f3ff
    11315 
    11316 > color sel #7273f3ff
    11317 
    11318 > color sel #7274f3ff
    11319 
    11320 > color sel #7375f3ff
    11321 
    11322 > color sel #7476f3ff
    11323 
    11324 > color sel #7477f3ff
    11325 
    11326 > color sel #7578f3ff
    11327 
    11328 > color sel #7579f3ff
    11329 
    11330 > color sel #7679f3ff
    11331 
    11332 > color sel #777af3ff
    11333 
    11334 > color sel #787cf3ff
    11335 
    11336 > color sel #777bf3ff
    11337 
    11338 > color sel #777af3ff
    11339 
    11340 > color sel #7679f3ff
    11341 
    11342 > color sel #7072f3ff
    11343 
    11344 > select add #3
    11345 
    11346 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    11347 
    11348 > select subtract #3
    11349 
    11350 Nothing selected 
    11351 
    11352 > select #3/B,A:300
    11353 
    11354 14 atoms, 12 bonds, 2 residues, 1 model selected 
    11355 
    11356 > select #3/B,A:300-309
    11357 
    11358 136 atoms, 134 bonds, 20 residues, 1 model selected 
    11359 
    11360 > color sel #4c4ef3ff
    11361 
    11362 > color sel #4242f3ff
    11363 
    11364 > select add #3
    11365 
    11366 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    11367 
    11368 > select subtract #3
    11369 
    11370 Nothing selected 
    11371 
    11372 > select #3/B,A:1-2
    11373 
    11374 28 atoms, 26 bonds, 4 residues, 1 model selected 
    11375 
    11376 > select #3/B,A:1-171
    11377 
    11378 2732 atoms, 2798 bonds, 342 residues, 1 model selected 
    11379 
    11380 > color sel #edeff3ff
    11381 
    11382 > color sel #c7c9ccff
    11383 
    11384 > color sel #c7c8ccff
    11385 
    11386 > color sel #c2c4c7ff
    11387 
    11388 > color sel #c1c2c6ff
    11389 
    11390 > color sel #c0c2c5ff
    11391 
    11392 > color sel #bfc0c4ff
    11393 
    11394 > color sel #bdbec2ff
    11395 
    11396 > color sel #bcbdc0ff
    11397 
    11398 > color sel #babcbfff
    11399 
    11400 > color sel #babbbeff
    11401 
    11402 > color sel #b9bbbeff
    11403 
    11404 > color sel #b9babeff
    11405 
    11406 > color sel #b6b7bbff
    11407 
    11408 > color sel #b2b3b6ff
    11409 
    11410 > color sel #afb0b3ff
    11411 
    11412 > color sel #abacafff
    11413 
    11414 > color sel #a6a7abff
    11415 
    11416 > color sel #a3a4a7ff
    11417 
    11418 > color sel #a1a2a5ff
    11419 
    11420 > color sel #9fa0a3ff
    11421 
    11422 > color sel #9c9da0ff
    11423 
    11424 > color sel #999a9cff
    11425 
    11426 > color sel #96979aff
    11427 
    11428 [Repeated 1 time(s)]
    11429 
    11430 > color sel #949597ff
    11431 
    11432 > color sel #919295ff
    11433 
    11434 > color sel #8b8b8eff
    11435 
    11436 > color sel #87888aff
    11437 
    11438 > color sel #7e7f81ff
    11439 
    11440 > color sel #727375ff
    11441 
    11442 > color sel #68686aff
    11443 
    11444 > color sel #616264ff
    11445 
    11446 > color sel #59595bff
    11447 
    11448 > color sel #545556ff
    11449 
    11450 > color sel #4d4e4fff
    11451 
    11452 > color sel #464748ff
    11453 
    11454 > color sel #444446ff
    11455 
    11456 > color sel #424244ff
    11457 
    11458 > color sel #3f3f40ff
    11459 
    11460 > color sel #3e3e3fff
    11461 
    11462 > color sel #3c3d3eff
    11463 
    11464 [Repeated 1 time(s)]
    11465 
    11466 > color sel #414243ff
    11467 
    11468 > color sel #4d4e4fff
    11469 
    11470 > color sel #565658ff
    11471 
    11472 > color sel #606162ff
    11473 
    11474 > color sel #656668ff
    11475 
    11476 > color sel #6a6b6dff
    11477 
    11478 > color sel #717274ff
    11479 
    11480 > color sel #737476ff
    11481 
    11482 > color sel #78797bff
    11483 
    11484 > color sel #7b7b7eff
    11485 
    11486 > color sel #818285ff
    11487 
    11488 > color sel #858689ff
    11489 
    11490 > color sel #88898cff
    11491 
    11492 > color sel #8b8c8eff
    11493 
    11494 > color sel #8c8d90ff
    11495 
    11496 > color sel #8f8f92ff
    11497 
    11498 > color sel #919295ff
    11499 
    11500 > color sel #959699ff
    11501 
    11502 > color sel #9a9b9eff
    11503 
    11504 > color sel #9e9fa2ff
    11505 
    11506 > color sel #a1a2a5ff
    11507 
    11508 > color sel #a5a6a9ff
    11509 
    11510 > color sel #a7a8abff
    11511 
    11512 > color sel #a8a9adff
    11513 
    11514 > color sel #a9aaaeff
    11515 
    11516 > color sel #aaabaeff
    11517 
    11518 [Repeated 1 time(s)]
    11519 
    11520 > color sel #adaeb1ff
    11521 
    11522 > color sel #afb0b3ff
    11523 
    11524 [Repeated 1 time(s)]
    11525 
    11526 > color sel #b0b1b4ff
    11527 
    11528 > color sel #b1b2b5ff
    11529 
    11530 > color sel #b2b3b6ff
    11531 
    11532 [Repeated 1 time(s)]
    11533 
    11534 > color sel #b2b3b6fa
    11535 
    11536 > color sel #b2b3b6f5
    11537 
    11538 > color sel #b2b3b6f3
    11539 
    11540 > color sel #b2b3b6ee
    11541 
    11542 [Repeated 2 time(s)]
    11543 
    11544 > color sel #b2b3b6ed
    11545 
    11546 [Repeated 1 time(s)]
    11547 
    11548 > color sel #b2b3b6eb
    11549 
    11550 [Repeated 1 time(s)]
    11551 
    11552 > color sel #b2b3b6ea
    11553 
    11554 > color sel #b2b3b6e9
    11555 
    11556 > color sel #b2b3b6e8
    11557 
    11558 [Repeated 1 time(s)]
    11559 
    11560 > color sel #b2b3b6e7
    11561 
    11562 [Repeated 1 time(s)]
    11563 
    11564 > color sel #b2b3b6e6
    11565 
    11566 > color sel #b2b3b6e5
    11567 
    11568 > color sel #b2b3b6e3
    11569 
    11570 > color sel #b2b3b6e2
    11571 
    11572 > color sel #b2b3b6e1
    11573 
    11574 > color sel #b2b3b6e0
    11575 
    11576 > color sel #b2b3b6df
    11577 
    11578 [Repeated 1 time(s)]
    11579 
    11580 > color sel #b2b3b6de
    11581 
    11582 > color sel #b2b3b6dd
    11583 
    11584 > color sel #b2b3b6dc
    11585 
    11586 > color sel #b2b3b6db
    11587 
    11588 > color sel #b2b3b6da
    11589 
    11590 [Repeated 1 time(s)]
    11591 
    11592 > color sel #b2b3b6d9
    11593 
    11594 > color sel #b2b3b6d8
    11595 
    11596 [Repeated 1 time(s)]
    11597 
    11598 > color sel #b2b3b6d7
    11599 
    11600 [Repeated 1 time(s)]
    11601 
    11602 > color sel #b2b3b6d6
    11603 
    11604 > color sel #b2b3b6d5
    11605 
    11606 > color sel #b2b3b6d4
    11607 
    11608 > color sel #b2b3b6d2
    11609 
    11610 > color sel #b2b3b6d1
    11611 
    11612 > color sel #b2b3b6d0
    11613 
    11614 [Repeated 1 time(s)]
    11615 
    11616 > color sel #b2b3b6cf
    11617 
    11618 > color sel #b2b3b6cd
    11619 
    11620 [Repeated 1 time(s)]
    11621 
    11622 > color sel #b1b3b6cd
    11623 
    11624 > color sel #b1b2b6cd
    11625 
    11626 > color sel #b1b2b5cd
    11627 
    11628 [Repeated 1 time(s)]
    11629 
    11630 > select add #3
    11631 
    11632 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    11633 
    11634 > select subtract #3
    11635 
    11636 Nothing selected 
    11637 
    11638 > select #3/B,A:1
    11639 
    11640 16 atoms, 14 bonds, 2 residues, 1 model selected 
    11641 
    11642 > select #3/B,A:1-171
    11643 
    11644 2732 atoms, 2798 bonds, 342 residues, 1 model selected 
    11645 
    11646 > color sel #b1b2b5cc
    11647 
    11648 > color sel #b1b2b5c8
    11649 
    11650 > color sel #b1b2b5c6
    11651 
    11652 > color sel #b1b2b5c5
    11653 
    11654 > color sel #b1b2b5c1
    11655 
    11656 > color sel #b1b2b5be
    11657 
    11658 > color sel #b1b2b5bb
    11659 
    11660 > color sel #b1b2b5b7
    11661 
    11662 > color sel #b1b2b5b5
    11663 
    11664 > color sel #b1b2b5b1
    11665 
    11666 > color sel #b1b2b5ad
    11667 
    11668 > color sel #b1b2b5aa
    11669 
    11670 > color sel #b1b2b5a7
    11671 
    11672 > color sel #b1b2b5a4
    11673 
    11674 > color sel #b1b2b5a0
    11675 
    11676 > color sel #b1b2b599
    11677 
    11678 > color sel #b1b2b592
    11679 
    11680 > color sel #b1b2b58c
    11681 
    11682 > color sel #b1b2b586
    11683 
    11684 > color sel #b1b2b576
    11685 
    11686 > color sel #b1b2b573
    11687 
    11688 > color sel #b1b2b56e
    11689 
    11690 > color sel #b1b2b56a
    11691 
    11692 > color sel #b1b2b568
    11693 
    11694 > color sel #b1b2b567
    11695 
    11696 > color sel #b1b2b565
    11697 
    11698 > color sel #b1b2b563
    11699 
    11700 [Repeated 1 time(s)]
    11701 
    11702 > color sel #b1b2b565
    11703 
    11704 > color sel #b1b2b569
    11705 
    11706 > color sel #b1b2b56c
    11707 
    11708 > color sel #b1b2b572
    11709 
    11710 > color sel #b1b2b575
    11711 
    11712 > color sel #b1b2b57b
    11713 
    11714 > color sel #b1b2b581
    11715 
    11716 > color sel #b1b2b587
    11717 
    11718 > color sel #b1b2b589
    11719 
    11720 > color sel #b1b2b58a
    11721 
    11722 [Repeated 1 time(s)]
    11723 
    11724 > color sel #b1b2b58d
    11725 
    11726 > color sel #b1b2b590
    11727 
    11728 > color sel #b1b2b591
    11729 
    11730 > color sel #b1b2b594
    11731 
    11732 > color sel #b1b2b596
    11733 
    11734 [Repeated 2 time(s)]
    11735 
    11736 > color sel #b1b2b597
    11737 
    11738 > color sel #b1b2b598
    11739 
    11740 [Repeated 1 time(s)]
    11741 
    11742 > color sel #b1b2b599
    11743 
    11744 > color sel #b1b2b59a
    11745 
    11746 > color sel #b1b2b59c
    11747 
    11748 > color sel #b1b2b59d
    11749 
    11750 > color sel #b1b2b59c
    11751 
    11752 [Repeated 1 time(s)]
    11753 
    11754 > color sel #b1b2b59b
    11755 
    11756 [Repeated 1 time(s)]
    11757 
    11758 > color sel #b1b2b59a
    11759 
    11760 [Repeated 1 time(s)]
    11761 
    11762 > color sel #b1b2b599
    11763 
    11764 [Repeated 1 time(s)]
    11765 
    11766 > color sel #b1b2b598
    11767 
    11768 > select add #3
    11769 
    11770 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    11771 
    11772 > select subtract #3
    11773 
    11774 Nothing selected 
    11775 
    11776 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    11777 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/sNS1wt-Ab562_EM-HDX.cxs"
    11778 > includeMaps true
    11779 
    11780 > show #!2 models
    11781 
    11782 > color #2 #cfbabb4d models
    11783 
    11784 > color #2 #c1acae4d models
    11785 
    11786 > color #2 #c1acae2e models
    11787 
    11788 > color #2 #c1acae34 models
    11789 
    11790 > show #!8 models
    11791 
    11792 > show #4 models
    11793 
    11794 > select add #4
    11795 
    11796 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    11797 
    11798 > ui mousemode right "translate selected models"
    11799 
    11800 > view matrix models
    11801 > #4,0.25081,-0.17578,-0.95194,337.54,0.94086,0.27565,0.19699,-69.227,0.22777,-0.94505,0.23452,277.17
    11802 
    11803 > view matrix models
    11804 > #4,0.25081,-0.17578,-0.95194,337.61,0.94086,0.27565,0.19699,-68.962,0.22777,-0.94505,0.23452,277.21
    11805 
    11806 > view matrix models
    11807 > #4,0.25081,-0.17578,-0.95194,338.3,0.94086,0.27565,0.19699,-67.778,0.22777,-0.94505,0.23452,276.56
    11808 
    11809 > ui mousemode right "rotate selected models"
    11810 
    11811 > view matrix models
    11812 > #4,0.28381,-0.20491,-0.93673,335.61,0.93973,0.25368,0.22923,-67.38,0.19066,-0.94534,0.26456,280.03
    11813 
    11814 > view matrix models
    11815 > #4,0.29033,-0.1329,-0.94765,322.58,0.93808,0.23513,0.25442,-66.671,0.18901,-0.96284,0.19293,291.98
    11816 
    11817 > view matrix models
    11818 > #4,0.35013,-0.063779,-0.93453,297.24,0.92612,0.17313,0.33516,-62.689,0.14042,-0.98283,0.11968,313.39
    11819 
    11820 > view matrix models
    11821 > #4,0.28929,-0.083154,-0.95362,314.43,0.94763,0.16569,0.27303,-58.03,0.1353,-0.98267,0.12673,313.48
    11822 
    11823 > view matrix models
    11824 > #4,0.29468,-0.086777,-0.95165,313.84,0.94725,0.15789,0.27892,-57.235,0.12605,-0.98364,0.12873,315.16
    11825 
    11826 > view matrix models
    11827 > #4,0.36145,-0.11336,-0.92548,303.06,0.89859,0.30718,0.31332,-79.332,0.24877,-0.94488,0.21289,275.15
    11828 
    11829 > hide #!2 models
    11830 
    11831 > view matrix models
    11832 > #4,0.75588,-0.11899,-0.6438,196.83,0.49521,0.74715,0.44333,-99.072,0.42827,-0.65392,0.62368,140.02
    11833 
    11834 > view matrix models
    11835 > #4,0.79244,-0.19913,-0.57652,196.6,0.59732,0.44467,0.66744,-89.678,0.12346,-0.87328,0.47133,255.09
    11836 
    11837 > show #!2 models
    11838 
    11839 > view matrix models
    11840 > #4,0.84088,0.043539,-0.53947,139,0.20748,0.89468,0.3956,-66.307,0.49988,-0.44458,0.74328,74.375
    11841 
    11842 > view matrix models
    11843 > #4,0.61732,-0.23939,-0.7494,257.2,0.45462,0.88598,0.091476,-75.144,0.64205,-0.39716,0.65577,49.425
    11844 
    11845 > view matrix models
    11846 > #4,0.38724,0.030398,-0.92148,271.6,0.61211,0.73893,0.28161,-100.4,0.68947,-0.6731,0.26753,136.6
    11847 
    11848 > view matrix models
    11849 > #4,0.32928,0.15127,-0.93204,261.73,0.67479,0.65276,0.34434,-103.89,0.66048,-0.74231,0.11286,172.9
    11850 
    11851 > view matrix models
    11852 > #4,0.83345,-0.16899,-0.52612,177.48,0.33798,0.90914,0.24338,-75.428,0.43719,-0.38066,0.81484,66.051
    11853 
    11854 > view matrix models
    11855 > #4,0.73197,-0.15661,-0.6631,210.44,0.61773,0.56316,0.54888,-101.05,0.28747,-0.81137,0.50895,208.62
    11856 
    11857 > view matrix models
    11858 > #4,0.70748,-0.11472,-0.69736,211.46,0.67078,0.41972,0.61146,-92.303,0.22255,-0.90037,0.3739,252.95
    11859 
    11860 > view matrix models
    11861 > #4,0.50475,-0.22825,-0.83254,286.11,0.80219,0.4803,0.35468,-97.631,0.31892,-0.84689,0.42553,219.04
    11862 
    11863 > view matrix models
    11864 > #4,0.43321,-0.14625,-0.88935,291.32,0.79138,0.53394,0.29769,-98.629,0.43133,-0.83278,0.34705,204.67
    11865 
    11866 > view matrix models
    11867 > #4,0.39985,-0.22492,-0.88856,311.79,0.73762,0.65442,0.16627,-94.936,0.54409,-0.7219,0.42757,153.83
    11868 
    11869 > hide #!8 models
    11870 
    11871 > view matrix models
    11872 > #4,0.40534,-0.24527,-0.88065,313.53,0.76932,0.61189,0.18368,-95.2,0.49381,-0.75196,0.43671,167.65
    11873 
    11874 > view matrix models
    11875 > #4,0.25068,-0.40305,-0.88017,371.18,0.81823,0.57411,-0.029862,-72.272,0.51736,-0.7127,0.47371,151.72
    11876 
    11877 > view matrix models
    11878 > #4,0.3665,-0.39401,-0.84287,343.41,0.8386,0.5323,0.11581,-85.696,0.40303,-0.74927,0.5255,173.7
    11879 
    11880 > view matrix models
    11881 > #4,0.48359,-0.37777,-0.78957,312.2,0.85036,0.41655,0.32152,-91.15,0.20743,-0.82691,0.52268,224.84
    11882 
    11883 > view matrix models
    11884 > #4,0.44767,-0.35695,-0.81986,318.73,0.84619,0.46549,0.25939,-91.93,0.28905,-0.80988,0.51043,207.88
    11885 
    11886 > show #5 models
    11887 
    11888 > hide #4 models
    11889 
    11890 > show #!8 models
    11891 
    11892 > hide #!2 models
    11893 
    11894 > ui tool show "Show Sequence Viewer"
    11895 
    11896 > sequence chain #5/B
    11897 
    11898 Alignment identifier is 5/B 
    11899 
    11900 > sequence chain #5/C
    11901 
    11902 Alignment identifier is 5/C 
    11903 
    11904 > ui tool show "Change Chain IDs"
    11905 
    11906 > select #5/C:1
    11907 
    11908 5 atoms, 4 bonds, 1 residue, 1 model selected 
    11909 
    11910 > select #5/C
    11911 
    11912 1632 atoms, 1668 bonds, 214 residues, 1 model selected 
    11913 
    11914 > changechains sel C L
    11915 
    11916 Chain IDs of 214 residues changed 
    11917 
    11918 > changechains sel C L
    11919 
    11920 No residues specified have any of the 'from' chain IDs 
    11921 
    11922 > ui tool show "Show Sequence Viewer"
    11923 
    11924 > sequence chain #5/L
    11925 
    11926 Alignment identifier is 5/L 
    11927 
    11928 > ui tool show "Change Chain IDs"
    11929 
    11930 > select
    11931 > #5/B:5-9,20-27,36-42,48-54,60-62,70-75,80-85,94-101,118-120,131-135,146-156,161-165,174-176,187-196,205-211,216-222
    11932 
    11933 837 atoms, 847 bonds, 101 residues, 1 model selected 
    11934 
    11935 > select #5/B:228
    11936 
    11937 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11938 
    11939 > select #5/B
    11940 
    11941 1769 atoms, 1825 bonds, 228 residues, 1 model selected 
    11942 
    11943 > ui tool show "Change Chain IDs"
    11944 
    11945 > changechains sel B H
    11946 
    11947 Chain IDs of 228 residues changed 
    11948 
    11949 > ui tool show "Show Sequence Viewer"
    11950 
    11951 > sequence chain #5/H
    11952 
    11953 Alignment identifier is 5/H 
    11954 
    11955 > select #5/H:1
    11956 
    11957 5 atoms, 4 bonds, 1 residue, 1 model selected 
    11958 
    11959 > select #5/H:1
    11960 
    11961 5 atoms, 4 bonds, 1 residue, 1 model selected 
    11962 
    11963 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    11964 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/Fab562_HDXMS_RelativeDchange_10min_recolored.defattr
    11965 
    11966 Summary of feedback from opening
    11967 /Users/alvinchew/Library/CloudStorage/OneDrive-
    11968 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/Fab562_HDXMS_RelativeDchange_10min_recolored.defattr 
    11969 --- 
    11970 note | Assigned attribute 'fab562_10min_relative_deuterium_uptake' to 1126
    11971 residues using match mode: any 
    11972  
    11973 
    11974 > color byattribute fab562_10min_relative_deuterium_uptake #3/A-B:174-361 key
    11975 > true palette bluered range -2.0,1.0 noValueColor grey
    11976 
    11977 All 'fab562_10min_relative_deuterium_uptake' values are None 
    11978 
    11979 > color byattribute fab562_10min_relative_deuterium_uptake #5 key true palette
    11980 > bluered range -2.0,1.0 noValueColor grey
    11981 
    11982 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    11983 
    11984 3401 atoms, 442 residues, atom fab562_10min_relative_deuterium_uptake range
    11985 -1.18 to 0.73 
    11986 
    11987 > hide #!8 models
    11988 
    11989 > select add #5
    11990 
    11991 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    11992 
    11993 > select subtract #5
    11994 
    11995 Nothing selected 
    11996 
    11997 > ui mousemode right zoom
    11998 
    11999 > select #5/H:1-2
    12000 
    12001 13 atoms, 12 bonds, 2 residues, 1 model selected 
    12002 
    12003 > select #5/H:1-3
    12004 
    12005 22 atoms, 21 bonds, 3 residues, 1 model selected 
    12006 
    12007 > select add #5
    12008 
    12009 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    12010 
    12011 > select subtract #5
    12012 
    12013 Nothing selected 
    12014 
    12015 > select add #5
    12016 
    12017 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    12018 
    12019 > select subtract #5
    12020 
    12021 Nothing selected 
    12022 
    12023 > select #5/H:5
    12024 
    12025 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12026 
    12027 > select #5/H:5-14
    12028 
    12029 71 atoms, 71 bonds, 10 residues, 1 model selected 
    12030 
    12031 > color sel #ddddffff
    12032 
    12033 > color sel #aab4ffff
    12034 
    12035 > color sel #8390ffff
    12036 
    12037 > select #5/H:15
    12038 
    12039 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12040 
    12041 > select #5/H:15-29
    12042 
    12043 120 atoms, 124 bonds, 15 residues, 1 model selected 
    12044 
    12045 > color sel #ffe6e6ff
    12046 
    12047 > color sel #ffe2ddff
    12048 
    12049 > color sel #ffe1ddff
    12050 
    12051 > color sel #ffe0dcff
    12052 
    12053 [Repeated 2 time(s)]
    12054 
    12055 > color sel #ffe0dbff
    12056 
    12057 > color sel #ffdfdaff
    12058 
    12059 [Repeated 1 time(s)]
    12060 
    12061 > color sel #ffdedaff
    12062 
    12063 > color sel #ffddd9ff
    12064 
    12065 [Repeated 1 time(s)]
    12066 
    12067 > color sel #ffdcd8ff
    12068 
    12069 > select #5/H:30
    12070 
    12071 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12072 
    12073 > select #5/H:30-35
    12074 
    12075 43 atoms, 43 bonds, 6 residues, 1 model selected 
    12076 
    12077 > ui tool show "Color Actions"
    12078 
    12079 > color sel #6f70ffff
    12080 
    12081 > color sel #4449ffff
    12082 
    12083 > color sel #1f28ffff
    12084 
    12085 > color sel #1f29ffff
    12086 
    12087 > color sel #202affff
    12088 
    12089 > color sel #212cffff
    12090 
    12091 > color sel #222cffff
    12092 
    12093 > color sel #222dffff
    12094 
    12095 > color sel #232effff
    12096 
    12097 > color sel #242fffff
    12098 
    12099 [Repeated 2 time(s)]
    12100 
    12101 > color sel #2531ffff
    12102 
    12103 > color sel #2631ffff
    12104 
    12105 > color sel #2632ffff
    12106 
    12107 > color sel #2732ffff
    12108 
    12109 > color sel #2733ffff
    12110 
    12111 > color sel #2935ffff
    12112 
    12113 > color sel #2a35ffff
    12114 
    12115 > color sel #2a36ffff
    12116 
    12117 > color sel #2b37ffff
    12118 
    12119 > select #5/H:36
    12120 
    12121 12 atoms, 12 bonds, 1 residue, 1 model selected 
    12122 
    12123 > select #5/H:36-47
    12124 
    12125 115 atoms, 120 bonds, 12 residues, 1 model selected 
    12126 
    12127 > color sel #ffcfe1ff
    12128 
    12129 > color sel #ffdddeff
    12130 
    12131 [Repeated 1 time(s)]
    12132 
    12133 > color sel #ffdddfff
    12134 
    12135 > color sel #ffdde2ff
    12136 
    12137 > color sel #ffdde3ff
    12138 
    12139 > color sel #ffdde5ff
    12140 
    12141 > color sel #ffdde8ff
    12142 
    12143 > color sel #ffdde9ff
    12144 
    12145 > color sel #ffdceaff
    12146 
    12147 [Repeated 1 time(s)]
    12148 
    12149 > color sel #ffdce9ff
    12150 
    12151 > color sel #ffdae7ff
    12152 
    12153 > color sel #ffd9e4ff
    12154 
    12155 > color sel #ffd8e2ff
    12156 
    12157 > color sel #ffd7e0ff
    12158 
    12159 > color sel #ffd7dfff
    12160 
    12161 > color sel #ffd6dcff
    12162 
    12163 > color sel #ffd5dbff
    12164 
    12165 > color sel #ffd3daff
    12166 
    12167 > color sel #ffd3d9ff
    12168 
    12169 > color sel #ffd2d7ff
    12170 
    12171 [Repeated 1 time(s)]
    12172 
    12173 > color sel #ffd1d6ff
    12174 
    12175 > color sel #ffd0d5ff
    12176 
    12177 > select #5/H:48
    12178 
    12179 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12180 
    12181 > select #5/H:48-61
    12182 
    12183 120 atoms, 123 bonds, 14 residues, 1 model selected 
    12184 
    12185 > color sel #6277ffff
    12186 
    12187 > select #5/H:62-63
    12188 
    12189 20 atoms, 20 bonds, 2 residues, 1 model selected 
    12190 
    12191 > select #5/H:62-72
    12192 
    12193 91 atoms, 92 bonds, 11 residues, 1 model selected 
    12194 
    12195 > color sel #ff7f7fff
    12196 
    12197 > color sel #ff9b9aff
    12198 
    12199 > select #5/H:79-80
    12200 
    12201 17 atoms, 16 bonds, 2 residues, 1 model selected 
    12202 
    12203 > select #5/H:79-81
    12204 
    12205 28 atoms, 28 bonds, 3 residues, 1 model selected 
    12206 
    12207 > select #5/H:78
    12208 
    12209 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12210 
    12211 > select #5/H:78-95
    12212 
    12213 142 atoms, 144 bonds, 18 residues, 1 model selected 
    12214 
    12215 > color sel #a9b9ffff
    12216 
    12217 > select #5/H:96
    12218 
    12219 12 atoms, 12 bonds, 1 residue, 1 model selected 
    12220 
    12221 > select #5/H:96-103
    12222 
    12223 75 atoms, 78 bonds, 8 residues, 1 model selected 
    12224 
    12225 > color sel #8493ffff
    12226 
    12227 > color sel #88a0ffff
    12228 
    12229 > select #5/H:104
    12230 
    12231 12 atoms, 12 bonds, 1 residue, 1 model selected 
    12232 
    12233 > select #5/H:104-112
    12234 
    12235 73 atoms, 78 bonds, 9 residues, 1 model selected 
    12236 
    12237 > color sel #8296ffff
    12238 
    12239 > color sel #8297ffff
    12240 
    12241 > color sel #8398ffff
    12242 
    12243 > color sel #8499ffff
    12244 
    12245 > color sel #849affff
    12246 
    12247 > color sel #849bffff
    12248 
    12249 > color sel #859cffff
    12250 
    12251 > color sel #859dffff
    12252 
    12253 [Repeated 1 time(s)]
    12254 
    12255 > color sel #869effff
    12256 
    12257 > color sel #869fffff
    12258 
    12259 > color sel #87a0ffff
    12260 
    12261 > color sel #88a1ffff
    12262 
    12263 > color sel #88a2ffff
    12264 
    12265 > color sel #89a3ffff
    12266 
    12267 [Repeated 1 time(s)]
    12268 
    12269 > color sel #8aa4ffff
    12270 
    12271 > color sel #8aa5ffff
    12272 
    12273 > select #5/H:113-114
    12274 
    12275 26 atoms, 28 bonds, 2 residues, 1 model selected 
    12276 
    12277 > select #5/H:113-120
    12278 
    12279 65 atoms, 67 bonds, 8 residues, 1 model selected 
    12280 
    12281 > color sel #aab4ffff
    12282 
    12283 > select #5/H:120-121
    12284 
    12285 14 atoms, 13 bonds, 2 residues, 1 model selected 
    12286 
    12287 > select #5/H:120-121
    12288 
    12289 14 atoms, 13 bonds, 2 residues, 1 model selected 
    12290 
    12291 > select #5/H:120
    12292 
    12293 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12294 
    12295 > select #5/H:120
    12296 
    12297 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12298 
    12299 > color sel #7e95ffff
    12300 
    12301 > select #5/H:121
    12302 
    12303 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12304 
    12305 > select #5/H:121-123
    12306 
    12307 25 atoms, 25 bonds, 3 residues, 1 model selected 
    12308 
    12309 > select #5/H:121
    12310 
    12311 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12312 
    12313 > select #5/H:121-122
    12314 
    12315 14 atoms, 13 bonds, 2 residues, 1 model selected 
    12316 
    12317 > color sel #eceeffff
    12318 
    12319 > color sel #73747cff
    12320 
    12321 [Repeated 1 time(s)]
    12322 
    12323 > color sel #74747dff
    12324 
    12325 > color sel #74757dff
    12326 
    12327 [Repeated 1 time(s)]
    12328 
    12329 > color sel #75757eff
    12330 
    12331 [Repeated 1 time(s)]
    12332 
    12333 > color sel #75767eff
    12334 
    12335 > undo
    12336 
    12337 [Repeated 1 time(s)]
    12338 
    12339 > select #5/H:123-124
    12340 
    12341 16 atoms, 16 bonds, 2 residues, 1 model selected 
    12342 
    12343 > select #5/H:123-145
    12344 
    12345 153 atoms, 157 bonds, 23 residues, 1 model selected 
    12346 
    12347 > color sel #6c6c7eff
    12348 
    12349 > color sel #dad8feff
    12350 
    12351 > color sel #d9d8fdff
    12352 
    12353 [Repeated 1 time(s)]
    12354 
    12355 > color sel #d8d7fcff
    12356 
    12357 > color sel #d6d5f9ff
    12358 
    12359 > color sel #d5d4f8ff
    12360 
    12361 > color sel #d4d3f7ff
    12362 
    12363 > color sel #d4d2f7ff
    12364 
    12365 > color sel #d3d2f6ff
    12366 
    12367 > color sel #d3d1f5ff
    12368 
    12369 > color sel #d2d1f5ff
    12370 
    12371 > color sel #d1d0f4ff
    12372 
    12373 > color sel #cbcaecff
    12374 
    12375 > color sel #c7c6e8ff
    12376 
    12377 > color sel #c5c4e6ff
    12378 
    12379 > color sel #b3c3e6ff
    12380 
    12381 > color sel #b6bee6ff
    12382 
    12383 > select #5/H:146-193
    12384 
    12385 349 atoms, 358 bonds, 48 residues, 1 model selected 
    12386 
    12387 > select #5/H:146-156
    12388 
    12389 79 atoms, 79 bonds, 11 residues, 1 model selected 
    12390 
    12391 > color sel #e6ced9ff
    12392 
    12393 > color sel #e6bfbaff
    12394 
    12395 > select #5/H:157-159
    12396 
    12397 27 atoms, 28 bonds, 3 residues, 1 model selected 
    12398 
    12399 > select #5/H:157-168
    12400 
    12401 93 atoms, 97 bonds, 12 residues, 1 model selected 
    12402 
    12403 > color sel #e6b7aeff
    12404 
    12405 > select #5/H:169-171
    12406 
    12407 20 atoms, 19 bonds, 3 residues, 1 model selected 
    12408 
    12409 > select #5/H:169-176
    12410 
    12411 54 atoms, 54 bonds, 8 residues, 1 model selected 
    12412 
    12413 > color sel #c1c4e6ff
    12414 
    12415 > select #5/H:177
    12416 
    12417 11 atoms, 11 bonds, 1 residue, 1 model selected 
    12418 
    12419 > select #5/H:177
    12420 
    12421 11 atoms, 11 bonds, 1 residue, 1 model selected 
    12422 
    12423 > color sel #e6d7dbff
    12424 
    12425 > color sel #e6bfc0ff
    12426 
    12427 > select #5/H:181
    12428 
    12429 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12430 
    12431 > select #5/H:181-184
    12432 
    12433 29 atoms, 28 bonds, 4 residues, 1 model selected 
    12434 
    12435 > select #5/H:180
    12436 
    12437 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12438 
    12439 > color sel #e6ced4ff
    12440 
    12441 > select #5/H:181
    12442 
    12443 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12444 
    12445 > select #5/H:181-186
    12446 
    12447 41 atoms, 40 bonds, 6 residues, 1 model selected 
    12448 
    12449 > color sel #e6c9cdff
    12450 
    12451 > color sel #e6c2c5ff
    12452 
    12453 [Repeated 1 time(s)]
    12454 
    12455 > color sel #e6c3c5ff
    12456 
    12457 > color sel #e6c3c6ff
    12458 
    12459 > color sel #e6c4c7ff
    12460 
    12461 [Repeated 1 time(s)]
    12462 
    12463 > color sel #e6c5c8ff
    12464 
    12465 > color sel #e6c5c7ff
    12466 
    12467 > color sel #e6c5c8ff
    12468 
    12469 > color sel #e6c6c8ff
    12470 
    12471 [Repeated 1 time(s)]
    12472 
    12473 > select #5/H:188
    12474 
    12475 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12476 
    12477 > select #5/H:188-198
    12478 
    12479 73 atoms, 73 bonds, 11 residues, 1 model selected 
    12480 
    12481 > color sel #b4b7e6ff
    12482 
    12483 > select #5/H:199-200
    12484 
    12485 14 atoms, 13 bonds, 2 residues, 1 model selected 
    12486 
    12487 > select #5/H:199-208
    12488 
    12489 75 atoms, 76 bonds, 10 residues, 1 model selected 
    12490 
    12491 > color sel #8999e6ff
    12492 
    12493 > color sel #7b90e6ff
    12494 
    12495 > color sel #7083e6ff
    12496 
    12497 > select #5/H:209
    12498 
    12499 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12500 
    12501 > select #5/H:209-212
    12502 
    12503 34 atoms, 34 bonds, 4 residues, 1 model selected 
    12504 
    12505 > color sel #95a4e6ff
    12506 
    12507 > color sel #b0b6e6ff
    12508 
    12509 > select #5/H:213-214
    12510 
    12511 13 atoms, 13 bonds, 2 residues, 1 model selected 
    12512 
    12513 > select #5/H:213-223
    12514 
    12515 86 atoms, 86 bonds, 11 residues, 1 model selected 
    12516 
    12517 > color sel #93a0e6ff
    12518 
    12519 > select #5/L:1
    12520 
    12521 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12522 
    12523 > select #5/L:1-6
    12524 
    12525 45 atoms, 44 bonds, 6 residues, 1 model selected 
    12526 
    12527 > select #5/L:7-8
    12528 
    12529 15 atoms, 14 bonds, 2 residues, 1 model selected 
    12530 
    12531 > select #5/L:7-14
    12532 
    12533 58 atoms, 58 bonds, 8 residues, 1 model selected 
    12534 
    12535 > color sel #9daae6ff
    12536 
    12537 > select #5/L:15
    12538 
    12539 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12540 
    12541 > select #5/L:15-21
    12542 
    12543 47 atoms, 46 bonds, 7 residues, 1 model selected 
    12544 
    12545 > color sel #e6c2caff
    12546 
    12547 > color sel #e6c3c3ff
    12548 
    12549 > select #5/L:22-23
    12550 
    12551 15 atoms, 14 bonds, 2 residues, 1 model selected 
    12552 
    12553 > select #5/L:22-26
    12554 
    12555 36 atoms, 35 bonds, 5 residues, 1 model selected 
    12556 
    12557 > color sel #e6cdceff
    12558 
    12559 > select #5/L:27-28
    12560 
    12561 11 atoms, 10 bonds, 2 residues, 1 model selected 
    12562 
    12563 > select #5/L:27-28
    12564 
    12565 11 atoms, 10 bonds, 2 residues, 1 model selected 
    12566 
    12567 > color sel #a5bbe6ff
    12568 
    12569 > color sel #a5b6e6ff
    12570 
    12571 > select #5/L:29-30
    12572 
    12573 12 atoms, 11 bonds, 2 residues, 1 model selected 
    12574 
    12575 > select #5/L:29-35
    12576 
    12577 51 atoms, 51 bonds, 7 residues, 1 model selected 
    12578 
    12579 > color sel #c4c6e6ff
    12580 
    12581 > color sel #d0d4e6ff
    12582 
    12583 > select #5/L:36-37
    12584 
    12585 24 atoms, 26 bonds, 2 residues, 1 model selected 
    12586 
    12587 > select #5/L:36
    12588 
    12589 10 atoms, 10 bonds, 1 residue, 1 model selected 
    12590 
    12591 > color sel #c7cfe6ff
    12592 
    12593 > select #5/L:37
    12594 
    12595 14 atoms, 15 bonds, 1 residue, 1 model selected 
    12596 
    12597 > select #5/L:37-38
    12598 
    12599 26 atoms, 28 bonds, 2 residues, 1 model selected 
    12600 
    12601 > color sel #b2bde6ff
    12602 
    12603 > color sel #abbae6ff
    12604 
    12605 > color sel #abbbe6ff
    12606 
    12607 > color sel #abbce6ff
    12608 
    12609 > color sel #acbce6ff
    12610 
    12611 > color sel #acbde6ff
    12612 
    12613 > color sel #adbee6ff
    12614 
    12615 [Repeated 1 time(s)]
    12616 
    12617 > color sel #adbfe6ff
    12618 
    12619 [Repeated 1 time(s)]
    12620 
    12621 > color sel #adc0e6ff
    12622 
    12623 > color sel #aec0e6ff
    12624 
    12625 > color sel #aec1e6ff
    12626 
    12627 > color sel #aec2e6ff
    12628 
    12629 > color sel #afc2e6ff
    12630 
    12631 > color sel #afc3e6ff
    12632 
    12633 > color sel #afc2e6ff
    12634 
    12635 > color sel #aec2e6ff
    12636 
    12637 > color sel #aec1e6ff
    12638 
    12639 > color sel #aec0e6ff
    12640 
    12641 [Repeated 1 time(s)]
    12642 
    12643 > color sel #aebfe6ff
    12644 
    12645 > color sel #adbee6ff
    12646 
    12647 > color sel #b0c3e6ff
    12648 
    12649 [Repeated 1 time(s)]
    12650 
    12651 > color sel #b0c2e6ff
    12652 
    12653 > color sel #b0c1e6ff
    12654 
    12655 [Repeated 2 time(s)]
    12656 
    12657 > color sel #b0c0e6ff
    12658 
    12659 [Repeated 2 time(s)]
    12660 
    12661 > color sel #b0bfe6ff
    12662 
    12663 [Repeated 1 time(s)]
    12664 
    12665 > color sel #b1bfe6ff
    12666 
    12667 [Repeated 2 time(s)]
    12668 
    12669 > color sel #b1bee6ff
    12670 
    12671 [Repeated 1 time(s)]
    12672 
    12673 > color sel #b2bee6ff
    12674 
    12675 > select #5/L:39
    12676 
    12677 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12678 
    12679 > select #5/L:39-48
    12680 
    12681 74 atoms, 74 bonds, 10 residues, 1 model selected 
    12682 
    12683 > color sel #abbbe6ff
    12684 
    12685 > select #5/L:49
    12686 
    12687 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12688 
    12689 > color sel #a1ace6ff
    12690 
    12691 > color sel #a1ade6ff
    12692 
    12693 > color sel #a0b1e6ff
    12694 
    12695 > color sel #a1b1e6ff
    12696 
    12697 > select #5/L:50
    12698 
    12699 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12700 
    12701 > select #5/L:50-55
    12702 
    12703 47 atoms, 47 bonds, 6 residues, 1 model selected 
    12704 
    12705 > color sel #6a88e6ff
    12706 
    12707 > color sel #5b80e6ff
    12708 
    12709 > color sel #5176e6ff
    12710 
    12711 > color sel #426be6ff
    12712 
    12713 > color sel #3b67e6ff
    12714 
    12715 > color sel #315ae6ff
    12716 
    12717 > select #5/L:56
    12718 
    12719 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12720 
    12721 > select #5/L:56
    12722 
    12723 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12724 
    12725 > color sel #3f64e6ff
    12726 
    12727 > select #5/L:57
    12728 
    12729 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12730 
    12731 > select #5/L:57
    12732 
    12733 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12734 
    12735 > color sel #b3b7e6ff
    12736 
    12737 > select #5/L:58
    12738 
    12739 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12740 
    12741 > select #5/L:58-69
    12742 
    12743 78 atoms, 79 bonds, 12 residues, 1 model selected 
    12744 
    12745 > color sel #b0b2e6ff
    12746 
    12747 > select #5/L:70-71
    12748 
    12749 11 atoms, 10 bonds, 2 residues, 1 model selected 
    12750 
    12751 > select #5/L:70-73
    12752 
    12753 34 atoms, 35 bonds, 4 residues, 1 model selected 
    12754 
    12755 > color sel #a9ace6ff
    12756 
    12757 > select #5/L:74-75
    12758 
    12759 14 atoms, 13 bonds, 2 residues, 1 model selected 
    12760 
    12761 > select #5/L:74-79
    12762 
    12763 41 atoms, 40 bonds, 6 residues, 1 model selected 
    12764 
    12765 > color sel #9eaae6ff
    12766 
    12767 > select #5/L:80
    12768 
    12769 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12770 
    12771 > select #5/L:80-82
    12772 
    12773 21 atoms, 20 bonds, 3 residues, 1 model selected 
    12774 
    12775 > color sel #d3cbe6ff
    12776 
    12777 > color sel #e6ced1ff
    12778 
    12779 > select #5/L:83
    12780 
    12781 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12782 
    12783 > select #5/L:83
    12784 
    12785 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12786 
    12787 > select #5/L:82
    12788 
    12789 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12790 
    12791 > select #5/L:82-83
    12792 
    12793 14 atoms, 13 bonds, 2 residues, 1 model selected 
    12794 
    12795 > volume #8 level 0.09283
    12796 
    12797 > color sel #b7bbe6ff
    12798 
    12799 > select #5/L:84
    12800 
    12801 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12802 
    12803 > select #5/L:84-87
    12804 
    12805 26 atoms, 25 bonds, 4 residues, 1 model selected 
    12806 
    12807 > color sel #d9cce6ff
    12808 
    12809 > color sel #e6d9e4ff
    12810 
    12811 > color sel #e6d2d0ff
    12812 
    12813 > select #5/L:98-99
    12814 
    12815 15 atoms, 15 bonds, 2 residues, 1 model selected 
    12816 
    12817 > select #5/L:98-100
    12818 
    12819 19 atoms, 19 bonds, 3 residues, 1 model selected 
    12820 
    12821 > select #5/L:97
    12822 
    12823 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12824 
    12825 > select #5/L:97
    12826 
    12827 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12828 
    12829 > color sel #d0d1e6ff
    12830 
    12831 > select #5/L:98-99
    12832 
    12833 15 atoms, 15 bonds, 2 residues, 1 model selected 
    12834 
    12835 > select #5/L:98-105
    12836 
    12837 56 atoms, 56 bonds, 8 residues, 1 model selected 
    12838 
    12839 > color sel #a9aee6ff
    12840 
    12841 > select #5/L:114-115
    12842 
    12843 13 atoms, 12 bonds, 2 residues, 1 model selected 
    12844 
    12845 > select #5/L:114-125
    12846 
    12847 97 atoms, 100 bonds, 12 residues, 1 model selected 
    12848 
    12849 > color sel #a8ace6ff
    12850 
    12851 > select #5/L:128-129
    12852 
    12853 11 atoms, 10 bonds, 2 residues, 1 model selected 
    12854 
    12855 > select #5/L:128-131
    12856 
    12857 22 atoms, 21 bonds, 4 residues, 1 model selected 
    12858 
    12859 > color sel #ccccffff
    12860 
    12861 > select #5/L:132
    12862 
    12863 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12864 
    12865 > select #5/L:132-137
    12866 
    12867 44 atoms, 43 bonds, 6 residues, 1 model selected 
    12868 
    12869 > color sel #ffeefaff
    12870 
    12871 > color sel #ffe4e2ff
    12872 
    12873 > color sel #ffe7ddff
    12874 
    12875 > color sel #ffe7dcff
    12876 
    12877 [Repeated 2 time(s)]
    12878 
    12879 > color sel #ffe7dbff
    12880 
    12881 [Repeated 1 time(s)]
    12882 
    12883 > color sel #ffe8daff
    12884 
    12885 > color sel #ffe7daff
    12886 
    12887 > color sel #ffe3d2ff
    12888 
    12889 > color sel #ffe1cdff
    12890 
    12891 > color sel #ffe2cdff
    12892 
    12893 > color sel #ffdbc2ff
    12894 
    12895 > color sel #ffdac2ff
    12896 
    12897 > color sel #ffd5c2ff
    12898 
    12899 > select #5/L:138
    12900 
    12901 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12902 
    12903 > select #5/L:138-146
    12904 
    12905 79 atoms, 81 bonds, 9 residues, 1 model selected 
    12906 
    12907 > color sel #d0d6ffff
    12908 
    12909 > color sel #c1c6ffff
    12910 
    12911 > color sel #b1bdffff
    12912 
    12913 > select #5/L:147
    12914 
    12915 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12916 
    12917 > select #5/L:147-158
    12918 
    12919 95 atoms, 96 bonds, 12 residues, 1 model selected 
    12920 
    12921 > color sel #ff5b5bff
    12922 
    12923 > color sel #ff484dff
    12924 
    12925 > color sel #ff4347ff
    12926 
    12927 > color sel #ff4247ff
    12928 
    12929 > color sel #ff4146ff
    12930 
    12931 > color sel #ff4145ff
    12932 
    12933 > color sel #ff4045ff
    12934 
    12935 > color sel #ff4044ff
    12936 
    12937 > color sel #ff3f43ff
    12938 
    12939 > color sel #ff3e43ff
    12940 
    12941 > color sel #ff3e42ff
    12942 
    12943 > color sel #ff3d42ff
    12944 
    12945 > color sel #ff3c41ff
    12946 
    12947 > color sel #ff3c40ff
    12948 
    12949 > color sel #ff3b40ff
    12950 
    12951 > color sel #ff3c40ff
    12952 
    12953 [Repeated 2 time(s)]
    12954 
    12955 > color sel #ff3d40ff
    12956 
    12957 > color sel #ff3e40ff
    12958 
    12959 [Repeated 1 time(s)]
    12960 
    12961 > color sel #ff3e41ff
    12962 
    12963 > color sel #ff3f41ff
    12964 
    12965 > color sel #ff3f40ff
    12966 
    12967 > color sel #ff4040ff
    12968 
    12969 [Repeated 2 time(s)]
    12970 
    12971 > color sel #ff3f3aff
    12972 
    12973 > color sel #ff3e39ff
    12974 
    12975 [Repeated 2 time(s)]
    12976 
    12977 > color sel #ff3e38ff
    12978 
    12979 [Repeated 1 time(s)]
    12980 
    12981 > select #5/L:159-160
    12982 
    12983 15 atoms, 14 bonds, 2 residues, 1 model selected 
    12984 
    12985 > select #5/L:159-160
    12986 
    12987 15 atoms, 14 bonds, 2 residues, 1 model selected 
    12988 
    12989 > select #5/L:161-162
    12990 
    12991 15 atoms, 14 bonds, 2 residues, 1 model selected 
    12992 
    12993 > select #5/L:161-179
    12994 
    12995 144 atoms, 144 bonds, 19 residues, 1 model selected 
    12996 
    12997 > select #5/L:180-181
    12998 
    12999 15 atoms, 14 bonds, 2 residues, 1 model selected 
    13000 
    13001 > select #5/L:180-182
    13002 
    13003 21 atoms, 20 bonds, 3 residues, 1 model selected 
    13004 
    13005 > select #5/L:183
    13006 
    13007 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13008 
    13009 > select #5/L:183-204
    13010 
    13011 176 atoms, 180 bonds, 22 residues, 1 model selected 
    13012 
    13013 > color sel #6f7bffff
    13014 
    13015 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    13016 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
    13017 
    13018 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    13019 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
    13020 > includeMaps true
    13021 
    13022 > show #!8 models
    13023 
    13024 > select add #5
    13025 
    13026 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13027 
    13028 > select subtract #5
    13029 
    13030 Nothing selected 
    13031 
    13032 > hide #!8 models
    13033 
    13034 > select add #8
    13035 
    13036 2 models selected 
    13037 
    13038 > select subtract #8
    13039 
    13040 Nothing selected 
    13041 
    13042 > color #8 #c5fdf81a models
    13043 
    13044 > show #!8 models
    13045 
    13046 > ui tool show "Show Sequence Viewer"
    13047 
    13048 > sequence chain #3/B
    13049 
    13050 Alignment identifier is 3/B 
    13051 
    13052 > select #3/B:111
    13053 
    13054 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13055 
    13056 > select #3/B:111-271
    13057 
    13058 1300 atoms, 1342 bonds, 161 residues, 1 model selected 
    13059 
    13060 > select #3/B:302
    13061 
    13062 7 atoms, 6 bonds, 1 residue, 1 model selected 
    13063 
    13064 > select #3/B:302-304
    13065 
    13066 18 atoms, 17 bonds, 3 residues, 1 model selected 
    13067 
    13068 > select #3/B:301-302
    13069 
    13070 14 atoms, 13 bonds, 2 residues, 1 model selected 
    13071 
    13072 > select #3/B:301-310
    13073 
    13074 70 atoms, 69 bonds, 10 residues, 1 model selected 
    13075 
    13076 > hide #5 models
    13077 
    13078 > show #5 models
    13079 
    13080 > select add #5
    13081 
    13082 3471 atoms, 3562 bonds, 452 residues, 2 models selected 
    13083 
    13084 > select subtract #5
    13085 
    13086 70 atoms, 69 bonds, 10 residues, 1 model selected 
    13087 
    13088 > select add #3
    13089 
    13090 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    13091 
    13092 > select subtract #3
    13093 
    13094 Nothing selected 
    13095 
    13096 > select add #5
    13097 
    13098 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13099 
    13100 > select #3/B:301
    13101 
    13102 7 atoms, 6 bonds, 1 residue, 1 model selected 
    13103 
    13104 > select #3/B:301-313
    13105 
    13106 96 atoms, 97 bonds, 13 residues, 1 model selected 
    13107 
    13108 > select add #5
    13109 
    13110 3497 atoms, 3590 bonds, 455 residues, 2 models selected 
    13111 
    13112 > select add #3
    13113 
    13114 9003 atoms, 9237 bonds, 1146 residues, 2 models selected 
    13115 
    13116 > select subtract #3
    13117 
    13118 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13119 
    13120 > ui mousemode right "translate selected models"
    13121 
    13122 > view matrix models
    13123 > #5,-0.17857,0.27184,0.94563,-4.5206,0.69023,0.71954,-0.076505,-64.572,-0.70121,0.63904,-0.31613,263.65
    13124 
    13125 > view matrix models
    13126 > #5,-0.17857,0.27184,0.94563,-4.1095,0.69023,0.71954,-0.076505,-65.814,-0.70121,0.63904,-0.31613,263.22
    13127 
    13128 > view matrix models
    13129 > #5,-0.17857,0.27184,0.94563,-4.2566,0.69023,0.71954,-0.076505,-65.556,-0.70121,0.63904,-0.31613,262.84
    13130 
    13131 > view matrix models
    13132 > #5,-0.17857,0.27184,0.94563,-3.5932,0.69023,0.71954,-0.076505,-65.573,-0.70121,0.63904,-0.31613,263.6
    13133 
    13134 > view matrix models
    13135 > #5,-0.17857,0.27184,0.94563,6.1172,0.69023,0.71954,-0.076505,-64.318,-0.70121,0.63904,-0.31613,265.1
    13136 
    13137 > view matrix models
    13138 > #5,-0.17857,0.27184,0.94563,6.2366,0.69023,0.71954,-0.076505,-63.955,-0.70121,0.63904,-0.31613,264.58
    13139 
    13140 > ui mousemode right "rotate selected models"
    13141 
    13142 > view matrix models
    13143 > #5,-0.50511,0.42112,0.75334,81.099,-0.58382,-0.80958,0.061111,408.82,0.63563,-0.40895,0.65478,-4.5259
    13144 
    13145 > view matrix models
    13146 > #5,-0.71614,0.48271,0.50412,165.69,-0.55355,-0.83274,0.011012,419.78,0.42512,-0.27117,0.86356,-43.167
    13147 
    13148 > view matrix models
    13149 > #5,-0.85245,0.30633,0.42367,241.3,-0.43531,-0.86468,-0.25067,467.41,0.28955,-0.39811,0.87044,2.3483
    13150 
    13151 > view matrix models
    13152 > #5,-0.93915,0.14358,0.31205,313.16,-0.24014,-0.924,-0.29757,455.63,0.24561,-0.3544,0.90226,-5.6943
    13153 
    13154 > ui mousemode right "translate selected models"
    13155 
    13156 > view matrix models
    13157 > #5,-0.93915,0.14358,0.31205,310.36,-0.24014,-0.924,-0.29757,454.57,0.24561,-0.3544,0.90226,-10.513
    13158 
    13159 > ui mousemode right "rotate selected models"
    13160 
    13161 > view matrix models
    13162 > #5,-0.92978,0.12057,0.3478,304.49,-0.25511,-0.89219,-0.3727,469.15,0.26537,-0.43526,0.86031,11.045
    13163 
    13164 > ui mousemode right "translate selected models"
    13165 
    13166 > view matrix models
    13167 > #5,-0.92978,0.12057,0.3478,301.55,-0.25511,-0.89219,-0.3727,465.8,0.26537,-0.43526,0.86031,10.049
    13168 
    13169 > ui mousemode right "rotate selected models"
    13170 
    13171 > view matrix models
    13172 > #5,-0.96388,-0.016383,0.26582,352.42,-0.11335,-0.87796,-0.46513,460.49,0.241,-0.47846,0.84439,26.097
    13173 
    13174 > view matrix models
    13175 > #5,-0.91826,0.06169,0.39115,300.16,-0.36231,-0.52952,-0.76703,510.97,0.15981,-0.84605,0.50859,188.38
    13176 
    13177 > view matrix models
    13178 > #5,-0.92676,0.077675,0.36753,304.3,-0.31305,-0.70047,-0.64136,504.23,0.20763,-0.70944,0.67349,115.46
    13179 
    13180 > view matrix models
    13181 > #5,-0.9834,-0.04765,0.17507,383.22,-0.094665,-0.6884,-0.71913,482.5,0.15478,-0.72376,0.67247,127.55
    13182 
    13183 > view matrix models
    13184 > #5,-0.95001,-0.19011,0.24767,386.58,-0.077458,-0.62494,-0.77682,481.46,0.30246,-0.75717,0.57898,130.31
    13185 
    13186 > view matrix models
    13187 > #5,-0.94393,-0.018851,0.3296,334.23,-0.26473,-0.55329,-0.7898,503.83,0.19725,-0.83277,0.51728,177.33
    13188 
    13189 > view matrix models
    13190 > #5,-0.84008,0.30007,0.45192,227.84,-0.54043,-0.53518,-0.64924,514.98,0.047043,-0.78964,0.61176,172.97
    13191 
    13192 > view matrix models
    13193 > #5,-0.90734,0.12615,0.40102,283.95,-0.29751,-0.86665,-0.40051,475.05,0.29702,-0.48271,0.82388,22.022
    13194 
    13195 > view matrix models
    13196 > #5,-0.89414,0.12288,0.43059,275.22,-0.30852,-0.866,-0.39353,475.19,0.32453,-0.48472,0.81224,20.379
    13197 
    13198 > view matrix models
    13199 > #5,-0.89988,0.10062,0.42437,281.83,-0.22953,-0.93663,-0.26465,443.88,0.37085,-0.33556,0.86595,-28.153
    13200 
    13201 > view matrix models
    13202 > #5,-0.91467,-0.052744,0.40075,318.49,-0.021786,-0.98358,-0.17917,396.11,0.40362,-0.17262,0.8985,-71.851
    13203 
    13204 > view matrix models
    13205 > #5,-0.83178,-0.098166,0.54635,277.86,0.12592,-0.99195,0.013478,326.12,0.54063,0.080008,0.83745,-128.06
    13206 
    13207 > view matrix models
    13208 > #5,-0.63629,-0.24728,0.73074,227.64,0.13032,-0.96808,-0.21411,375.09,0.76036,-0.041004,0.6482,-98.781
    13209 
    13210 > view matrix models
    13211 > #5,-0.61952,-0.21214,0.75577,212.25,0.091718,-0.97576,-0.19871,379.56,0.7796,-0.05379,0.62396,-93.986
    13212 
    13213 > view matrix models
    13214 > #5,-0.75135,-0.11146,0.65042,241.56,0.10086,-0.99345,-0.053733,346.75,0.65215,0.025229,0.75767,-118.3
    13215 
    13216 > view matrix models
    13217 > #5,-0.66332,-0.23987,0.70885,236.18,0.33554,-0.94201,-0.0047814,284.72,0.6689,0.23468,0.70534,-147.64
    13218 
    13219 > view matrix models
    13220 > #5,-0.7722,0.036461,0.63433,221.56,0.075095,-0.98612,0.1481,301.84,0.63093,0.162,0.75874,-140.25
    13221 
    13222 > view matrix models
    13223 > #5,-0.77412,-0.056826,0.63048,240.13,0.10514,-0.99367,0.039532,323.85,0.62424,0.096891,0.7752,-130.92
    13224 
    13225 > view matrix models
    13226 > #5,-0.82608,-0.15163,0.54277,287.64,0.13237,-0.98838,-0.074658,345.31,0.54779,0.010175,0.83655,-116.13
    13227 
    13228 > ui mousemode right "translate selected models"
    13229 
    13230 > view matrix models
    13231 > #5,-0.82608,-0.15163,0.54277,287.24,0.13237,-0.98838,-0.074658,345.43,0.54779,0.010175,0.83655,-116.45
    13232 
    13233 > view matrix models
    13234 > #5,-0.82608,-0.15163,0.54277,287.21,0.13237,-0.98838,-0.074658,345.17,0.54779,0.010175,0.83655,-116.29
    13235 
    13236 > select subtract #5
    13237 
    13238 Nothing selected 
    13239 
    13240 > select #3/B:301
    13241 
    13242 7 atoms, 6 bonds, 1 residue, 1 model selected 
    13243 
    13244 > select #3/B:301-313
    13245 
    13246 96 atoms, 97 bonds, 13 residues, 1 model selected 
    13247 
    13248 > select #3/B:310
    13249 
    13250 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13251 
    13252 > select #3/B:300-310
    13253 
    13254 77 atoms, 76 bonds, 11 residues, 1 model selected 
    13255 
    13256 > ui mousemode right "rotate selected models"
    13257 
    13258 > select add #5
    13259 
    13260 3478 atoms, 3569 bonds, 453 residues, 2 models selected 
    13261 
    13262 > select add #3
    13263 
    13264 9003 atoms, 9237 bonds, 1146 residues, 2 models selected 
    13265 
    13266 > select subtract #3
    13267 
    13268 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13269 
    13270 > view matrix models
    13271 > #5,-0.57941,0.69777,0.4212,115.54,-0.37625,0.22943,-0.89766,403.45,-0.723,-0.67859,0.1296,400.92
    13272 
    13273 > view matrix models
    13274 > #5,-0.42133,0.73627,0.52952,55.111,0.43201,0.67631,-0.59663,108.23,-0.7974,-0.022616,-0.60303,466.45
    13275 
    13276 > view matrix models
    13277 > #5,-0.21413,0.8577,0.46743,11.295,0.513,0.50597,-0.69341,148.79,-0.83125,0.091314,-0.54835,438.17
    13278 
    13279 > view matrix models
    13280 > #5,-0.1885,0.67264,0.71556,-17.862,0.29998,0.73323,-0.61023,123.87,-0.93514,0.09963,-0.33999,405.12
    13281 
    13282 > log thumbnail
    13283 
    13284 ![](data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAABkCAIAAAD/gAIDAAAXEklEQVR4nO1deZgdVZX/1Xuvu9NJ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%0AaB9Y06B9YE2D9oE1Dfo/aRiVuzY0Nb4AAAAASUVORK5CYII=%0A) 
    13285 
    13286 > view matrix models
    13287 > #5,-0.31715,0.77532,0.54617,25.775,0.1619,0.61171,-0.77434,209.51,-0.93445,-0.15716,-0.31953,447.8
    13288 
    13289 > view matrix models
    13290 > #5,-0.32237,0.77028,0.55023,26.653,0.15917,0.61709,-0.77062,208.1,-0.93313,-0.16085,-0.32154,448.73
    13291 
    13292 > view matrix models
    13293 > #5,-0.35979,0.63359,0.68492,26.481,0.1023,0.75644,-0.64601,162.47,-0.92741,-0.16236,-0.33698,451.69
    13294 
    13295 > select subtract #5
    13296 
    13297 Nothing selected 
    13298 
    13299 > select add #5
    13300 
    13301 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13302 
    13303 > view matrix models
    13304 > #5,-0.22546,0.76745,0.60016,-1.5674,0.19788,0.63926,-0.7431,190.7,-0.95395,-0.048776,-0.29599,425.47
    13305 
    13306 > view matrix models
    13307 > #5,0.070979,0.66168,0.74642,-68.315,0.16435,0.73032,-0.66304,160.57,-0.98385,0.16974,-0.056909,333.2
    13308 
    13309 > view matrix models
    13310 > #5,0.11489,0.59902,0.79245,-75.277,0.39981,0.70238,-0.5889,107.15,-0.90937,0.38449,-0.1588,304.63
    13311 
    13312 > view matrix models
    13313 > #5,0.18754,0.5726,0.7981,-84.357,0.35537,0.71792,-0.59858,114.3,-0.91572,0.39588,-0.068839,282.21
    13314 
    13315 > view matrix models
    13316 > #5,0.12973,0.70112,0.70114,-75.082,0.32499,0.63799,-0.6981,158.11,-0.93678,0.31843,-0.14509,318.4
    13317 
    13318 > view matrix models
    13319 > #5,0.012151,0.66827,0.74382,-58.685,0.27803,0.71228,-0.64448,139.73,-0.9605,0.21463,-0.17714,349.42
    13320 
    13321 > view matrix models
    13322 > #5,0.087714,-0.77021,0.63174,221.89,0.82852,-0.29568,-0.47553,190.87,0.55305,0.56511,0.61219,-166.83
    13323 
    13324 > view matrix models
    13325 > #5,-0.33436,-0.81985,0.46481,344.26,0.68971,-0.54897,-0.47216,261.24,0.64227,0.16271,0.74901,-140.21
    13326 
    13327 > view matrix models
    13328 > #5,-0.44895,-0.57242,0.68614,265.59,0.52883,-0.78916,-0.31235,295.78,0.72027,0.22263,0.657,-143
    13329 
    13330 > view matrix models
    13331 > #5,-0.4442,-0.59383,0.67086,272.37,0.54224,-0.77427,-0.32633,294.01,0.7132,0.21881,0.66593,-143.19
    13332 
    13333 > view matrix models
    13334 > #5,-0.46401,-0.4815,0.74354,237.67,0.47306,-0.84435,-0.25157,301.26,0.74894,0.23501,0.61957,-141.38
    13335 
    13336 > view matrix models
    13337 > #5,-0.44441,-0.50908,0.73711,240.91,0.50441,-0.8222,-0.26373,294.59,0.74031,0.25461,0.62218,-144.14
    13338 
    13339 > ui mousemode right "translate selected models"
    13340 
    13341 > view matrix models
    13342 > #5,-0.44441,-0.50908,0.73711,237.62,0.50441,-0.8222,-0.26373,296.55,0.74031,0.25461,0.62218,-146.91
    13343 
    13344 > ui mousemode right "rotate selected models"
    13345 
    13346 > view matrix models
    13347 > #5,-0.60143,-0.49924,0.62373,290.1,0.509,-0.8412,-0.18249,279.94,0.61579,0.20772,0.76004,-149.35
    13348 
    13349 > view matrix models
    13350 > #5,-0.74827,-0.24752,0.61549,270.87,0.3197,-0.94749,0.0076404,287.36,0.58128,0.20249,0.78811,-149.06
    13351 
    13352 > view matrix models
    13353 > #5,-0.81926,-0.51039,0.26136,416.31,0.4815,-0.85984,-0.1698,285.16,0.31139,-0.013269,0.95019,-100.62
    13354 
    13355 > view matrix models
    13356 > #5,-0.8197,-0.3099,0.48172,326.72,0.29937,-0.94878,-0.10096,316.98,0.48834,0.061452,0.87049,-126.31
    13357 
    13358 > view matrix models
    13359 > #5,-0.74081,-0.34591,0.57581,297.29,0.14449,-0.91921,-0.3663,401.59,0.65599,-0.18816,0.73094,-75.929
    13360 
    13361 > view matrix models
    13362 > #5,-0.81757,-0.07895,0.57039,262.37,-0.070004,-0.96958,-0.23455,416.9,0.57155,-0.23169,0.78718,-66.543
    13363 
    13364 > view matrix models
    13365 > #5,-0.91951,-0.12462,0.37278,335.62,0.063486,-0.98304,-0.17204,381.3,0.3879,-0.13453,0.91183,-82.295
    13366 
    13367 > view matrix models
    13368 > #5,-0.90793,0.0064486,0.41907,298.25,-0.059509,-0.99174,-0.11367,390.42,0.41488,-0.12814,0.90081,-85.551
    13369 
    13370 > view matrix models
    13371 > #5,-0.91351,-0.073219,0.40017,318.51,-0.028011,-0.97001,-0.24143,411.31,0.40585,-0.23176,0.88407,-60.76
    13372 
    13373 > view matrix models
    13374 > #5,-0.89133,0.0016103,0.45335,288.11,-0.071877,-0.98785,-0.13781,397.59,0.44762,-0.15542,0.88062,-81.377
    13375 
    13376 > view matrix models
    13377 > #5,-0.88255,0.076297,0.46398,270.18,-0.18199,-0.96527,-0.18743,424.37,0.43356,-0.24986,0.86579,-57.872
    13378 
    13379 > ui mousemode right select
    13380 
    13381 > select clear
    13382 
    13383 > ui mousemode right "translate selected models"
    13384 
    13385 > ui mousemode right "rotate selected models"
    13386 
    13387 > select add #5
    13388 
    13389 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13390 
    13391 > view matrix models
    13392 > #5,-0.90173,0.066834,0.42711,284.05,-0.16494,-0.96643,-0.197,423.89,0.3996,-0.24809,0.88248,-56.263
    13393 
    13394 > view matrix models
    13395 > #5,-0.91899,-0.040079,0.39223,315.2,-0.062389,-0.9675,-0.24504,417.68,0.3893,-0.24966,0.88663,-55.168
    13396 
    13397 > ui mousemode right "translate selected models"
    13398 
    13399 > view matrix models
    13400 > #5,-0.91899,-0.040079,0.39223,315,-0.062389,-0.9675,-0.24504,417.81,0.3893,-0.24966,0.88663,-53.939
    13401 
    13402 > view matrix models
    13403 > #5,-0.91899,-0.040079,0.39223,318.19,-0.062389,-0.9675,-0.24504,417.19,0.3893,-0.24966,0.88663,-52.686
    13404 
    13405 > view matrix models
    13406 > #5,-0.91899,-0.040079,0.39223,318.14,-0.062389,-0.9675,-0.24504,417.21,0.3893,-0.24966,0.88663,-52.699
    13407 
    13408 > view matrix models
    13409 > #5,-0.91899,-0.040079,0.39223,317.71,-0.062389,-0.9675,-0.24504,417.12,0.3893,-0.24966,0.88663,-52.726
    13410 
    13411 > view matrix models
    13412 > #5,-0.91899,-0.040079,0.39223,317.53,-0.062389,-0.9675,-0.24504,417.02,0.3893,-0.24966,0.88663,-52.524
    13413 
    13414 > ui mousemode right "rotate selected models"
    13415 
    13416 > view matrix models
    13417 > #5,-0.94446,-0.024801,0.32768,334.49,-0.074776,-0.95477,-0.28779,426.99,0.31999,-0.29631,0.89989,-34.96
    13418 
    13419 > view matrix models
    13420 > #5,-0.9387,-0.13701,0.31634,357.02,0.018467,-0.93629,-0.35073,422.31,0.34424,-0.32339,0.88143,-29.758
    13421 
    13422 > view matrix models
    13423 > #5,-0.97606,-0.21236,0.047016,441.6,0.10357,-0.64388,-0.75808,450.17,0.19126,-0.73506,0.65046,128.25
    13424 
    13425 > view matrix models
    13426 > #5,-0.97665,-0.2075,0.055729,438.73,0.092906,-0.64173,-0.76128,452.39,0.19373,-0.73832,0.64603,129.48
    13427 
    13428 > view matrix models
    13429 > #5,-0.9734,-0.14293,0.17908,396.82,-0.057279,-0.60498,-0.79418,479.52,0.22185,-0.78331,0.5807,148.49
    13430 
    13431 > view matrix models
    13432 > #5,-0.9046,-0.16174,0.39438,337.11,-0.12194,-0.78835,-0.60302,479.32,0.40844,-0.59359,0.69342,53.977
    13433 
    13434 > view matrix models
    13435 > #5,-0.88062,-0.11723,0.45909,309.27,-0.22079,-0.75576,-0.61651,493.68,0.41923,-0.64427,0.63965,74.305
    13436 
    13437 > view matrix models
    13438 > #5,-0.77365,-0.13721,0.61857,256.41,-0.084758,-0.94508,-0.31565,433.55,0.62792,-0.29663,0.71954,-45.551
    13439 
    13440 > view matrix models
    13441 > #5,-0.73239,-0.017561,0.68065,212.25,-0.29602,-0.89204,-0.34153,466.62,0.61317,-0.45162,0.64812,2.7847
    13442 
    13443 > view matrix models
    13444 > #5,-0.75559,0.045501,0.65347,211.04,-0.31215,-0.90204,-0.29812,460.96,0.57589,-0.42924,0.69578,-6.2267
    13445 
    13446 > ui mousemode right select
    13447 
    13448 > select clear
    13449 
    13450 > volume #8 level 0.04382
    13451 
    13452 > select add #5
    13453 
    13454 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13455 
    13456 > ui mousemode right "translate selected models"
    13457 
    13458 > ui mousemode right "rotate selected models"
    13459 
    13460 > view matrix models
    13461 > #5,-0.81035,-0.039349,0.58462,252.71,-0.22376,-0.90134,-0.37083,462.75,0.54153,-0.43132,0.7216,-6.0096
    13462 
    13463 > view matrix models
    13464 > #5,-0.75411,-0.09465,0.64989,237.66,-0.18462,-0.9191,-0.34808,453.83,0.63026,-0.38248,0.67563,-19.574
    13465 
    13466 > view matrix models
    13467 > #5,-0.82045,-0.19006,0.5392,293.25,-0.01249,-0.93694,-0.34926,427.47,0.57158,-0.29329,0.76634,-47.509
    13468 
    13469 > view matrix models
    13470 > #5,-0.8334,-0.14541,0.5332,288.65,-0.074442,-0.92644,-0.36901,441,0.54764,-0.34723,0.76127,-32.123
    13471 
    13472 > view matrix models
    13473 > #5,-0.86676,-0.2008,0.45651,322.99,-0.01989,-0.90071,-0.43396,442.19,0.49833,-0.38522,0.77671,-20.166
    13474 
    13475 > view matrix models
    13476 > #5,-0.91778,-0.012999,0.39688,311.19,-0.033872,-0.99326,-0.11086,384.91,0.39565,-0.11519,0.91115,-84.427
    13477 
    13478 > view matrix models
    13479 > #5,-0.92008,-0.092652,0.38063,330.24,0.036985,-0.98783,-0.15106,381.14,0.38999,-0.12491,0.91231,-81.914
    13480 
    13481 > view matrix models
    13482 > #5,-0.92081,-0.14037,0.36387,343.22,0.070303,-0.97744,-0.19917,384.86,0.38362,-0.15781,0.90991,-74.125
    13483 
    13484 > view matrix models
    13485 > #5,-0.90137,-0.23742,0.36216,358.26,0.18937,-0.96821,-0.16341,353.92,0.38944,-0.078707,0.91768,-91.674
    13486 
    13487 > view matrix models
    13488 > #5,-0.91318,-0.21739,0.34475,360.74,0.15071,-0.96603,-0.20993,371.32,0.37867,-0.13975,0.91492,-77.812
    13489 
    13490 > view matrix models
    13491 > #5,-0.79261,-0.38378,0.47381,339.94,0.3287,-0.92343,-0.1981,329.62,0.51355,-0.0012739,0.85806,-113.45
    13492 
    13493 > view matrix models
    13494 > #5,-0.82527,-0.3527,0.44105,347.65,0.32765,-0.93514,-0.13475,316.9,0.45997,0.033307,0.88731,-117.51
    13495 
    13496 > view matrix models
    13497 > #5,-0.84093,-0.3241,0.43335,346.89,0.26592,-0.94495,-0.1907,342.78,0.4713,-0.045133,0.88082,-103.37
    13498 
    13499 > view matrix models
    13500 > #5,-0.8011,-0.41235,0.43383,356.23,0.35913,-0.911,-0.20275,323.13,0.47883,-0.0066236,0.87788,-111.14
    13501 
    13502 > view matrix models
    13503 > #5,-0.84269,-0.41546,0.34245,385.79,0.3308,-0.90136,-0.2795,344.54,0.4248,-0.12225,0.897,-84.819
    13504 
    13505 > view matrix models
    13506 > #5,-0.79168,-0.41509,0.44827,351.66,0.24249,-0.88697,-0.39305,384.25,0.56075,-0.20247,0.80285,-71.174
    13507 
    13508 > view matrix models
    13509 > #5,-0.80765,-0.39545,0.43739,353.39,0.27696,-0.90927,-0.31067,362.79,0.52056,-0.12977,0.8439,-87.449
    13510 
    13511 > view matrix models
    13512 > #5,-0.80048,-0.3248,0.50372,323.24,0.18817,-0.93413,-0.3033,381.1,0.56905,-0.148,0.80887,-84.163
    13513 
    13514 > view matrix models
    13515 > #5,-0.83802,-0.27227,0.47285,327.36,0.14615,-0.94695,-0.28624,386.73,0.5257,-0.17076,0.83336,-78.221
    13516 
    13517 > view matrix models
    13518 > #5,-0.82968,-0.2976,0.47229,330.75,0.18414,-0.9446,-0.27172,376.23,0.52699,-0.13847,0.83852,-85.669
    13519 
    13520 > volume #8 level 0.07251
    13521 
    13522 > select subtract #5
    13523 
    13524 Nothing selected 
    13525 
    13526 > ui tool show Rotamers
    13527 
    13528 > select #3/B:1
    13529 
    13530 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13531 
    13532 > select #3/B:1-2
    13533 
    13534 14 atoms, 13 bonds, 2 residues, 1 model selected 
    13535 
    13536 > select #5/L:1-2
    13537 
    13538 14 atoms, 13 bonds, 2 residues, 1 model selected 
    13539 
    13540 > select #5/L:1-3
    13541 
    13542 22 atoms, 21 bonds, 3 residues, 1 model selected 
    13543 
    13544 > ui tool show "Show Sequence Viewer"
    13545 
    13546 > sequence chain #5/H
    13547 
    13548 Alignment identifier is 5/H 
    13549 
    13550 > select #5/H:1-2
    13551 
    13552 13 atoms, 12 bonds, 2 residues, 1 model selected 
    13553 
    13554 > select #5/H:1-3
    13555 
    13556 22 atoms, 21 bonds, 3 residues, 1 model selected 
    13557 
    13558 > ui tool show "Model Loops"
    13559 
    13560 > modeller refine 5/H:1:all-missing numModels 5 fast false adjacentFlexible 1
    13561 > protocol standard
    13562 
    13563 Webservices job id: VWCNQFID77H03PPS 
    13564 Modeller job (ID VWCNQFID77H03PPS) finished 
    13565 Modeller failure; standard error: 
    13566 Traceback (most recent call last): 
    13567 File "ModellerModelling.py", line 93, in   
    13568 a.make() 
    13569 File "/usr/lib64/python3.6/site-packages/modeller/automodel/loopmodel.py",
    13570 line 42, in make 
    13571 AutoModel.make(self, exit_stage) 
    13572 File "/usr/lib64/python3.6/site-packages/modeller/automodel/automodel.py",
    13573 line 151, in make 
    13574 atmsel = self._check_select_atoms() 
    13575 File "/usr/lib64/python3.6/site-packages/modeller/automodel/automodel.py",
    13576 line 701, in _check_select_atoms 
    13577 raise ModellerError("no atoms selected for optimization") 
    13578 _modeller.ModellerError: no atoms selected for optimization 
    13579  
    13580 
    13581 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    13582 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
    13583 > includeMaps true
    13584 
    13585 > ui tool show "Side View"
    13586 
    13587 > show #9 models
    13588 
    13589 > hide #9 models
    13590 
    13591 > show #9 models
    13592 
    13593 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    13594 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
    13595 > includeMaps true
    13596 
    13597 > select #5/H:89
    13598 
    13599 7 atoms, 6 bonds, 1 residue, 1 model selected 
    13600 
    13601 > select #5/H:89-116
    13602 
    13603 230 atoms, 242 bonds, 28 residues, 1 model selected 
    13604 
    13605 > select #5/H:28
    13606 
    13607 4 atoms, 3 bonds, 1 residue, 1 model selected 
    13608 
    13609 > select #5/H:28-36
    13610 
    13611 71 atoms, 73 bonds, 9 residues, 1 model selected 
    13612 
    13613 > select #5/H:28
    13614 
    13615 4 atoms, 3 bonds, 1 residue, 1 model selected 
    13616 
    13617 > select #5/H:28-35
    13618 
    13619 59 atoms, 60 bonds, 8 residues, 1 model selected 
    13620 
    13621 > select #5/H:29
    13622 
    13623 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13624 
    13625 > select #5/H:29-34
    13626 
    13627 43 atoms, 43 bonds, 6 residues, 1 model selected 
    13628 
    13629 > select #5/H:29
    13630 
    13631 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13632 
    13633 > select #5/H:29-35
    13634 
    13635 55 atoms, 56 bonds, 7 residues, 1 model selected 
    13636 
    13637 > select #5/H:36
    13638 
    13639 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13640 
    13641 > select #5/H:36
    13642 
    13643 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13644 
    13645 > select add #5
    13646 
    13647 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13648 
    13649 > select subtract #5
    13650 
    13651 Nothing selected 
    13652 
    13653 > select add #5
    13654 
    13655 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13656 
    13657 > view matrix models
    13658 > #5,-0.78057,-0.25347,0.57136,290.43,0.14361,-0.96236,-0.23074,376.82,0.60834,-0.098055,0.78759,-95.206
    13659 
    13660 > view matrix models
    13661 > #5,-0.70706,-0.3336,0.62352,280.11,0.24945,-0.94271,-0.22152,352.57,0.6617,-0.0010907,0.74977,-113.49
    13662 
    13663 > view matrix models
    13664 > #5,-0.69694,-0.29889,0.65187,265.15,0.22036,-0.95428,-0.20196,355.12,0.68243,0.0028993,0.73094,-113.36
    13665 
    13666 > view matrix models
    13667 > #5,-0.71926,-0.31911,0.61712,281.06,0.26188,-0.94728,-0.18461,342.47,0.6435,0.028824,0.7649,-119.48
    13668 
    13669 > view matrix models
    13670 > #5,-0.73098,-0.35003,0.58579,296.3,0.27751,-0.93672,-0.21342,344.64,0.62342,0.0065603,0.78186,-115.89
    13671 
    13672 > view matrix models
    13673 > #5,-0.744,-0.38717,0.54457,315.27,0.29793,-0.92173,-0.24828,346.61,0.59808,-0.022477,0.80112,-110.67
    13674 
    13675 > view matrix models
    13676 > #5,-0.64878,-0.44583,0.6167,292.42,0.35923,-0.89386,-0.26827,335.52,0.67084,0.047487,0.74008,-121.79
    13677 
    13678 > view matrix models
    13679 > #5,-0.62439,-0.46334,0.62884,288.54,0.36562,-0.88479,-0.2889,337.64,0.69026,0.049536,0.72187,-121.21
    13680 
    13681 > view matrix models
    13682 > #5,-0.63478,-0.46697,0.61562,294.17,0.35225,-0.88401,-0.30733,344.2,0.68773,0.021768,0.72564,-116.52
    13683 
    13684 > view matrix models
    13685 > #5,-0.61524,-0.38128,0.69001,257.16,0.33568,-0.91865,-0.20832,329.96,0.71331,0.10345,0.69318,-128.41
    13686 
    13687 > view matrix models
    13688 > #5,-0.76581,-0.22867,0.60103,276.2,0.13893,-0.9714,-0.19256,370.23,0.62788,-0.063967,0.77568,-102.1
    13689 
    13690 > view matrix models
    13691 > #5,-0.78982,-0.28243,0.54445,303.82,0.18289,-0.95574,-0.23046,368.69,0.58544,-0.082452,0.80651,-98.621
    13692 
    13693 > view matrix models
    13694 > #5,-0.79292,-0.27196,0.54527,302.22,0.18011,-0.95949,-0.21664,366.58,0.5821,-0.073569,0.80978,-100.47
    13695 
    13696 > view matrix models
    13697 > #5,-0.79401,-0.27238,0.54346,302.92,0.18004,-0.95926,-0.21773,366.81,0.58063,-0.075037,0.8107,-100.16
    13698 
    13699 > view matrix models
    13700 > #5,-0.80028,-0.30121,0.51848,315.31,0.14171,-0.93519,-0.32456,394.44,0.58264,-0.18627,0.7911,-75.192
    13701 
    13702 > view matrix models
    13703 > #5,-0.78732,-0.26873,0.55489,298.36,0.10956,-0.94667,-0.303,397.03,0.60673,-0.17777,0.77478,-77.078
    13704 
    13705 > view matrix models
    13706 > #5,-0.77396,-0.26304,0.57601,289.95,0.10485,-0.95032,-0.29309,396.17,0.62449,-0.16645,0.76309,-79.488
    13707 
    13708 > ui mousemode right "move picked models"
    13709 
    13710 > ui mousemode right "translate selected models"
    13711 
    13712 > view matrix models
    13713 > #5,-0.77396,-0.26304,0.57601,289.63,0.10485,-0.95032,-0.29309,395.77,0.62449,-0.16645,0.76309,-79.465
    13714 
    13715 > select subtract #5
    13716 
    13717 Nothing selected 
    13718 
    13719 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    13720 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
    13721 > includeMaps true
    13722 
    13723 > select #5/H:29
    13724 
    13725 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13726 
    13727 > select #5/H:29-35
    13728 
    13729 55 atoms, 56 bonds, 7 residues, 1 model selected 
    13730 
    13731 > ui tool show "Model Loops"
    13732 
    13733 [Repeated 2 time(s)]
    13734 
    13735 > ui tool show "Modeller Comparative"
    13736 
    13737 > select #5/H:56
    13738 
    13739 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13740 
    13741 > select #5/H:56-62
    13742 
    13743 58 atoms, 59 bonds, 7 residues, 1 model selected 
    13744 
    13745 > select #5/H:55
    13746 
    13747 11 atoms, 10 bonds, 1 residue, 1 model selected 
    13748 
    13749 > select #5/H:55-62
    13750 
    13751 69 atoms, 70 bonds, 8 residues, 1 model selected 
    13752 
    13753 > select #5/H:55
    13754 
    13755 11 atoms, 10 bonds, 1 residue, 1 model selected 
    13756 
    13757 > select #5/H:55-58
    13758 
    13759 35 atoms, 35 bonds, 4 residues, 1 model selected 
    13760 
    13761 > select #5/H:54-55
    13762 
    13763 19 atoms, 18 bonds, 2 residues, 1 model selected 
    13764 
    13765 > select #5/H:54-59
    13766 
    13767 49 atoms, 49 bonds, 6 residues, 1 model selected 
    13768 
    13769 > select #5/H:55-56
    13770 
    13771 23 atoms, 23 bonds, 2 residues, 1 model selected 
    13772 
    13773 > select #5/H:55-59
    13774 
    13775 41 atoms, 41 bonds, 5 residues, 1 model selected 
    13776 
    13777 > select #5/H:60
    13778 
    13779 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13780 
    13781 > select #5/H:60
    13782 
    13783 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13784 
    13785 > select #5/H:59
    13786 
    13787 6 atoms, 5 bonds, 1 residue, 1 model selected 
    13788 
    13789 > select #5/H:55-59
    13790 
    13791 41 atoms, 41 bonds, 5 residues, 1 model selected 
    13792 
    13793 > select #5/H:100-144
    13794 
    13795 341 atoms, 356 bonds, 45 residues, 1 model selected 
    13796 
    13797 > select #5/H:100-112
    13798 
    13799 113 atoms, 120 bonds, 13 residues, 1 model selected 
    13800 
    13801 > select #5/H:174
    13802 
    13803 7 atoms, 6 bonds, 1 residue, 1 model selected 
    13804 
    13805 > select #5/H:174-185
    13806 
    13807 87 atoms, 89 bonds, 12 residues, 1 model selected 
    13808 
    13809 > select #5/H:102
    13810 
    13811 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13812 
    13813 > select #5/H:102-107
    13814 
    13815 54 atoms, 56 bonds, 6 residues, 1 model selected 
    13816 
    13817 > select #3/B:290-291
    13818 
    13819 14 atoms, 13 bonds, 2 residues, 1 model selected 
    13820 
    13821 > select #3/B:290-310
    13822 
    13823 150 atoms, 150 bonds, 21 residues, 1 model selected 
    13824 
    13825 > select #3/B:290-315
    13826 
    13827 193 atoms, 195 bonds, 26 residues, 1 model selected 
    13828 
    13829 > hide #3 models
    13830 
    13831 > show #3 models
    13832 
    13833 > hide #3 models
    13834 
    13835 > show #3 models
    13836 
    13837 > select #3/B:352
    13838 
    13839 5 atoms, 4 bonds, 1 residue, 1 model selected 
    13840 
    13841 > select #3/B:341-352
    13842 
    13843 91 atoms, 90 bonds, 12 residues, 1 model selected 
    13844 
    13845 > select
    13846 > #5/H:5-9,20-27,36-42,48-54,60-62,70-75,80-85,94-101,118-120,131-135,146-156,161-165,174-176,187-196,205-211,216-222
    13847 
    13848 837 atoms, 847 bonds, 101 residues, 1 model selected 
    13849 
    13850 > select #5/H:127
    13851 
    13852 7 atoms, 6 bonds, 1 residue, 1 model selected 
    13853 
    13854 > select #5/H:127-130
    13855 
    13856 27 atoms, 27 bonds, 4 residues, 1 model selected 
    13857 
    13858 > view matrix models
    13859 > #5,-0.77396,-0.26304,0.57601,280.18,0.10485,-0.95032,-0.29309,395.64,0.62449,-0.16645,0.76309,-74.626
    13860 
    13861 > hide #!8 models
    13862 
    13863 > show #!2 models
    13864 
    13865 > hide #!2 models
    13866 
    13867 > select #5/L:22
    13868 
    13869 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13870 
    13871 > select #5/L:22-28
    13872 
    13873 47 atoms, 46 bonds, 7 residues, 1 model selected 
    13874 
    13875 > select #5/L:29
    13876 
    13877 6 atoms, 5 bonds, 1 residue, 1 model selected 
    13878 
    13879 > select #5/L:29-34
    13880 
    13881 43 atoms, 43 bonds, 6 residues, 1 model selected 
    13882 
    13883 > select #5/L:29
    13884 
    13885 6 atoms, 5 bonds, 1 residue, 1 model selected 
    13886 
    13887 > select #5/L:29-35
    13888 
    13889 51 atoms, 51 bonds, 7 residues, 1 model selected 
    13890 
    13891 > select #5/L:22
    13892 
    13893 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13894 
    13895 > select #5/L:22-26
    13896 
    13897 36 atoms, 35 bonds, 5 residues, 1 model selected 
    13898 
    13899 > select #5/L:29
    13900 
    13901 6 atoms, 5 bonds, 1 residue, 1 model selected 
    13902 
    13903 > select #5/L:29-34
    13904 
    13905 43 atoms, 43 bonds, 6 residues, 1 model selected 
    13906 
    13907 > select #5/L:50
    13908 
    13909 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13910 
    13911 > select #5/L:50-54
    13912 
    13913 39 atoms, 39 bonds, 5 residues, 1 model selected 
    13914 
    13915 > select #5/L:51
    13916 
    13917 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13918 
    13919 > select #5/L:51-55
    13920 
    13921 39 atoms, 39 bonds, 5 residues, 1 model selected 
    13922 
    13923 > select #5/L:51
    13924 
    13925 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13926 
    13927 > select #5/L:51-56
    13928 
    13929 47 atoms, 47 bonds, 6 residues, 1 model selected 
    13930 
    13931 > select #5/L:51
    13932 
    13933 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13934 
    13935 > select #5/L:51-62
    13936 
    13937 82 atoms, 83 bonds, 12 residues, 1 model selected 
    13938 
    13939 > select add #8
    13940 
    13941 82 atoms, 83 bonds, 12 residues, 3 models selected 
    13942 
    13943 > select subtract #8
    13944 
    13945 82 atoms, 83 bonds, 12 residues, 1 model selected 
    13946 
    13947 > select add #8
    13948 
    13949 82 atoms, 83 bonds, 12 residues, 3 models selected 
    13950 
    13951 > select subtract #8
    13952 
    13953 82 atoms, 83 bonds, 12 residues, 1 model selected 
    13954 
    13955 > select add #8
    13956 
    13957 82 atoms, 83 bonds, 12 residues, 3 models selected 
    13958 
    13959 > show #!8 models
    13960 
    13961 > select subtract #8
    13962 
    13963 82 atoms, 83 bonds, 12 residues, 1 model selected 
    13964 
    13965 > select add #8
    13966 
    13967 82 atoms, 83 bonds, 12 residues, 3 models selected 
    13968 
    13969 > select subtract #8
    13970 
    13971 82 atoms, 83 bonds, 12 residues, 1 model selected 
    13972 
    13973 > hide #!8 models
    13974 
    13975 > hide #8.1 models
    13976 
    13977 > select add #9
    13978 
    13979 3416 atoms, 3463 bonds, 426 residues, 2 models selected 
    13980 
    13981 > select subtract #9
    13982 
    13983 82 atoms, 83 bonds, 12 residues, 1 model selected 
    13984 
    13985 > select add #5
    13986 
    13987 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13988 
    13989 > select subtract #5
    13990 
    13991 Nothing selected 
    13992 
    13993 > select add #5
    13994 
    13995 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    13996 
    13997 > view matrix models
    13998 > #5,-0.77396,-0.26304,0.57601,281.01,0.10485,-0.95032,-0.29309,395.7,0.62449,-0.16645,0.76309,-74.661
    13999 
    14000 > view matrix models
    14001 > #5,-0.77396,-0.26304,0.57601,281.22,0.10485,-0.95032,-0.29309,395.6,0.62449,-0.16645,0.76309,-74.86
    14002 
    14003 > view matrix models
    14004 > #5,-0.77396,-0.26304,0.57601,282.28,0.10485,-0.95032,-0.29309,396.27,0.62449,-0.16645,0.76309,-74.987
    14005 
    14006 > view matrix models
    14007 > #5,-0.77396,-0.26304,0.57601,283.04,0.10485,-0.95032,-0.29309,396.66,0.62449,-0.16645,0.76309,-75.111
    14008 
    14009 > view matrix models
    14010 > #5,-0.77396,-0.26304,0.57601,282.9,0.10485,-0.95032,-0.29309,397.32,0.62449,-0.16645,0.76309,-75.13
    14011 
    14012 > view matrix models
    14013 > #5,-0.77396,-0.26304,0.57601,283.39,0.10485,-0.95032,-0.29309,397.2,0.62449,-0.16645,0.76309,-75.14
    14014 
    14015 > view matrix models
    14016 > #5,-0.77396,-0.26304,0.57601,285.17,0.10485,-0.95032,-0.29309,397.62,0.62449,-0.16645,0.76309,-75.184
    14017 
    14018 > view matrix models
    14019 > #5,-0.77396,-0.26304,0.57601,285.99,0.10485,-0.95032,-0.29309,397.56,0.62449,-0.16645,0.76309,-75.367
    14020 
    14021 > view matrix models
    14022 > #5,-0.77396,-0.26304,0.57601,286.16,0.10485,-0.95032,-0.29309,397.36,0.62449,-0.16645,0.76309,-75.361
    14023 
    14024 > select add #8.1
    14025 
    14026 3401 atoms, 3493 bonds, 442 residues, 2 models selected 
    14027 
    14028 > show #8.1 models
    14029 
    14030 > select subtract #5
    14031 
    14032 1 model selected 
    14033 
    14034 > select add #8
    14035 
    14036 2 models selected 
    14037 
    14038 > select subtract #8
    14039 
    14040 Nothing selected 
    14041 
    14042 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    14043 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms_10min_recolored.cxs"
    14044 > includeMaps true
    14045 
    14046 > select #5/L:50
    14047 
    14048 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14049 
    14050 > select #5/L:50
    14051 
    14052 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14053 
    14054 > select #5/L:66
    14055 
    14056 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14057 
    14058 > select #5/L:66-68
    14059 
    14060 14 atoms, 13 bonds, 3 residues, 1 model selected 
    14061 
    14062 > select #5/L:115
    14063 
    14064 7 atoms, 6 bonds, 1 residue, 1 model selected 
    14065 
    14066 > select #5/L:115-121
    14067 
    14068 57 atoms, 60 bonds, 7 residues, 1 model selected 
    14069 
    14070 > select #5/L:102
    14071 
    14072 7 atoms, 6 bonds, 1 residue, 1 model selected 
    14073 
    14074 > select #5/L:102-106
    14075 
    14076 41 atoms, 40 bonds, 5 residues, 1 model selected 
    14077 
    14078 > select #5/L:96
    14079 
    14080 14 atoms, 15 bonds, 1 residue, 1 model selected 
    14081 
    14082 > select #5/L:94-96
    14083 
    14084 26 atoms, 27 bonds, 3 residues, 1 model selected 
    14085 
    14086 > select #5/L:75
    14087 
    14088 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14089 
    14090 > select #5/L:75-77
    14091 
    14092 23 atoms, 22 bonds, 3 residues, 1 model selected 
    14093 
    14094 > select #5/L:80
    14095 
    14096 7 atoms, 6 bonds, 1 residue, 1 model selected 
    14097 
    14098 > select #5/L:80-81
    14099 
    14100 16 atoms, 15 bonds, 2 residues, 1 model selected 
    14101 
    14102 > select #5/L:98
    14103 
    14104 11 atoms, 11 bonds, 1 residue, 1 model selected 
    14105 
    14106 > select #5/L:98-99
    14107 
    14108 15 atoms, 15 bonds, 2 residues, 1 model selected 
    14109 
    14110 > select #5/L:94
    14111 
    14112 6 atoms, 5 bonds, 1 residue, 1 model selected 
    14113 
    14114 > select #5/L:93-94
    14115 
    14116 20 atoms, 21 bonds, 2 residues, 1 model selected 
    14117 
    14118 > select #5/L:91
    14119 
    14120 10 atoms, 10 bonds, 1 residue, 1 model selected 
    14121 
    14122 > select #5/L:91
    14123 
    14124 10 atoms, 10 bonds, 1 residue, 1 model selected 
    14125 
    14126 > select #5/L:92
    14127 
    14128 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14129 
    14130 > select #5/L:92-93
    14131 
    14132 23 atoms, 24 bonds, 2 residues, 1 model selected 
    14133 
    14134 > select #5/L:92-93
    14135 
    14136 23 atoms, 24 bonds, 2 residues, 1 model selected 
    14137 
    14138 > select #5/L:92-97
    14139 
    14140 56 atoms, 59 bonds, 6 residues, 1 model selected 
    14141 
    14142 > select #5/L:1
    14143 
    14144 5 atoms, 4 bonds, 1 residue, 1 model selected 
    14145 
    14146 > select #5/L:1-100
    14147 
    14148 750 atoms, 769 bonds, 100 residues, 1 model selected 
    14149 
    14150 > select #5/L:1
    14151 
    14152 5 atoms, 4 bonds, 1 residue, 1 model selected 
    14153 
    14154 > select #5/L:1-111
    14155 
    14156 834 atoms, 853 bonds, 111 residues, 1 model selected 
    14157 
    14158 > select #5/L:108
    14159 
    14160 11 atoms, 10 bonds, 1 residue, 1 model selected 
    14161 
    14162 > select #5/L:1-108
    14163 
    14164 815 atoms, 834 bonds, 108 residues, 1 model selected 
    14165 
    14166 > select #5/L:95
    14167 
    14168 6 atoms, 5 bonds, 1 residue, 1 model selected 
    14169 
    14170 > select #5/L:95-96
    14171 
    14172 20 atoms, 21 bonds, 2 residues, 1 model selected 
    14173 
    14174 > select #5/L:95
    14175 
    14176 6 atoms, 5 bonds, 1 residue, 1 model selected 
    14177 
    14178 > select #5/L:95-105
    14179 
    14180 83 atoms, 85 bonds, 11 residues, 1 model selected 
    14181 
    14182 > select #5/L:95
    14183 
    14184 6 atoms, 5 bonds, 1 residue, 1 model selected 
    14185 
    14186 > select #5/L:95-102
    14187 
    14188 57 atoms, 59 bonds, 8 residues, 1 model selected 
    14189 
    14190 > select #5/L:93
    14191 
    14192 14 atoms, 15 bonds, 1 residue, 1 model selected 
    14193 
    14194 > select #5/L:93-101
    14195 
    14196 70 atoms, 74 bonds, 9 residues, 1 model selected 
    14197 
    14198 > ui tool show "Show Sequence Viewer"
    14199 
    14200 > sequence chain #9/B #9/C
    14201 
    14202 Alignment identifier is 1 
    14203 
    14204 > ui mousemode right select
    14205 
    14206 > select clear
    14207 
    14208 > toolshed show
    14209 
    14210 Downloading bundle ChimeraX_XMAS-1.1.2-py3-none-any.whl 
    14211 
    14212 Errors may have occurred when running pip: 
    14213 
    14214 pip standard error: 
    14215 \--- 
    14216  
    14217 [notice] A new release of pip available: 22.2.2 -> 23.0.1 
    14218 [notice] To update, run:
    14219 /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX -m pip install
    14220 --upgrade pip 
    14221 \--- 
    14222 
    14223 pip standard output: 
    14224 \--- 
    14225 Looking in indexes: https://pypi.org/simple,
    14226 https://cxtoolshed.rbvi.ucsf.edu/pypi/ 
    14227 Processing /Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl 
    14228 Requirement already satisfied: ChimeraX-UI~=1.3 in
    14229 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14230 packages (from ChimeraX-XMAS==1.1.2) (1.24.3) 
    14231 Requirement already satisfied: ChimeraX-Core~=1.3 in
    14232 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14233 packages (from ChimeraX-XMAS==1.1.2) (1.5) 
    14234 Collecting openpyxl 
    14235 Downloading openpyxl-3.1.2-py2.py3-none-any.whl (249 kB) 
    14236 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.0/250.0 kB 8.0 MB/s eta 0:00:00 
    14237 Collecting seaborn 
    14238 Downloading seaborn-0.12.2-py3-none-any.whl (293 kB) 
    14239 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 293.3/293.3 kB 18.8 MB/s eta 0:00:00 
    14240 Collecting pandas 
    14241 Downloading pandas-1.5.3-cp39-cp39-macosx_10_9_x86_64.whl (12.0 MB) 
    14242 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.0/12.0 MB 8.1 MB/s eta 0:00:00 
    14243 Collecting qtrangeslider 
    14244 Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB) 
    14245 Requirement already satisfied: ChimeraX-Graphics~=1.0 in
    14246 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14247 packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1) 
    14248 Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
    14249 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14250 packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1.1) 
    14251 Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
    14252 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14253 packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.0) 
    14254 Collecting et-xmlfile 
    14255 Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB) 
    14256 Requirement already satisfied: python-dateutil>=2.8.1 in
    14257 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14258 packages (from pandas->ChimeraX-XMAS==1.1.2) (2.8.2) 
    14259 Requirement already satisfied: numpy>=1.20.3 in
    14260 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14261 packages (from pandas->ChimeraX-XMAS==1.1.2) (1.23.1) 
    14262 Requirement already satisfied: pytz>=2020.1 in
    14263 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14264 packages (from pandas->ChimeraX-XMAS==1.1.2) (2022.6) 
    14265 Requirement already satisfied: matplotlib!=3.6.1,>=3.1 in
    14266 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14267 packages (from seaborn->ChimeraX-XMAS==1.1.2) (3.5.2) 
    14268 Requirement already satisfied: ChimeraX-Geometry~=1.0 in
    14269 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14270 packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
    14271 (1.2) 
    14272 Requirement already satisfied: ChimeraX-Arrays~=1.0 in
    14273 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14274 packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
    14275 (1.0) 
    14276 Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
    14277 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14278 packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX-
    14279 XMAS==1.1.2) (1.0.1) 
    14280 Requirement already satisfied: pyparsing>=2.2.1 in
    14281 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14282 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (3.0.9) 
    14283 Requirement already satisfied: fonttools>=4.22.0 in
    14284 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14285 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
    14286 (4.38.0) 
    14287 Requirement already satisfied: packaging>=20.0 in
    14288 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14289 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (21.3) 
    14290 Requirement already satisfied: kiwisolver>=1.0.1 in
    14291 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14292 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (1.4.4) 
    14293 Requirement already satisfied: cycler>=0.10 in
    14294 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14295 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
    14296 (0.11.0) 
    14297 Requirement already satisfied: pillow>=6.2.0 in
    14298 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14299 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (9.2.0) 
    14300 Requirement already satisfied: six>=1.5 in
    14301 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    14302 packages (from python-dateutil>=2.8.1->pandas->ChimeraX-XMAS==1.1.2) (1.16.0) 
    14303 Installing collected packages: qtrangeslider, et-xmlfile, pandas, openpyxl,
    14304 seaborn, ChimeraX-XMAS 
    14305 Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2
    14306 pandas-1.5.3 qtrangeslider-0.1.5 seaborn-0.12.2 
    14307 \--- 
    14308 
    14309 Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2
    14310 pandas-1.5.3 qtrangeslider-0.1.5 seaborn-0.12.2 
    14311 Installed ChimeraX-XMAS (1.1.2) 
    14312 
    14313 > toolshed install Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl
    14314 
    14315 Missing or invalid "bundleNames" argument: Expected a bundle name or a wheel
    14316 file name 
    14317 
    14318 > toolshed install /Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-
    14319 > any.whl
    14320 
    14321 bundle '/Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl'
    14322 already installed 
    14323 
    14324 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    14325 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms_10min_recolored.cxs"
    14326 > includeMaps true
    14327 
    14328 ——— End of log from Thu Mar 30 23:52:24 2023 ———
    14329 
    14330 opened ChimeraX session 
    14331 
    14332 > select down
    14333 
    14334 Nothing selected 
    14335 
    14336 > select down
    14337 
    14338 Nothing selected 
    14339 
    14340 > ui tool show "Show Sequence Viewer"
    14341 
    14342 > ui tool show "Change Chain IDs"
    14343 
    14344 > select add #3
    14345 
    14346 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    14347 
    14348 > select subtract #3
    14349 
    14350 Nothing selected 
    14351 
    14352 > select #3/B:1
    14353 
    14354 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14355 
    14356 > select #3/B:1-20
    14357 
    14358 149 atoms, 151 bonds, 20 residues, 1 model selected 
    14359 
    14360 > select #3/B:1-20
    14361 
    14362 149 atoms, 151 bonds, 20 residues, 1 model selected 
    14363 
    14364 > select #3/B:1-20,136-352
    14365 
    14366 1872 atoms, 1920 bonds, 237 residues, 1 model selected 
    14367 
    14368 > select #3/B:1-20,136-352
    14369 
    14370 1872 atoms, 1920 bonds, 237 residues, 1 model selected 
    14371 
    14372 > select #3/B:1
    14373 
    14374 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14375 
    14376 > select #3/B:1-180
    14377 
    14378 1439 atoms, 1472 bonds, 180 residues, 1 model selected 
    14379 
    14380 > select #3/A
    14381 
    14382 2801 atoms, 2872 bonds, 352 residues, 1 model selected 
    14383 
    14384 > save /Users/alvinchew/Downloads/NS1chainA.pdb selectedOnly true relModel
    14385 > #8.1
    14386 
    14387 > open /Users/alvinchew/Downloads/NS1chainA.pdb
    14388 
    14389 Summary of feedback from opening /Users/alvinchew/Downloads/NS1chainA.pdb 
    14390 --- 
    14391 warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
    14392 GLU B 51 1 13 
    14393 Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
    14394 11 
    14395 Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
    14396 9 
    14397 Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
    14398 1 7 
    14399 Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
    14400 1 3 
    14401 26 messages similar to the above omitted 
    14402  
    14403 Chain information for NS1chainA.pdb #6 
    14404 --- 
    14405 Chain | Description 
    14406 A | No description available 
    14407  
    14408 
    14409 > undo
    14410 
    14411 > close #6
    14412 
    14413 > select add #3
    14414 
    14415 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    14416 
    14417 > select subtract #3
    14418 
    14419 Nothing selected 
    14420 
    14421 > toolshed show
    14422 
    14423 > xmas
    14424 
    14425 Unknown command: xmas 
    14426 
    14427 > runscript xmas
    14428 
    14429 Missing or invalid "scriptFile" argument: File 'xmas' does not exist 
    14430 
    14431 > select #3/B:1
    14432 
    14433 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14434 
    14435 > select #3/B:1-120
    14436 
    14437 956 atoms, 977 bonds, 120 residues, 1 model selected 
    14438 
    14439 > select #3/A
    14440 
    14441 2801 atoms, 2872 bonds, 352 residues, 1 model selected 
    14442 
    14443 > save /Users/alvinchew/Downloads/NS1chainA.pdb models #3 selectedOnly true
    14444 > relModel #3
    14445 
    14446 > open /Users/alvinchew/Downloads/NS1chainA.pdb
    14447 
    14448 Summary of feedback from opening /Users/alvinchew/Downloads/NS1chainA.pdb 
    14449 --- 
    14450 warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
    14451 GLU B 51 1 13 
    14452 Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
    14453 11 
    14454 Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
    14455 9 
    14456 Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
    14457 1 7 
    14458 Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
    14459 1 3 
    14460 26 messages similar to the above omitted 
    14461  
    14462 Chain information for NS1chainA.pdb #6 
    14463 --- 
    14464 Chain | Description 
    14465 A | No description available 
    14466  
    14467 
    14468 > close #6
    14469 
    14470 > hide #3 models
    14471 
    14472 > show #3 models
    14473 
    14474 > save /Users/alvinchew/Downloads/D2NS1_A #3/A relModel #3/B
    14475 
    14476 Cannot determine format for '/Users/alvinchew/Downloads/D2NS1_A' 
    14477 
    14478 > save /Users/alvinchew/Downloads/D2NS1_A.pdb #3/A relModel #3/B
    14479 
    14480 > open /Users/alvinchew/Downloads/D2NS1_A.pdb
    14481 
    14482 Chain information for D2NS1_A.pdb #6 
    14483 --- 
    14484 Chain | Description 
    14485 A B | No description available 
    14486  
    14487 
    14488 > hide #3 models
    14489 
    14490 > show #3 models
    14491 
    14492 > hide #6 models
    14493 
    14494 > show #6 models
    14495 
    14496 > hide #6 models
    14497 
    14498 > show #6 models
    14499 
    14500 > close #6
    14501 
    14502 > save /Users/alvinchew/Downloads/D2NS1_A.pdb #3/A selectedOnly true relModel
    14503 > #3/B
    14504 
    14505 > open /Users/alvinchew/Downloads/D2NS1_A.pdb
    14506 
    14507 Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_A.pdb 
    14508 --- 
    14509 warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
    14510 GLU B 51 1 13 
    14511 Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
    14512 11 
    14513 Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
    14514 9 
    14515 Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
    14516 1 7 
    14517 Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
    14518 1 3 
    14519 26 messages similar to the above omitted 
    14520  
    14521 Chain information for D2NS1_A.pdb #6 
    14522 --- 
    14523 Chain | Description 
    14524 A | No description available 
    14525  
    14526 
    14527 > hide #3 models
    14528 
    14529 > select #3/B:1-2
    14530 
    14531 14 atoms, 13 bonds, 2 residues, 1 model selected 
    14532 
    14533 > select #3/B:1-14
    14534 
    14535 110 atoms, 111 bonds, 14 residues, 1 model selected 
    14536 
    14537 > show #3 models
    14538 
    14539 > select add #8
    14540 
    14541 110 atoms, 111 bonds, 14 residues, 5 models selected 
    14542 
    14543 > select subtract #8
    14544 
    14545 110 atoms, 111 bonds, 14 residues, 1 model selected 
    14546 
    14547 > hide #!8 models
    14548 
    14549 > hide #3 models
    14550 
    14551 > show #3 models
    14552 
    14553 > mmaker #6 to #3/A
    14554 
    14555 Parameters 
    14556 --- 
    14557 Chain pairing | bb 
    14558 Alignment algorithm | Needleman-Wunsch 
    14559 Similarity matrix | BLOSUM-62 
    14560 SS fraction | 0.3 
    14561 Gap open (HH/SS/other) | 18/18/6 
    14562 Gap extend | 1 
    14563 SS matrix |  |  | H | S | O 
    14564 ---|---|---|--- 
    14565 H | 6 | -9 | -6 
    14566 S |  | 6 | -6 
    14567 O |  |  | 4 
    14568 Iteration cutoff | 2 
    14569  
    14570 Matchmaker eden2ns1.pdb, chain A (#3) with D2NS1_A.pdb, chain A (#6), sequence
    14571 alignment score = 1853.9 
    14572 RMSD between 352 pruned atom pairs is 0.000 angstroms; (across all 352 pairs:
    14573 0.000) 
    14574  
    14575 
    14576 > hide #3 models
    14577 
    14578 > show #3 models
    14579 
    14580 > hide #3 models
    14581 
    14582 > show #3 models
    14583 
    14584 > hide #3 models
    14585 
    14586 > show #3 models
    14587 
    14588 > hide #6 models
    14589 
    14590 > show #6 models
    14591 
    14592 > hide #6 models
    14593 
    14594 > show #6 models
    14595 
    14596 > select add #3
    14597 
    14598 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    14599 
    14600 > select subtract #3
    14601 
    14602 Nothing selected 
    14603 
    14604 > hide #3 models
    14605 
    14606 > show #3 models
    14607 
    14608 > hide #3 models
    14609 
    14610 > show #3 models
    14611 
    14612 > hide #3 models
    14613 
    14614 > show #3 models
    14615 
    14616 > hide #3 models
    14617 
    14618 > show #3 models
    14619 
    14620 > save /Users/alvinchew/Downloads/D2NS1_A.pdb #6
    14621 
    14622 > open /Users/alvinchew/Downloads/D2NS1_A.pdb
    14623 
    14624 Chain information for D2NS1_A.pdb #7 
    14625 --- 
    14626 Chain | Description 
    14627 A | No description available 
    14628  
    14629 
    14630 > select #3/B:1
    14631 
    14632 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14633 
    14634 > select #3/B
    14635 
    14636 2801 atoms, 2872 bonds, 352 residues, 1 model selected 
    14637 
    14638 > save /Users/alvinchew/Downloads/D2NS1_B.pdb #3/B selectedOnly true relModel
    14639 > #3/A
    14640 
    14641 > open /Users/alvinchew/Downloads/D2NS1_B.pdb
    14642 
    14643 Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb 
    14644 --- 
    14645 warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
    14646 39 GLU A 51 1 13 
    14647 Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
    14648 1 11 
    14649 Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
    14650 1 9 
    14651 Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
    14652 121 1 7 
    14653 Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
    14654 147 1 3 
    14655 26 messages similar to the above omitted 
    14656  
    14657 Chain information for D2NS1_B.pdb #10 
    14658 --- 
    14659 Chain | Description 
    14660 B | No description available 
    14661  
    14662 
    14663 > close #10
    14664 
    14665 > save /Users/alvinchew/Downloads/D2NS1_B.pdb #3/B selectedOnly true
    14666 
    14667 > open /Users/alvinchew/Downloads/D2NS1_B.pdb
    14668 
    14669 Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb 
    14670 --- 
    14671 warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
    14672 39 GLU A 51 1 13 
    14673 Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
    14674 1 11 
    14675 Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
    14676 1 9 
    14677 Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
    14678 121 1 7 
    14679 Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
    14680 147 1 3 
    14681 26 messages similar to the above omitted 
    14682  
    14683 Chain information for D2NS1_B.pdb #10 
    14684 --- 
    14685 Chain | Description 
    14686 B | No description available 
    14687  
    14688 
    14689 > close #6
    14690 
    14691 > hide #9 models
    14692 
    14693 > show #9 models
    14694 
    14695 > hide #9 models
    14696 
    14697 > show #9 models
    14698 
    14699 > select #9/B-C:1
    14700 
    14701 12 atoms, 10 bonds, 2 residues, 1 model selected 
    14702 
    14703 > select #9/B-C:1-8
    14704 
    14705 114 atoms, 112 bonds, 16 residues, 1 model selected 
    14706 
    14707 > ui tool show "Show Sequence Viewer"
    14708 
    14709 > sequence chain #9/B
    14710 
    14711 Alignment identifier is 9/B 
    14712 
    14713 > sequence chain #9/C
    14714 
    14715 Alignment identifier is 9/C 
    14716 
    14717 > select #9/C:2-149,151-206
    14718 
    14719 1648 atoms, 1670 bonds, 204 residues, 1 model selected 
    14720 
    14721 > select #9/C:1
    14722 
    14723 6 atoms, 5 bonds, 1 residue, 1 model selected 
    14724 
    14725 > select #9/C
    14726 
    14727 1667 atoms, 1690 bonds, 207 residues, 1 model selected 
    14728 
    14729 > save /Users/alvinchew/Downloads/ApoA1_Y.pdb #9/C selectedOnly true
    14730 
    14731 > open /Users/alvinchew/Downloads/ApoA1_Y.pdb
    14732 
    14733 Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_Y.pdb 
    14734 --- 
    14735 warnings | Start residue of secondary structure not found: HELIX 1 1 ALA B 2
    14736 ALA B 129 1 128 
    14737 Start residue of secondary structure not found: HELIX 2 2 PRO B 130 GLY B 149
    14738 1 20 
    14739 Start residue of secondary structure not found: HELIX 3 3 GLY B 151 ALA B 206
    14740 1 56 
    14741  
    14742 Chain information for ApoA1_Y.pdb #6 
    14743 --- 
    14744 Chain | Description 
    14745 C | No description available 
    14746  
    14747 
    14748 > select #9/B:1
    14749 
    14750 6 atoms, 5 bonds, 1 residue, 1 model selected 
    14751 
    14752 > select #9/B
    14753 
    14754 1667 atoms, 1690 bonds, 207 residues, 1 model selected 
    14755 
    14756 > save /Users/alvinchew/Downloads/ApoA1_X.pdb #9/B selectedOnly true
    14757 
    14758 > open /Users/alvinchew/Downloads/ApoA1_X.pdb
    14759 
    14760 Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_X.pdb 
    14761 --- 
    14762 warnings | Start residue of secondary structure not found: HELIX 4 4 ALA C 2
    14763 ALA C 129 1 128 
    14764 Start residue of secondary structure not found: HELIX 5 5 PRO C 130 GLY C 149
    14765 1 20 
    14766 Start residue of secondary structure not found: HELIX 6 6 GLY C 151 ALA C 206
    14767 1 56 
    14768  
    14769 Chain information for ApoA1_X.pdb #11 
    14770 --- 
    14771 Chain | Description 
    14772 B | No description available 
    14773  
    14774 
    14775 > hide #11 models
    14776 
    14777 > show #11 models
    14778 
    14779 > hide #11 models
    14780 
    14781 > show #11 models
    14782 
    14783 > hide #9 models
    14784 
    14785 > hide #8.1 models
    14786 
    14787 > hide #10 models
    14788 
    14789 > hide #11 models
    14790 
    14791 > select add #9
    14792 
    14793 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    14794 
    14795 > select subtract #9
    14796 
    14797 Nothing selected 
    14798 
    14799 > hide #5 models
    14800 
    14801 > show #5 models
    14802 
    14803 > hide #5 models
    14804 
    14805 > show #5 models
    14806 
    14807 > hide #3 models
    14808 
    14809 > show #3 models
    14810 
    14811 > hide #7 models
    14812 
    14813 > hide #6 models
    14814 
    14815 > show #!8 models
    14816 
    14817 > hide #!8 models
    14818 
    14819 > show #8.1 models
    14820 
    14821 > hide #8.1 models
    14822 
    14823 > show #7 models
    14824 
    14825 > hide #7 models
    14826 
    14827 > show #6 models
    14828 
    14829 > hide #6 models
    14830 
    14831 > show #6 models
    14832 
    14833 > hide #6 models
    14834 
    14835 > hide #!8 models
    14836 
    14837 > show #!8 models
    14838 
    14839 > hide #!8 models
    14840 
    14841 > show #!8 models
    14842 
    14843 > hide #!8 models
    14844 
    14845 > hide #5 models
    14846 
    14847 > show #5 models
    14848 
    14849 > hide #5 models
    14850 
    14851 > show #5 models
    14852 
    14853 > hide #5 models
    14854 
    14855 > show #5 models
    14856 
    14857 > hide #5 models
    14858 
    14859 > show #5 models
    14860 
    14861 > hide #5 models
    14862 
    14863 > show #5 models
    14864 
    14865 [Repeated 1 time(s)]
    14866 
    14867 > save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min.defattr attrName
    14868 > Fab_rDeutdelta_10min models #5
    14869 
    14870 No known/registered attribute Fab_rDeutdelta_10min 
    14871 
    14872 > setattr #5 residues Fab_rDeutdelta_10min_color models create true type color
    14873 
    14874 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    14875 Invalid color name or specifier 
    14876 
    14877 > setattr #5 residues Fab_rDeutdelta_10min_color create true type color
    14878 
    14879 Expected a keyword 
    14880 
    14881 > setattr #5 residues Fab_rDeutdelta_10min_color value create true type color
    14882 
    14883 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    14884 Invalid color name or specifier 
    14885 
    14886 > save /Users/alvinchew/Downloads/ Fab_rDeutdelta_10min_color.defattr attrName
    14887 > Fab_rDeutdelta_10min_color models #5
    14888 
    14889 Cannot determine format for '/Users/alvinchew/Downloads/' 
    14890 
    14891 > save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
    14892 > Fab_rDeutdelta_10min_color models #5
    14893 
    14894 No known/registered attribute Fab_rDeutdelta_10min_color 
    14895 
    14896 > save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
    14897 > Fab_rDeutdelta_10min_color models #5
    14898 
    14899 No known/registered attribute Fab_rDeutdelta_10min_color 
    14900 
    14901 > setattr #5 residues Fab_rDeutdelta_10min_color value create true type color
    14902 
    14903 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    14904 Invalid color name or specifier 
    14905 
    14906 > setattr #5 residues Fab_rDeutdelta_10min_color value create true type float
    14907 
    14908 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    14909 Expected a number 
    14910 
    14911 > setattr #5 residues Fab_rDeutdelta_10min_color value create true
    14912 
    14913 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    14914 Invalid color name or specifier 
    14915 
    14916 > setattr #5 residues Fab_rDeutdelta_10min_color value create true type string
    14917 
    14918 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    14919 
    14920 > save /Users/alvinchew/Downloads/ Fab_rDeutdelta_10min_color.defattr attrName
    14921 > Fab_rDeutdelta_10min_color models #5
    14922 
    14923 Cannot determine format for '/Users/alvinchew/Downloads/' 
    14924 
    14925 > save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
    14926 > Fab_rDeutdelta_10min_color models #5
    14927 
    14928 Saved attribute 'Fab_rDeutdelta_10min_color' of 442 residues using match mode:
    14929 1-to-1 to /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr 
    14930 
    14931 > ui tool show "Color Actions"
    14932 
    14933 > close session
    14934 
    14935 > open /Users/alvinchew/Downloads/ApoA1_X.pdb
    14936 
    14937 Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_X.pdb 
    14938 --- 
    14939 warnings | Start residue of secondary structure not found: HELIX 4 4 ALA C 2
    14940 ALA C 129 1 128 
    14941 Start residue of secondary structure not found: HELIX 5 5 PRO C 130 GLY C 149
    14942 1 20 
    14943 Start residue of secondary structure not found: HELIX 6 6 GLY C 151 ALA C 206
    14944 1 56 
    14945  
    14946 Chain information for ApoA1_X.pdb #1 
    14947 --- 
    14948 Chain | Description 
    14949 B | No description available 
    14950  
    14951 
    14952 > open /Users/alvinchew/Downloads/ApoA1_Y.pdb
    14953 
    14954 Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_Y.pdb 
    14955 --- 
    14956 warnings | Start residue of secondary structure not found: HELIX 1 1 ALA B 2
    14957 ALA B 129 1 128 
    14958 Start residue of secondary structure not found: HELIX 2 2 PRO B 130 GLY B 149
    14959 1 20 
    14960 Start residue of secondary structure not found: HELIX 3 3 GLY B 151 ALA B 206
    14961 1 56 
    14962  
    14963 Chain information for ApoA1_Y.pdb #2 
    14964 --- 
    14965 Chain | Description 
    14966 C | No description available 
    14967  
    14968 
    14969 > open /Users/alvinchew/Downloads/D2NS1_B.pdb
    14970 
    14971 Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb 
    14972 --- 
    14973 warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
    14974 39 GLU A 51 1 13 
    14975 Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
    14976 1 11 
    14977 Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
    14978 1 9 
    14979 Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
    14980 121 1 7 
    14981 Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
    14982 147 1 3 
    14983 26 messages similar to the above omitted 
    14984  
    14985 Chain information for D2NS1_B.pdb #3 
    14986 --- 
    14987 Chain | Description 
    14988 B | No description available 
    14989  
    14990 
    14991 > open /Users/alvinchew/Downloads/D2NS1_A.pdb
    14992 
    14993 Chain information for D2NS1_A.pdb #4 
    14994 --- 
    14995 Chain | Description 
    14996 A | No description available 
    14997  
    14998 
    14999 > color #2 #e0e6ecff
    15000 
    15001 > color #2 #b1b6bbff
    15002 
    15003 > color #1 #d7d0cbff
    15004 
    15005 > color #3 #93a3e1ff
    15006 
    15007 > color #3 #8a9ae1ff
    15008 
    15009 > color #3 #969ae1ff
    15010 
    15011 > color #3 #8496e1ff
    15012 
    15013 > color #4 #b7d7ecff
    15014 
    15015 > save /Users/alvinchew/Downloads/NS1-apoAI_monomers-forwint.cxs includeMaps
    15016 > true
    15017 
    15018 ——— End of log from Sat Apr 1 16:55:32 2023 ———
    15019 
    15020 opened ChimeraX session 
    15021 
    15022 > ui tool show XMAS
    15023 
    15024  
    15025 Peptide pair mapping of XlinkX evidence file:
    15026 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy.txt 
    15027 428 Peptide pairs are disregarded due to lacking/decoy sequence 
    15028 Unique peptide pairs: 28 out of 33 
    15029 Unique peptide pairs with pseudobonds: 28 
    15030 Pseudobonds are stored in
    15031 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy_1,2,3,4.pb 
    15032 Mapping information is stored in
    15033 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy_1,2,3,4.tsv 
    15034 Please select pseudobonds 
    15035 Please select pseudobonds 
    15036 Please select pseudobonds 
    15037 
    15038 > select subtract #5
    15039 
    15040 Nothing selected 
    15041 
    15042 > save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    15043 
    15044 ——— End of log from Mon Apr 3 15:19:20 2023 ———
    15045 
    15046 opened ChimeraX session 
    15047  
    15048 Peptide pair mapping of XlinkX evidence file:
    15049 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS.txt 
    15050 432 Peptide pairs are disregarded due to lacking/decoy sequence 
    15051 Unique peptide pairs: 29 out of 29 
    15052 Unique peptide pairs with pseudobonds: 26 
    15053 Pseudobonds are stored in
    15054 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2.pb 
    15055 Mapping information is stored in
    15056 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2.tsv 
    15057 
    15058 > save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    15059 
    15060 Please select pseudobonds 
    15061 /Users/wintwintphoo/Library/Application Support/ChimeraX/1.5/site-
    15062 packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette
    15063 using color= is deprecated and will be removed in version 0.13. Set
    15064 `palette='dark:gray'` for same effect. 
    15065 warnings.warn(msg, FutureWarning) 
    15066 
    15067 > color #1 #684bdfff
    15068 
    15069 > undo
    15070 
    15071 > select subtract #6
    15072 
    15073 Nothing selected 
    15074 
    15075 > select add #5
    15076 
    15077 102 pseudobonds, 1 model selected 
    15078 
    15079 > select subtract #5
    15080 
    15081 Nothing selected 
    15082 
    15083 > save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    15084 
    15085  
    15086 Peptide pair mapping of XlinkX evidence file:
    15087 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS.txt 
    15088 432 Peptide pairs are disregarded due to lacking/decoy sequence 
    15089 Unique peptide pairs: 29 out of 29 
    15090 Unique peptide pairs with pseudobonds: 26 
    15091 Pseudobonds are stored in
    15092 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2,3,4.pb 
    15093 Mapping information is stored in
    15094 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2,3,4.tsv 
    15095  
    15096 Peptide pair mapping of XlinkX evidence file:
    15097 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS.txt 
    15098 436 Peptide pairs are disregarded due to lacking/decoy sequence 
    15099 Unique peptide pairs: 25 out of 25 
    15100 Unique peptide pairs with pseudobonds: 20 
    15101 Pseudobonds are stored in
    15102 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS_1,2,3,4.pb 
    15103 Mapping information is stored in
    15104 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS_1,2,3,4.tsv 
    15105 
    15106 > select subtract #7
    15107 
    15108 Nothing selected 
    15109 
    15110 > close #7
    15111 
    15112 > save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    15113 
    15114 [Repeated 1 time(s)]Pseudobonds are stored in
    15115 /Users/wintwintphoo/Downloads/20220215_denv_ns1_apoA1_xmas_xlinks_list.pb 
    15116 
    15117 > select subtract #8
    15118 
    15119 195 pseudobonds, 2 models selected 
    15120 
    15121 > select add #8
    15122 
    15123 275 pseudobonds, 3 models selected 
    15124 
    15125 > hide #8 models
    15126 
    15127 > show #8 models
    15128 
    15129 > hide #7 models
    15130 
    15131 > save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    15132 
    15133 ——— End of log from Mon Apr 3 16:43:31 2023 ———
    15134 
    15135 opened ChimeraX session 
    15136 
    15137 > show #7 models
    15138 
    15139 > hide #7 models
    15140 
    15141 > show #7 models
    15142 
    15143 > hide #7 models
    15144 
    15145 > select subtract #7
    15146 
    15147 275 pseudobonds, 3 models selected 
    15148 
    15149 > hide #5 models
    15150 
    15151 > show #5 models
    15152 
    15153 > hide #6 models
    15154 
    15155 > show #6 models
    15156 
    15157 > hide #6 models
    15158 
    15159 > show #6 models
    15160 
    15161 > hide #6 models
    15162 
    15163 > show #6 models
    15164 
    15165 > hide #8 models
    15166 
    15167 > show #8 models
    15168 
    15169 > hide #8 models
    15170 
    15171 > show #8 models
    15172 
    15173 > hide #6 models
    15174 
    15175 > show #6 models
    15176 
    15177 > hide #6 models
    15178 
    15179 > show #6 models
    15180 
    15181 > hide #6 models
    15182 
    15183 > show #6 models
    15184 
    15185 > hide #6 models
    15186 
    15187 > show #6 models
    15188 
    15189 > hide #5 models
    15190 
    15191 > show #5 models
    15192 
    15193 > hide #5 models
    15194 
    15195 > show #5 models
    15196 
    15197 > hide #5 models
    15198 
    15199 > show #5 models
    15200 
    15201 > open "/Users/alvinchew/Library/CloudStorage/OneDrive-
    15202 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM
    15203 > Maps_docked structures/EDEN2 sNS1wt-Fab562/sNS1wt-Fab562.mrc"
    15204 
    15205 Opened sNS1wt-Fab562.mrc as #9, grid size 416,416,416, pixel 0.85, shown at
    15206 level 0.0324, step 2, values float32 
    15207 
    15208 > volume #9 step 1
    15209 
    15210 > volume #9 color #b2b2b25f
    15211 
    15212 > volume #9 color #b2b2b24d
    15213 
    15214 > volume #9 color #aebfbb4d
    15215 
    15216 > volume #9 color #96bdbf4d
    15217 
    15218 > volume #9 color #b4e3e64d
    15219 
    15220 > select subtract #5
    15221 
    15222 173 pseudobonds, 2 models selected 
    15223 
    15224 > select subtract #6
    15225 
    15226 80 pseudobonds, 1 model selected 
    15227 
    15228 > select subtract #8
    15229 
    15230 Nothing selected 
    15231 
    15232 > select add #9
    15233 
    15234 2 models selected 
    15235 
    15236 > ui mousemode right "rotate selected models"
    15237 
    15238 > view matrix models
    15239 > #9,-0.87886,-0.26868,-0.39424,454.61,-2.4853e-05,0.82637,-0.56313,136.08,0.47709,-0.4949,-0.72627,325.9
    15240 
    15241 > view matrix models
    15242 > #9,-0.58078,0.6843,0.44094,79.244,0.37206,0.7049,-0.6039,98.706,-0.72406,-0.18668,-0.66399,474.16
    15243 
    15244 > volume #9 level 0.08346
    15245 
    15246 > view matrix models
    15247 > #9,-0.62302,0.6249,0.47048,91.383,0.37769,0.76704,-0.51866,70.685,-0.68498,-0.14544,-0.71389,469.61
    15248 
    15249 > view matrix models
    15250 > #9,-0.59735,0.62471,0.5029,80.705,0.44544,0.7799,-0.43971,41.448,-0.6669,-0.038648,-0.74414,453.65
    15251 
    15252 > view matrix models
    15253 > #9,-0.73179,-0.006901,0.6815,180.03,-0.57374,0.54594,-0.61055,294.56,-0.36785,-0.83779,-0.40347,474.63
    15254 
    15255 > view matrix models
    15256 > #9,-0.79319,-0.093028,0.60182,221,-0.596,0.32149,-0.73582,361.32,-0.12503,-0.94233,-0.31045,432.17
    15257 
    15258 > view matrix models
    15259 > #9,-0.58382,-0.31126,0.74985,193.7,-0.73407,0.59693,-0.32375,259.38,-0.34683,-0.73946,-0.57698,486.91
    15260 
    15261 > view matrix models
    15262 > #9,-0.34202,-0.16644,0.92484,92.532,-0.84723,0.48035,-0.22687,281.13,-0.40649,-0.86114,-0.3053,466.79
    15263 
    15264 > view matrix models
    15265 > #9,-0.55882,0.49146,0.66797,65.577,-0.45981,0.4867,-0.74277,309.92,-0.69014,-0.72222,-0.045999,443.36
    15266 
    15267 > view matrix models
    15268 > #9,-0.54201,-0.3239,0.77544,183.64,-0.79241,0.50424,-0.34326,289.48,-0.27982,-0.80052,-0.52997,476.72
    15269 
    15270 > view matrix models
    15271 > #9,-0.58956,-0.063726,0.80521,141.21,-0.57182,0.737,-0.36035,213.39,-0.57047,-0.67289,-0.47094,494.64
    15272 
    15273 > view matrix models
    15274 > #9,-0.39155,-0.00207,0.92016,73.642,-0.67059,0.68539,-0.28381,225.21,-0.63008,-0.72818,-0.26975,476.42
    15275 
    15276 > view matrix models
    15277 > #9,-0.28776,-0.19817,0.93698,86.145,-0.87695,0.44774,-0.17463,282.08,-0.38491,-0.87193,-0.30263,464.35
    15278 
    15279 > view matrix models
    15280 > #9,-0.25456,-0.094965,0.96238,57.53,-0.75216,0.64493,-0.13531,218.34,-0.60782,-0.75832,-0.2356,471.22
    15281 
    15282 > view matrix models
    15283 > #9,0.08179,0.053136,0.99523,-33.823,-0.83033,0.55594,0.038556,214.45,-0.55124,-0.82952,0.089591,411.62
    15284 
    15285 > view matrix models
    15286 > #9,-0.066864,0.18014,0.98137,-26.974,-0.92402,0.35991,-0.12902,296.95,-0.37644,-0.91543,0.14239,385.61
    15287 
    15288 > view matrix models
    15289 > #9,-0.1796,0.42981,0.88488,-32.014,-0.68511,0.59085,-0.42605,271.28,-0.70595,-0.68276,0.18835,394.65
    15290 
    15291 > view matrix models
    15292 > #9,-0.38938,-0.35219,0.85108,147.19,-0.71886,0.6939,-0.041736,186.13,-0.57587,-0.62806,-0.52337,497.8
    15293 
    15294 > ui mousemode right "translate selected models"
    15295 
    15296 > view matrix models
    15297 > #9,-0.38938,-0.35219,0.85108,163.76,-0.71886,0.6939,-0.041736,188.56,-0.57587,-0.62806,-0.52337,496.31
    15298 
    15299 > view matrix models
    15300 > #9,-0.38938,-0.35219,0.85108,168.86,-0.71886,0.6939,-0.041736,197.29,-0.57587,-0.62806,-0.52337,495.68
    15301 
    15302 > view matrix models
    15303 > #9,-0.38938,-0.35219,0.85108,169.85,-0.71886,0.6939,-0.041736,197.13,-0.57587,-0.62806,-0.52337,494.81
    15304 
    15305 > volume #9 level 0.09622
    15306 
    15307 > volume #9 level 0.1218
    15308 
    15309 > volume #9 level 0.1102
    15310 
    15311 > ui mousemode right "rotate selected models"
    15312 
    15313 > view matrix models
    15314 > #9,-0.37051,-0.036777,0.9281,96.88,-0.68448,0.68625,-0.24606,231.42,-0.62786,-0.72644,-0.27943,474.52
    15315 
    15316 > view matrix models
    15317 > #9,-0.31168,-0.049862,0.94888,84.726,-0.69125,0.69707,-0.19043,220.1,-0.65194,-0.71527,-0.25173,471.56
    15318 
    15319 > view matrix models
    15320 > #9,-0.1857,-0.07265,0.97992,60.36,-0.66701,0.74162,-0.07142,185.28,-0.72154,-0.66687,-0.18618,462.98
    15321 
    15322 > view matrix models
    15323 > #9,-0.23942,-0.0021906,0.97091,59.372,-0.51422,0.84851,-0.12489,149.75,-0.82356,-0.52917,-0.20428,460.62
    15324 
    15325 > view matrix models
    15326 > #9,-0.22507,0.022971,0.97407,51.838,-0.51742,0.84429,-0.13947,153.84,-0.8256,-0.5354,-0.17814,457.06
    15327 
    15328 > view matrix models
    15329 > #9,-0.22651,0.020133,0.9738,52.639,-0.51714,0.84474,-0.13775,153.38,-0.82538,-0.5348,-0.18093,457.45
    15330 
    15331 > view matrix models
    15332 > #9,-0.21551,0.029869,0.97604,48.561,-0.50806,0.85017,-0.1382,150.91,-0.83393,-0.52567,-0.16805,454.92
    15333 
    15334 > view matrix models
    15335 > #9,-0.26159,0.28099,0.92337,23.126,-0.7227,0.57709,-0.38035,282.89,-0.63974,-0.76682,0.052114,420.27
    15336 
    15337 > view matrix models
    15338 > #9,-0.41669,0.2104,0.88436,70.441,-0.68255,0.57014,-0.45725,291.66,-0.60041,-0.79415,-0.093959,445.96
    15339 
    15340 > view matrix models
    15341 > #9,-0.43816,0.2546,0.86209,70.827,-0.46829,0.75397,-0.46068,222.24,-0.76728,-0.60556,-0.21113,465.21
    15342 
    15343 > view matrix models
    15344 > #9,-0.40829,0.25984,0.87509,62.119,-0.47771,0.75607,-0.44739,221.01,-0.77788,-0.6007,-0.18457,461.17
    15345 
    15346 > view matrix models
    15347 > #9,-0.44661,0.14869,0.88229,86.897,-0.5092,0.76859,-0.38728,212.93,-0.7357,-0.62223,-0.26755,473.29
    15348 
    15349 > view matrix models
    15350 > #9,-0.44407,0.15675,0.88217,85.065,-0.50686,0.76795,-0.3916,213.45,-0.73884,-0.62104,-0.26158,472.5
    15351 
    15352 > ui mousemode right "move picked models"
    15353 
    15354 > ui mousemode right "rotate selected models"
    15355 
    15356 > ui mousemode right "translate selected models"
    15357 
    15358 > view matrix models
    15359 > #9,-0.44407,0.15675,0.88217,83.534,-0.50686,0.76795,-0.3916,214.96,-0.73884,-0.62104,-0.26158,474.33
    15360 
    15361 > ui mousemode right "rotate selected models"
    15362 
    15363 > view matrix models
    15364 > #9,-0.47173,0.10261,0.87575,99.098,-0.49372,0.79217,-0.35876,202.13,-0.73056,-0.60161,-0.32303,481.23
    15365 
    15366 > view matrix models
    15367 > #9,-0.46188,0.17351,0.86981,86.145,-0.45527,0.79525,-0.40039,202.72,-0.76118,-0.58093,-0.28831,476.44
    15368 
    15369 > view matrix models
    15370 > #9,-0.17678,0.17743,0.96813,15.981,-0.55919,0.79135,-0.24714,192.57,-0.80997,-0.58505,-0.040674,438.48
    15371 
    15372 > view matrix models
    15373 > #9,-0.20822,0.22068,0.95286,16.964,-0.47946,0.8261,-0.2961,181.71,-0.8525,-0.51851,-0.066201,439.34
    15374 
    15375 > view matrix models
    15376 > #9,-0.23313,0.22067,0.94708,22.5,-0.51218,0.80002,-0.31248,195.19,-0.82664,-0.55792,-0.073484,442.99
    15377 
    15378 > view matrix models
    15379 > #9,-0.272,0.31817,0.90818,19.883,-0.43497,0.80119,-0.41096,200.1,-0.85838,-0.50681,-0.07953,440.9
    15380 
    15381 > ui mousemode right "translate selected models"
    15382 
    15383 > view matrix models
    15384 > #9,-0.272,0.31817,0.90818,20.776,-0.43497,0.80119,-0.41096,197.63,-0.85838,-0.50681,-0.07953,443.72
    15385 
    15386 > view matrix models
    15387 > #9,-0.272,0.31817,0.90818,21.653,-0.43497,0.80119,-0.41096,197.64,-0.85838,-0.50681,-0.07953,444.39
    15388 
    15389 > view matrix models
    15390 > #9,-0.272,0.31817,0.90818,21.578,-0.43497,0.80119,-0.41096,197.39,-0.85838,-0.50681,-0.07953,444.75
    15391 
    15392 > ui mousemode right "rotate selected models"
    15393 
    15394 > view matrix models
    15395 > #9,-0.34138,0.16793,0.9248,56.875,-0.43348,0.8449,-0.31343,170.87,-0.834,-0.50788,-0.21564,466.63
    15396 
    15397 > hide #1 models
    15398 
    15399 > show #1 models
    15400 
    15401 > hide #2 models
    15402 
    15403 > show #2 models
    15404 
    15405 > hide #3 models
    15406 
    15407 > show #3 models
    15408 
    15409 > hide #4 models
    15410 
    15411 > show #4 models
    15412 
    15413 > combine #1-4
    15414 
    15415 Remapping chain ID 'B' in D2NS1_B.pdb #3 to 'D' 
    15416 
    15417 > hide #10 models
    15418 
    15419 > show #10 models
    15420 
    15421 > hide #1 models
    15422 
    15423 > hide #2 models
    15424 
    15425 > hide #3 models
    15426 
    15427 > hide #4 models
    15428 
    15429 > hide #10 models
    15430 
    15431 > show #10 models
    15432 
    15433 > hide #5 models
    15434 
    15435 > show #5 models
    15436 
    15437 > show #1 models
    15438 
    15439 > hide #1 models
    15440 
    15441 > show #1 models
    15442 
    15443 > hide #1 models
    15444 
    15445 > show #2 models
    15446 
    15447 > show #3 models
    15448 
    15449 > show #4 models
    15450 
    15451 > view matrix models
    15452 > #9,0.52951,-0.025333,0.84793,-49.614,-0.39781,0.87542,0.27457,46.784,-0.74925,-0.4827,0.45346,319.24
    15453 
    15454 > undo
    15455 
    15456 > select subtract #9
    15457 
    15458 Nothing selected 
    15459 
    15460 > ui mousemode right zoom
    15461 
    15462 > molmap #1-4 onGrid #9 sigmaFactor 6
    15463 
    15464 Missing or invalid "resolution" argument: Expected a number 
    15465 
    15466 > molmap #1-4 resolution 8 onGrid #9
    15467 
    15468 Missing or invalid "resolution" argument: Expected a number 
    15469 
    15470 > molmap #1-4 8 onGrid #9
    15471 
    15472 Opened map 8 as #11, grid size 416,416,416, pixel 0.85, shown at level 0.0635,
    15473 step 1, values float32 
    15474 
    15475 > volume #11 level 0.03753
    15476 
    15477 > mmaker #9 to #11
    15478 
    15479 No 'to' model specified 
    15480 
    15481 > fitmap #9 to #11
    15482 
    15483 Expected a keyword 
    15484 
    15485 > Fit #9 in map #11
    15486 
    15487 Unknown command: Fit #9 in map #11 
    15488 
    15489 > fitmap #9 inMap map #11
    15490 
    15491 Invalid "inMap" argument: invalid density map specifier 
    15492 
    15493 > fitmap #9 inMap #11
    15494 
    15495 Fit map sNS1wt-Fab562.mrc in map map 8 using 131473 points 
    15496 correlation = 0.6323, correlation about mean = 0.08876, overlap = 2834 
    15497 steps = 292, shift = 12.1, angle = 16.9 degrees 
    15498  
    15499 Position of sNS1wt-Fab562.mrc (#9) relative to map 8 (#11) coordinates: 
    15500 Matrix rotation and translation 
    15501 0.96199493 -0.17308261 0.21120645 -4.02299000 
    15502 0.19395657 0.97754937 -0.08232910 -24.62700524 
    15503 -0.19221500 0.12016506 0.97396805 10.65384009 
    15504 Axis 0.34805838 0.69342351 0.63088763 
    15505 Axis point 91.81802475 0.00000000 16.19663836 
    15506 Rotation angle (degrees) 16.91131195 
    15507 Shift along axis -11.75580388 
    15508  
    15509 
    15510 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    15511 > (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
    15512 > MS_recolored.cxs" includeMaps true
    15513 
    15514 ——— End of log from Wed Apr 19 14:11:57 2023 ———
    15515 
    15516 opened ChimeraX session 
    15517 
    15518 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    15519 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/F562a.pdb
    15520 
    15521 Chain information for F562a.pdb #12 
    15522 --- 
    15523 Chain | Description 
    15524 C | No description available 
    15525 D | No description available 
    15526  
    15527 
    15528 > color #12 #8b92d7ff
    15529 
    15530 > color #12 #718dd7ff
    15531 
    15532 > color #12 #7693d7ff
    15533 
    15534 > color #12 #849ed7ff
    15535 
    15536 > select add #12
    15537 
    15538 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    15539 
    15540 > ui mousemode right zoom
    15541 
    15542 > ui mousemode right "translate selected models"
    15543 
    15544 > ui mousemode right "rotate selected models"
    15545 
    15546 > view matrix models
    15547 > #12,0.59826,0.23414,-0.76633,188.86,-0.29309,-0.82615,-0.48122,476.1,-0.74578,0.5125,-0.42563,337.4
    15548 
    15549 > view matrix models
    15550 > #12,0.8198,-0.22926,-0.52475,175.64,-0.56234,-0.49535,-0.66212,513.22,-0.10814,0.8379,-0.53501,149.05
    15551 
    15552 > view matrix models
    15553 > #12,0.70505,-0.47588,-0.52578,246.35,-0.42704,-0.87682,0.22096,392.51,-0.56617,0.068741,-0.82142,443.24
    15554 
    15555 > ui mousemode right "translate selected models"
    15556 
    15557 > view matrix models
    15558 > #12,0.70505,-0.47588,-0.52578,242.09,-0.42704,-0.87682,0.22096,378.11,-0.56617,0.068741,-0.82142,460.51
    15559 
    15560 > ui mousemode right zoom
    15561 
    15562 > ui mousemode right "rotate selected models"
    15563 
    15564 > view matrix models
    15565 > #12,0.89785,-0.43928,-0.030063,102.58,-0.37117,-0.71836,-0.58838,480.03,0.23687,0.53943,-0.80803,185.85
    15566 
    15567 > ui mousemode right "translate selected models"
    15568 
    15569 > view matrix models
    15570 > #12,0.89785,-0.43928,-0.030063,97.925,-0.37117,-0.71836,-0.58838,480.91,0.23687,0.53943,-0.80803,179.17
    15571 
    15572 > ui mousemode right "rotate selected models"
    15573 
    15574 > view matrix models
    15575 > #12,0.96357,-0.26121,-0.057389,55.865,-0.25517,-0.8337,-0.48973,456.47,0.080078,0.48653,-0.86998,236.41
    15576 
    15577 > view matrix models
    15578 > #12,0.90596,-0.39388,-0.15525,110.13,-0.42323,-0.85213,-0.30783,467.19,-0.011043,0.34459,-0.93869,295.05
    15579 
    15580 > view matrix models
    15581 > #12,0.89108,-0.41763,-0.17768,121.79,-0.45249,-0.84775,-0.2767,467.81,-0.035067,0.32696,-0.94439,304.83
    15582 
    15583 > ui mousemode right "translate selected models"
    15584 
    15585 > view matrix models
    15586 > #12,0.89108,-0.41763,-0.17768,121.19,-0.45249,-0.84775,-0.2767,465.74,-0.035067,0.32696,-0.94439,307.63
    15587 
    15588 > view matrix models
    15589 > #12,0.89108,-0.41763,-0.17768,120.89,-0.45249,-0.84775,-0.2767,466.02,-0.035067,0.32696,-0.94439,307.05
    15590 
    15591 > ui mousemode right "rotate selected models"
    15592 
    15593 > view matrix models
    15594 > #12,0.90549,-0.36137,-0.22248,115.49,-0.40743,-0.88694,-0.21757,451.86,-0.11871,0.28765,-0.95035,334.75
    15595 
    15596 Must specify one map, got 0 
    15597 
    15598 > fitmap #12 inMap #9
    15599 
    15600 Fit molecule F562a.pdb (#12) to map sNS1wt-Fab562.mrc (#9) using 3401 atoms 
    15601 average map value = 0.09851, steps = 92 
    15602 shifted from previous position = 4.5 
    15603 rotated from previous position = 18.4 degrees 
    15604 atoms outside contour = 1988, contour level = 0.11015 
    15605  
    15606 Position of F562a.pdb (#12) relative to sNS1wt-Fab562.mrc (#9) coordinates: 
    15607 Matrix rotation and translation 
    15608 -0.10510217 -0.15771336 0.98187577 53.64785327 
    15609 -0.09250566 -0.98151278 -0.16755707 397.45943422 
    15610 0.99014960 -0.10843968 0.08856975 -3.70781985 
    15611 Axis 0.66871425 -0.09359056 0.73760562 
    15612 Axis point 22.55285651 199.33929044 0.00000000 
    15613 Rotation angle (degrees) 177.46657060 
    15614 Shift along axis -4.05827537 
    15615  
    15616 
    15617 > select subtract #12
    15618 
    15619 Nothing selected 
    15620 
    15621 > ui tool show "Show Sequence Viewer"
    15622 
    15623 > sequence chain #12/C
    15624 
    15625 Alignment identifier is 12/C 
    15626 
    15627 > select #12/C:1-2
    15628 
    15629 13 atoms, 12 bonds, 2 residues, 1 model selected 
    15630 
    15631 > select #12/C:1-18
    15632 
    15633 131 atoms, 132 bonds, 18 residues, 1 model selected 
    15634 
    15635 > color #12 #d0d2dfff
    15636 
    15637 > select #12/C:5
    15638 
    15639 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15640 
    15641 > select #12/C:5-14
    15642 
    15643 71 atoms, 71 bonds, 10 residues, 1 model selected 
    15644 
    15645 > ui tool show "Color Actions"
    15646 
    15647 > color sel #cbd8ffff
    15648 
    15649 > color sel #9fbcffff
    15650 
    15651 > color sel #93abffff
    15652 
    15653 > color sel #88a4ffff
    15654 
    15655 > color sel #8484f7ff
    15656 
    15657 > select #12/C:15
    15658 
    15659 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15660 
    15661 > select #12/C:15-35
    15662 
    15663 163 atoms, 168 bonds, 21 residues, 1 model selected 
    15664 
    15665 > color sel #fdf2f2ff
    15666 
    15667 > select #12/C:21
    15668 
    15669 6 atoms, 5 bonds, 1 residue, 1 model selected 
    15670 
    15671 > select #12/C:21
    15672 
    15673 6 atoms, 5 bonds, 1 residue, 1 model selected 
    15674 
    15675 > color sel #fae0e0ff
    15676 
    15677 > select #12/C:22
    15678 
    15679 11 atoms, 11 bonds, 1 residue, 1 model selected 
    15680 
    15681 > select #12/C:22-35
    15682 
    15683 112 atoms, 116 bonds, 14 residues, 1 model selected 
    15684 
    15685 > color sel #fbe8e7ff
    15686 
    15687 > select #12/C:36-37
    15688 
    15689 26 atoms, 28 bonds, 2 residues, 1 model selected 
    15690 
    15691 > select #12/C:36-42
    15692 
    15693 77 atoms, 81 bonds, 7 residues, 1 model selected 
    15694 
    15695 > select #12/C:30
    15696 
    15697 6 atoms, 5 bonds, 1 residue, 1 model selected 
    15698 
    15699 > select #12/C:30-35
    15700 
    15701 43 atoms, 43 bonds, 6 residues, 1 model selected 
    15702 
    15703 > color sel #3535f5ff
    15704 
    15705 > select #12/C:36-37
    15706 
    15707 26 atoms, 28 bonds, 2 residues, 1 model selected 
    15708 
    15709 > select #12/C:36-47
    15710 
    15711 115 atoms, 120 bonds, 12 residues, 1 model selected 
    15712 
    15713 > color sel #fbe8e7ff
    15714 
    15715 > select #12/C:48-49
    15716 
    15717 17 atoms, 16 bonds, 2 residues, 1 model selected 
    15718 
    15719 > select #12/C:48-57
    15720 
    15721 94 atoms, 97 bonds, 10 residues, 1 model selected 
    15722 
    15723 > select #12/C:58-59
    15724 
    15725 10 atoms, 9 bonds, 2 residues, 1 model selected 
    15726 
    15727 > select #12/C:58-61
    15728 
    15729 26 atoms, 25 bonds, 4 residues, 1 model selected 
    15730 
    15731 > color sel #f1f1feff
    15732 
    15733 > select #12/C:62-63
    15734 
    15735 20 atoms, 20 bonds, 2 residues, 1 model selected 
    15736 
    15737 > select #12/C:62-73
    15738 
    15739 99 atoms, 100 bonds, 12 residues, 1 model selected 
    15740 
    15741 > color sel #fadfdfff
    15742 
    15743 > select #12/C:79
    15744 
    15745 8 atoms, 7 bonds, 1 residue, 1 model selected 
    15746 
    15747 > select #12/C:79-94
    15748 
    15749 126 atoms, 128 bonds, 16 residues, 1 model selected 
    15750 
    15751 > color sel #efeffeff
    15752 
    15753 > select #12/C:95
    15754 
    15755 7 atoms, 6 bonds, 1 residue, 1 model selected 
    15756 
    15757 > select #12/C:95-103
    15758 
    15759 82 atoms, 85 bonds, 9 residues, 1 model selected 
    15760 
    15761 > color sel #ddddfcff
    15762 
    15763 > select #12/C:102
    15764 
    15765 12 atoms, 12 bonds, 1 residue, 1 model selected 
    15766 
    15767 > select #12/C:102-103
    15768 
    15769 24 atoms, 25 bonds, 2 residues, 1 model selected 
    15770 
    15771 > color sel #c9d0ffff
    15772 
    15773 > hide #!9 models
    15774 
    15775 > select #12/C:104
    15776 
    15777 12 atoms, 12 bonds, 1 residue, 1 model selected 
    15778 
    15779 > select #12/C:104-105
    15780 
    15781 18 atoms, 18 bonds, 2 residues, 1 model selected 
    15782 
    15783 > set bgColor white
    15784 
    15785 > select #12/C:104
    15786 
    15787 12 atoms, 12 bonds, 1 residue, 1 model selected 
    15788 
    15789 > select #12/C:104-112
    15790 
    15791 73 atoms, 78 bonds, 9 residues, 1 model selected 
    15792 
    15793 > color sel #d3d3fbff
    15794 
    15795 > color sel #bec7feff
    15796 
    15797 > select #12/C:113
    15798 
    15799 12 atoms, 12 bonds, 1 residue, 1 model selected 
    15800 
    15801 > select #12/C:113-120
    15802 
    15803 65 atoms, 67 bonds, 8 residues, 1 model selected 
    15804 
    15805 > color sel #d3d9feff
    15806 
    15807 > select #12/C:123
    15808 
    15809 11 atoms, 11 bonds, 1 residue, 1 model selected 
    15810 
    15811 > select #12/C:123-145
    15812 
    15813 153 atoms, 157 bonds, 23 residues, 1 model selected 
    15814 
    15815 > color sel #f6f6feff
    15816 
    15817 > color sel #e7e8ffff
    15818 
    15819 > color sel #edf0ffff
    15820 
    15821 > select #12/C:146
    15822 
    15823 7 atoms, 6 bonds, 1 residue, 1 model selected 
    15824 
    15825 > select #12/C:146-156
    15826 
    15827 79 atoms, 79 bonds, 11 residues, 1 model selected 
    15828 
    15829 > color sel #fdf1f1ff
    15830 
    15831 > select #12/C:157
    15832 
    15833 11 atoms, 11 bonds, 1 residue, 1 model selected 
    15834 
    15835 > select #12/C:157-168
    15836 
    15837 93 atoms, 97 bonds, 12 residues, 1 model selected 
    15838 
    15839 > color sel #fbeae9ff
    15840 
    15841 > select #12/C:169
    15842 
    15843 5 atoms, 4 bonds, 1 residue, 1 model selected 
    15844 
    15845 > select #12/C:169-176
    15846 
    15847 54 atoms, 54 bonds, 8 residues, 1 model selected 
    15848 
    15849 > color sel #f0f0feff
    15850 
    15851 > select #12/C:177-178
    15852 
    15853 18 atoms, 19 bonds, 2 residues, 1 model selected 
    15854 
    15855 > select #12/C:177-179
    15856 
    15857 23 atoms, 24 bonds, 3 residues, 1 model selected 
    15858 
    15859 > select #12/C:177
    15860 
    15861 11 atoms, 11 bonds, 1 residue, 1 model selected 
    15862 
    15863 > select #12/C:177-178
    15864 
    15865 18 atoms, 19 bonds, 2 residues, 1 model selected 
    15866 
    15867 > color sel #ffe7efff
    15868 
    15869 > color sel #fdf6ffff
    15870 
    15871 > color sel #fff0ffff
    15872 
    15873 > color sel #ffeffdff
    15874 
    15875 > color sel #ffedfaff
    15876 
    15877 > color sel #ffecf9ff
    15878 
    15879 > color sel #ffecfaff
    15880 
    15881 > color sel #ffebf9ff
    15882 
    15883 > color sel #ffecfaff
    15884 
    15885 > color sel #ffecfbff
    15886 
    15887 > color sel #ffecfcff
    15888 
    15889 > color sel #ffedfdff
    15890 
    15891 > color sel #ffecfdff
    15892 
    15893 > color sel #ffedfdff
    15894 
    15895 > color sel #ffeaffff
    15896 
    15897 > color sel #ffeafeff
    15898 
    15899 > color sel #ffe9feff
    15900 
    15901 > color sel #ffe8feff
    15902 
    15903 > color sel #ffe8fdff
    15904 
    15905 > color sel #ffe8fcff
    15906 
    15907 > color sel #ffe8fbff
    15908 
    15909 > color sel #ffe8faff
    15910 
    15911 > color sel #ffe8f8ff
    15912 
    15913 > color sel #ffe8f7ff
    15914 
    15915 > color sel #ffe9f7ff
    15916 
    15917 > color sel #ffe8f6ff
    15918 
    15919 > color sel #ffe9f6ff
    15920 
    15921 > color sel #ffe9f5ff
    15922 
    15923 > color sel #ffeaf5ff
    15924 
    15925 > color sel #ffeaf4ff
    15926 
    15927 > color sel #ffebf4ff
    15928 
    15929 > color sel #ffebf3ff
    15930 
    15931 > color sel #ffecf2ff
    15932 
    15933 > color sel #ffecf1ff
    15934 
    15935 > color sel #ffecf0ff
    15936 
    15937 > color sel #ffebefff
    15938 
    15939 > color sel #ffebeeff
    15940 
    15941 > color sel #ffeaedff
    15942 
    15943 > color sel #ffe9ecff
    15944 
    15945 > color sel #ffe8ebff
    15946 
    15947 > color sel #ffe7ebff
    15948 
    15949 > color sel #ffe6eaff
    15950 
    15951 > color sel #ffe6e9ff
    15952 
    15953 > select #12/C:181
    15954 
    15955 8 atoms, 7 bonds, 1 residue, 1 model selected 
    15956 
    15957 > select #12/C:181-187
    15958 
    15959 53 atoms, 53 bonds, 7 residues, 1 model selected 
    15960 
    15961 > color sel #fff7fdff
    15962 
    15963 > color sel #f9f3ffff
    15964 
    15965 > select #12/C:188-189
    15966 
    15967 14 atoms, 13 bonds, 2 residues, 1 model selected 
    15968 
    15969 > select #12/C:188-198
    15970 
    15971 73 atoms, 73 bonds, 11 residues, 1 model selected 
    15972 
    15973 > color sel #f4efffff
    15974 
    15975 > select #12/C:200
    15976 
    15977 8 atoms, 7 bonds, 1 residue, 1 model selected 
    15978 
    15979 > select #12/C:200-208
    15980 
    15981 69 atoms, 70 bonds, 9 residues, 1 model selected 
    15982 
    15983 > color sel #cdd3ffff
    15984 
    15985 > color sel #8e8ef8ff
    15986 
    15987 > color sel #9da0ffff
    15988 
    15989 > color sel #9c9fffff
    15990 
    15991 > color sel #9c9effff
    15992 
    15993 > color sel #9b9effff
    15994 
    15995 > color sel #9b9dffff
    15996 
    15997 > color sel #9a9cffff
    15998 
    15999 > color sel #9696f8ff
    16000 
    16001 > select #12/C:209
    16002 
    16003 7 atoms, 6 bonds, 1 residue, 1 model selected 
    16004 
    16005 > select #12/C:209-213
    16006 
    16007 41 atoms, 42 bonds, 5 residues, 1 model selected 
    16008 
    16009 > color sel #f1f1feff
    16010 
    16011 > select #12/C:214-215
    16012 
    16013 14 atoms, 13 bonds, 2 residues, 1 model selected 
    16014 
    16015 > select #12/C:214-223
    16016 
    16017 79 atoms, 78 bonds, 10 residues, 1 model selected 
    16018 
    16019 > color sel #b8b8faff
    16020 
    16021 > select #12/C:224-225
    16022 
    16023 16 atoms, 16 bonds, 2 residues, 1 model selected 
    16024 
    16025 > select #12/C:224-228
    16026 
    16027 36 atoms, 36 bonds, 5 residues, 1 model selected 
    16028 
    16029 > color sel #f8f6ffff
    16030 
    16031 > color sel #dad8e0ff
    16032 
    16033 > color sel #c5c3caff
    16034 
    16035 > color sel #c4c3caff
    16036 
    16037 > color sel #b5b4baff
    16038 
    16039 > color sel #b4b3baff
    16040 
    16041 > color sel dim gray
    16042 
    16043 > select #12/C:1
    16044 
    16045 5 atoms, 4 bonds, 1 residue, 1 model selected 
    16046 
    16047 > select #12/C:1-4
    16048 
    16049 29 atoms, 28 bonds, 4 residues, 1 model selected 
    16050 
    16051 > color sel dim gray
    16052 
    16053 > select #12/C:122
    16054 
    16055 7 atoms, 6 bonds, 1 residue, 1 model selected 
    16056 
    16057 > select #12/C:121-122
    16058 
    16059 14 atoms, 13 bonds, 2 residues, 1 model selected 
    16060 
    16061 > color sel dim gray
    16062 
    16063 > select #12/C:178-179
    16064 
    16065 12 atoms, 12 bonds, 2 residues, 1 model selected 
    16066 
    16067 > select #12/C:178-180
    16068 
    16069 19 atoms, 19 bonds, 3 residues, 1 model selected 
    16070 
    16071 > color sel dim gray
    16072 
    16073 > select #12/C:73-74
    16074 
    16075 19 atoms, 18 bonds, 2 residues, 1 model selected 
    16076 
    16077 > select #12/C:73-78
    16078 
    16079 54 atoms, 54 bonds, 6 residues, 1 model selected 
    16080 
    16081 > color sel dim gray
    16082 
    16083 > select add #12
    16084 
    16085 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    16086 
    16087 > select subtract #12
    16088 
    16089 Nothing selected 
    16090 
    16091 > ui tool show "Show Sequence Viewer"
    16092 
    16093 > sequence chain #12/D
    16094 
    16095 Alignment identifier is 12/D 
    16096 
    16097 > select #12/D:1
    16098 
    16099 5 atoms, 4 bonds, 1 residue, 1 model selected 
    16100 
    16101 > select #12/D
    16102 
    16103 1632 atoms, 1668 bonds, 214 residues, 1 model selected 
    16104 
    16105 > color sel dim gray
    16106 
    16107 > view matrix models
    16108 > #12,0.71436,-0.39661,-0.57653,226.88,-0.66803,-0.63185,-0.39307,496.97,-0.20839,0.66593,-0.71632,245.16
    16109 
    16110 > undo
    16111 
    16112 > ui mousemode right select
    16113 
    16114 > select clear
    16115 
    16116 > ui mousemode right zoom
    16117 
    16118 > select #12/D:7-8
    16119 
    16120 15 atoms, 14 bonds, 2 residues, 1 model selected 
    16121 
    16122 > select #12/D:7-14
    16123 
    16124 58 atoms, 58 bonds, 8 residues, 1 model selected 
    16125 
    16126 > color sel #e0e0fcff
    16127 
    16128 > select #12/D:15
    16129 
    16130 6 atoms, 5 bonds, 1 residue, 1 model selected 
    16131 
    16132 > select #12/D:15-21
    16133 
    16134 47 atoms, 46 bonds, 7 residues, 1 model selected 
    16135 
    16136 > color sel #fdf4f4ff
    16137 
    16138 > color sel #ffefedff
    16139 
    16140 > select #12/D:22
    16141 
    16142 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16143 
    16144 > select #12/D:22-26
    16145 
    16146 36 atoms, 35 bonds, 5 residues, 1 model selected 
    16147 
    16148 > color sel #fff1f0ff
    16149 
    16150 > color sel #fff2f0ff
    16151 
    16152 > select #12/D:27
    16153 
    16154 6 atoms, 5 bonds, 1 residue, 1 model selected 
    16155 
    16156 > select #12/D:27-28
    16157 
    16158 11 atoms, 10 bonds, 2 residues, 1 model selected 
    16159 
    16160 > color sel #e0e0fcff
    16161 
    16162 > select #12/D:29
    16163 
    16164 6 atoms, 5 bonds, 1 residue, 1 model selected 
    16165 
    16166 > select #12/D:29-36
    16167 
    16168 61 atoms, 62 bonds, 8 residues, 1 model selected 
    16169 
    16170 > color sel #f9f9ffff
    16171 
    16172 > select #12/D:37
    16173 
    16174 14 atoms, 15 bonds, 1 residue, 1 model selected 
    16175 
    16176 > select #12/D:37-38
    16177 
    16178 26 atoms, 28 bonds, 2 residues, 1 model selected 
    16179 
    16180 > color sel #ededfdff
    16181 
    16182 > select #12/D:39
    16183 
    16184 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16185 
    16186 > select #12/D:39-48
    16187 
    16188 74 atoms, 74 bonds, 10 residues, 1 model selected 
    16189 
    16190 > color sel #dcdcfcff
    16191 
    16192 > select
    16193 > #12/D:7-10,13-17,22-28,35-40,47-50,64-69,72-77,86-92,102-107,114-118,129-137,144-150,153-155,159-163,175-182,191-198,205-210
    16194 
    16195 797 atoms, 797 bonds, 102 residues, 1 model selected 
    16196 
    16197 > select #12/D:49
    16198 
    16199 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16200 
    16201 > select #12/D:49
    16202 
    16203 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16204 
    16205 > color sel #e4e4fdff
    16206 
    16207 > select #12/D:50
    16208 
    16209 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16210 
    16211 > select #12/D:50-56
    16212 
    16213 55 atoms, 55 bonds, 7 residues, 1 model selected 
    16214 
    16215 > color sel #5c5cf6ff
    16216 
    16217 > select #12/D:57
    16218 
    16219 5 atoms, 4 bonds, 1 residue, 1 model selected 
    16220 
    16221 > select #12/D:57-58
    16222 
    16223 11 atoms, 10 bonds, 2 residues, 1 model selected 
    16224 
    16225 > select #12/D:57-58
    16226 
    16227 11 atoms, 10 bonds, 2 residues, 1 model selected 
    16228 
    16229 > select #12/D:57
    16230 
    16231 5 atoms, 4 bonds, 1 residue, 1 model selected 
    16232 
    16233 > color sel #fdf6f6ff
    16234 
    16235 > select #12/D:58
    16236 
    16237 6 atoms, 5 bonds, 1 residue, 1 model selected 
    16238 
    16239 > select #12/D:58-67
    16240 
    16241 68 atoms, 69 bonds, 10 residues, 1 model selected 
    16242 
    16243 > color sel #efeffeff
    16244 
    16245 > select #12/D:58-67
    16246 
    16247 68 atoms, 69 bonds, 10 residues, 1 model selected 
    16248 
    16249 > select #12/D:58
    16250 
    16251 6 atoms, 5 bonds, 1 residue, 1 model selected 
    16252 
    16253 > select #12/D:58-69
    16254 
    16255 78 atoms, 79 bonds, 12 residues, 1 model selected 
    16256 
    16257 > color sel #e8e8fdff
    16258 
    16259 > select #12/D:70
    16260 
    16261 4 atoms, 3 bonds, 1 residue, 1 model selected 
    16262 
    16263 > select #12/D:70-73
    16264 
    16265 34 atoms, 35 bonds, 4 residues, 1 model selected 
    16266 
    16267 > color sel #d8d8fcff
    16268 
    16269 > select #12/D:74-75
    16270 
    16271 14 atoms, 13 bonds, 2 residues, 1 model selected 
    16272 
    16273 > select #12/D:74-79
    16274 
    16275 41 atoms, 40 bonds, 6 residues, 1 model selected 
    16276 
    16277 > color sel #f4f4feff
    16278 
    16279 > select #12/D:80
    16280 
    16281 7 atoms, 6 bonds, 1 residue, 1 model selected 
    16282 
    16283 > select #12/D:80-81
    16284 
    16285 16 atoms, 15 bonds, 2 residues, 1 model selected 
    16286 
    16287 > color sel #fff6f4ff
    16288 
    16289 > select #12/D:82
    16290 
    16291 5 atoms, 4 bonds, 1 residue, 1 model selected 
    16292 
    16293 > select #12/D:82-84
    16294 
    16295 22 atoms, 21 bonds, 3 residues, 1 model selected 
    16296 
    16297 > color sel #efeffeff
    16298 
    16299 > select #12/D:85
    16300 
    16301 5 atoms, 4 bonds, 1 residue, 1 model selected 
    16302 
    16303 > select #12/D:85-87
    16304 
    16305 18 atoms, 17 bonds, 3 residues, 1 model selected 
    16306 
    16307 > select #12/D:84-85
    16308 
    16309 13 atoms, 12 bonds, 2 residues, 1 model selected 
    16310 
    16311 > select #12/D:84-87
    16312 
    16313 26 atoms, 25 bonds, 4 residues, 1 model selected 
    16314 
    16315 > color sel #ffdedeff
    16316 
    16317 > color sel #ffe8e9ff
    16318 
    16319 > select #12/D:88
    16320 
    16321 12 atoms, 12 bonds, 1 residue, 1 model selected 
    16322 
    16323 > select #12/D:88-97
    16324 
    16325 96 atoms, 102 bonds, 10 residues, 1 model selected 
    16326 
    16327 > select #12/D:98
    16328 
    16329 11 atoms, 11 bonds, 1 residue, 1 model selected 
    16330 
    16331 > select #12/D:98-105
    16332 
    16333 56 atoms, 56 bonds, 8 residues, 1 model selected 
    16334 
    16335 > color sel #d0d0fbff
    16336 
    16337 > select #12/D:114
    16338 
    16339 6 atoms, 5 bonds, 1 residue, 1 model selected 
    16340 
    16341 > select #12/D:114-125
    16342 
    16343 97 atoms, 100 bonds, 12 residues, 1 model selected 
    16344 
    16345 > color sel #d6d6fcff
    16346 
    16347 > select #12/D:128-129
    16348 
    16349 11 atoms, 10 bonds, 2 residues, 1 model selected 
    16350 
    16351 > select #12/D:128-131
    16352 
    16353 22 atoms, 21 bonds, 4 residues, 1 model selected 
    16354 
    16355 > color sel #dfdffcff
    16356 
    16357 > select #12/D:132-133
    16358 
    16359 14 atoms, 13 bonds, 2 residues, 1 model selected 
    16360 
    16361 > select #12/D:132-137
    16362 
    16363 44 atoms, 43 bonds, 6 residues, 1 model selected 
    16364 
    16365 > color sel #fbeae9ff
    16366 
    16367 > color sel #ffeeeaff
    16368 
    16369 > select #12/D:138
    16370 
    16371 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16372 
    16373 > select #12/D:138-146
    16374 
    16375 79 atoms, 81 bonds, 9 residues, 1 model selected 
    16376 
    16377 > color sel #c9c9fbff
    16378 
    16379 > select #12/D:147
    16380 
    16381 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16382 
    16383 > select #12/D:147-158
    16384 
    16385 95 atoms, 96 bonds, 12 residues, 1 model selected 
    16386 
    16387 > color sel #f7cbcaff
    16388 
    16389 > select #12/D:161
    16390 
    16391 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16392 
    16393 > select #12/D:161-179
    16394 
    16395 144 atoms, 144 bonds, 19 residues, 1 model selected 
    16396 
    16397 > color sel #c9c9fbff
    16398 
    16399 > select #12/D:183
    16400 
    16401 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16402 
    16403 > select #12/D:183-204
    16404 
    16405 176 atoms, 180 bonds, 22 residues, 1 model selected 
    16406 
    16407 > color sel #bbbbfaff
    16408 
    16409 > select #12/D:205
    16410 
    16411 7 atoms, 6 bonds, 1 residue, 1 model selected 
    16412 
    16413 > select #12/D:205-213
    16414 
    16415 72 atoms, 72 bonds, 9 residues, 1 model selected 
    16416 
    16417 > color sel #fbebffff
    16418 
    16419 > color sel #f1eaffff
    16420 
    16421 > color sel #f6eeffff
    16422 
    16423 > color sel #f7eeffff
    16424 
    16425 > select add #12
    16426 
    16427 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    16428 
    16429 > select subtract #12
    16430 
    16431 Nothing selected 
    16432 
    16433 > ui tool show "Show Sequence Viewer"
    16434 
    16435 > sequence chain #3/B #4/A #10/D #10/A
    16436 
    16437 Alignment identifier is 1 
    16438 
    16439 > show #!9 models
    16440 
    16441 > hide #8 models
    16442 
    16443 > show #8 models
    16444 
    16445 > hide #8 models
    16446 
    16447 > show #8 models
    16448 
    16449 > hide #8 models
    16450 
    16451 > show #8 models
    16452 
    16453 > hide #8 models
    16454 
    16455 > show #8 models
    16456 
    16457 > show #7 models
    16458 
    16459 > hide #7 models
    16460 
    16461 > show #7 models
    16462 
    16463 > hide #7 models
    16464 
    16465 > show #7 models
    16466 
    16467 > hide #7 models
    16468 
    16469 > select #3/B:1-81 #4/A:1-81 #10/D,A:1-81
    16470 
    16471 2576 atoms, 2632 bonds, 14 pseudobonds, 324 residues, 5 models selected 
    16472 
    16473 > select #3/B:1-275 #4/A:1-275 #10/D,A:1-275
    16474 
    16475 8808 atoms, 9044 bonds, 154 pseudobonds, 1100 residues, 5 models selected 
    16476 
    16477 > select #3/B:276 #4/A:276 #10/D,A:276
    16478 
    16479 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16480 
    16481 > select #3/B:276-352 #4/A:276-352 #10/D,A:276-352
    16482 
    16483 2396 atoms, 2440 bonds, 1 pseudobond, 308 residues, 4 models selected 
    16484 
    16485 > select #3/B:101-352 #4/A:101-352 #10/D,A:101-352
    16486 
    16487 8076 atoms, 8300 bonds, 31 pseudobonds, 1008 residues, 5 models selected 
    16488 
    16489 > select #3/B #4/A #10/D,A
    16490 
    16491 11204 atoms, 11488 bonds, 155 pseudobonds, 1408 residues, 5 models selected 
    16492 
    16493 > select subtract #5
    16494 
    16495 11204 atoms, 11488 bonds, 53 pseudobonds, 1408 residues, 4 models selected 
    16496 
    16497 > select subtract #4
    16498 
    16499 8403 atoms, 8616 bonds, 21 pseudobonds, 1056 residues, 3 models selected 
    16500 
    16501 > select subtract #3
    16502 
    16503 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    16504 
    16505 > select add #10
    16506 
    16507 8936 atoms, 9124 bonds, 1118 residues, 1 model selected 
    16508 
    16509 > select subtract #10
    16510 
    16511 Nothing selected 
    16512 
    16513 > select add #3
    16514 
    16515 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    16516 
    16517 > select add #4
    16518 
    16519 5602 atoms, 5744 bonds, 90 pseudobonds, 704 residues, 4 models selected 
    16520 
    16521 > select add #5
    16522 
    16523 5602 atoms, 5744 bonds, 144 pseudobonds, 704 residues, 4 models selected 
    16524 
    16525 > select subtract #5
    16526 
    16527 5602 atoms, 5744 bonds, 42 pseudobonds, 704 residues, 3 models selected 
    16528 
    16529 > select add #7
    16530 
    16531 5602 atoms, 5744 bonds, 97 pseudobonds, 704 residues, 3 models selected 
    16532 
    16533 > select subtract #7
    16534 
    16535 5602 atoms, 5744 bonds, 704 residues, 2 models selected 
    16536 
    16537 > color sel dim gray
    16538 
    16539 > select subtract #3
    16540 
    16541 2801 atoms, 2872 bonds, 352 residues, 1 model selected 
    16542 
    16543 > select subtract #4
    16544 
    16545 Nothing selected 
    16546 
    16547 > select #3/B:175 #4/A:175 #10/D,A:175
    16548 
    16549 36 atoms, 32 bonds, 4 residues, 3 models selected 
    16550 
    16551 > select #3/B:175-178 #4/A:175-178 #10/D,A:175-178
    16552 
    16553 120 atoms, 116 bonds, 16 residues, 3 models selected 
    16554 
    16555 > ui tool show "Color Actions"
    16556 
    16557 > color sel #d8d8fcff
    16558 
    16559 > select #3/B:180 #4/A:180 #10/D,A:180
    16560 
    16561 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16562 
    16563 > select #3/B:180-185 #4/A:180-185 #10/D,A:180-185
    16564 
    16565 180 atoms, 176 bonds, 24 residues, 3 models selected 
    16566 
    16567 > select #3/B:179 #4/A:179 #10/D,A:179
    16568 
    16569 24 atoms, 20 bonds, 4 residues, 3 models selected 
    16570 
    16571 > select #3/B:179-186 #4/A:179-186 #10/D,A:179-186
    16572 
    16573 224 atoms, 220 bonds, 32 residues, 3 models selected 
    16574 
    16575 > color sel #e5e3ffff
    16576 
    16577 > select #3/B:187-188 #4/A:187-188 #10/D,A:187-188
    16578 
    16579 52 atoms, 48 bonds, 8 residues, 3 models selected 
    16580 
    16581 > select #3/B:187-198 #4/A:187-198 #10/D,A:187-198
    16582 
    16583 368 atoms, 368 bonds, 48 residues, 3 models selected 
    16584 
    16585 > color sel #dbdcffff
    16586 
    16587 > select #3/B:199-200 #4/A:199-200 #10/D,A:199-200
    16588 
    16589 64 atoms, 64 bonds, 8 residues, 3 models selected 
    16590 
    16591 > select #3/B:199-200 #4/A:199-200 #10/D,A:199-200
    16592 
    16593 64 atoms, 64 bonds, 8 residues, 3 models selected 
    16594 
    16595 > color sel #d2d5ffff
    16596 
    16597 > select #3/B:201 #4/A:201 #10/D,A:201
    16598 
    16599 56 atoms, 60 bonds, 4 residues, 3 models selected 
    16600 
    16601 > select #3/B:201-211 #4/A:201-211 #10/D,A:201-211
    16602 
    16603 384 atoms, 396 bonds, 44 residues, 3 models selected 
    16604 
    16605 > color sel #d9dbffff
    16606 
    16607 > select #3/B:212 #4/A:212 #10/D,A:212
    16608 
    16609 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16610 
    16611 > select #3/B:212-217 #4/A:212-217 #10/D,A:212-217
    16612 
    16613 192 atoms, 192 bonds, 24 residues, 3 models selected 
    16614 
    16615 > color sel #f7f5ffff
    16616 
    16617 > select #3/B:218 #4/A:218 #10/D,A:218
    16618 
    16619 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16620 
    16621 > select #3/B:218-220 #4/A:218-220 #10/D,A:218-220
    16622 
    16623 96 atoms, 92 bonds, 12 residues, 3 models selected 
    16624 
    16625 > select #3/B:218-219 #4/A:218-219 #10/D,A:218-219
    16626 
    16627 68 atoms, 64 bonds, 8 residues, 3 models selected 
    16628 
    16629 > select #3/B:218-219 #4/A:218-219 #10/D,A:218-219
    16630 
    16631 68 atoms, 64 bonds, 8 residues, 3 models selected 
    16632 
    16633 > color sel #c9d5ffff
    16634 
    16635 > color sel #cad4ffff
    16636 
    16637 > color sel #cbd4ffff
    16638 
    16639 > color sel #ccd4ffff
    16640 
    16641 > color sel #cdd3ffff
    16642 
    16643 > color sel #ced3ffff
    16644 
    16645 > color sel #cfd3ffff
    16646 
    16647 > color sel #cfd2ffff
    16648 
    16649 > color sel #d0d2ffff
    16650 
    16651 > color sel #d1d2ffff
    16652 
    16653 > color sel #d1d1ffff
    16654 
    16655 > select #3/B:220 #4/A:220 #10/D,A:220
    16656 
    16657 28 atoms, 24 bonds, 4 residues, 3 models selected 
    16658 
    16659 > select #3/B:220-231 #4/A:220-231 #10/D,A:220-231
    16660 
    16661 396 atoms, 412 bonds, 48 residues, 3 models selected 
    16662 
    16663 > color sel #c8c9ffff
    16664 
    16665 > select #3/B:232-233 #4/A:232-233 #10/D,A:232-233
    16666 
    16667 80 atoms, 84 bonds, 8 residues, 3 models selected 
    16668 
    16669 > select #3/B:232-240 #4/A:232-240 #10/D,A:232-240
    16670 
    16671 284 atoms, 288 bonds, 36 residues, 3 models selected 
    16672 
    16673 > color sel #d4d6ffff
    16674 
    16675 > select #3/B:241 #4/A:241 #10/D,A:241
    16676 
    16677 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16678 
    16679 > select #3/B:241-242 #4/A:241-242 #10/D,A:241-242
    16680 
    16681 64 atoms, 60 bonds, 8 residues, 3 models selected 
    16682 
    16683 > select #3/B:242 #4/A:242 #10/D,A:242
    16684 
    16685 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16686 
    16687 > select #3/B:241-242 #4/A:241-242 #10/D,A:241-242
    16688 
    16689 64 atoms, 60 bonds, 8 residues, 3 models selected 
    16690 
    16691 > select #3/B:241 #4/A:241 #10/D,A:241
    16692 
    16693 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16694 
    16695 > select #3/B:241-242 #4/A:241-242 #10/D,A:241-242
    16696 
    16697 64 atoms, 60 bonds, 8 residues, 3 models selected 
    16698 
    16699 > select #3/B:241 #4/A:241 #10/D,A:241
    16700 
    16701 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16702 
    16703 > select #3/B:241 #4/A:241 #10/D,A:241
    16704 
    16705 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16706 
    16707 > color sel #dddfffff
    16708 
    16709 > select #3/B:242 #4/A:242 #10/D,A:242
    16710 
    16711 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16712 
    16713 > select #3/B:242-247 #4/A:242-247 #10/D,A:242-247
    16714 
    16715 204 atoms, 208 bonds, 24 residues, 3 models selected 
    16716 
    16717 > color sel #d3d6ffff
    16718 
    16719 > select #3/B:248 #4/A:248 #10/D,A:248
    16720 
    16721 20 atoms, 16 bonds, 4 residues, 3 models selected 
    16722 
    16723 > select #3/B:248-254 #4/A:248-254 #10/D,A:248-254
    16724 
    16725 192 atoms, 196 bonds, 28 residues, 3 models selected 
    16726 
    16727 > select #3/B:254 #4/A:254 #10/D,A:254
    16728 
    16729 40 atoms, 40 bonds, 4 residues, 3 models selected 
    16730 
    16731 > select #3/B:254 #4/A:254 #10/D,A:254
    16732 
    16733 40 atoms, 40 bonds, 4 residues, 3 models selected 
    16734 
    16735 > select #3/B:253 #4/A:253 #10/D,A:253
    16736 
    16737 36 atoms, 32 bonds, 4 residues, 3 models selected 
    16738 
    16739 > select #3/B:248-253 #4/A:248-253 #10/D,A:248-253
    16740 
    16741 152 atoms, 152 bonds, 24 residues, 3 models selected 
    16742 
    16743 > color sel #dedfffff
    16744 
    16745 > color sel #e1e1ffff
    16746 
    16747 > select #3/B:254-255 #4/A:254-255 #10/D,A:254-255
    16748 
    16749 72 atoms, 72 bonds, 8 residues, 3 models selected 
    16750 
    16751 > select #3/B:254-262 #4/A:254-262 #10/D,A:254-262
    16752 
    16753 324 atoms, 340 bonds, 36 residues, 3 models selected 
    16754 
    16755 > color sel #d6d6ffff
    16756 
    16757 > select #3/B:263 #4/A:263 #10/D,A:263
    16758 
    16759 36 atoms, 32 bonds, 4 residues, 3 models selected 
    16760 
    16761 > select #3/B:263-265 #4/A:263-265 #10/D,A:263-265
    16762 
    16763 84 atoms, 80 bonds, 12 residues, 3 models selected 
    16764 
    16765 > color sel #dad9ffff
    16766 
    16767 > select #3/B:266 #4/A:266 #10/D,A:266
    16768 
    16769 16 atoms, 12 bonds, 4 residues, 3 models selected 
    16770 
    16771 > select #3/B:266-267 #4/A:266-267 #10/D,A:266-267
    16772 
    16773 44 atoms, 44 bonds, 8 residues, 3 models selected 
    16774 
    16775 > color sel #cfcfffff
    16776 
    16777 > color sel #d0cfffff
    16778 
    16779 > color sel #d0d0ffff
    16780 
    16781 > color sel #cecbffff
    16782 
    16783 > select #3/B:268-269 #4/A:268-269 #10/D,A:268-269
    16784 
    16785 96 atoms, 104 bonds, 8 residues, 3 models selected 
    16786 
    16787 > select #3/B:268-273 #4/A:268-273 #10/D,A:268-273
    16788 
    16789 220 atoms, 228 bonds, 24 residues, 3 models selected 
    16790 
    16791 > color sel #d3d1ffff
    16792 
    16793 > select #3/B:274 #4/A:274 #10/D,A:274
    16794 
    16795 36 atoms, 32 bonds, 4 residues, 3 models selected 
    16796 
    16797 > select #3/B:274-275 #4/A:274-275 #10/D,A:274-275
    16798 
    16799 68 atoms, 64 bonds, 8 residues, 3 models selected 
    16800 
    16801 > color sel #c3c6ffff
    16802 
    16803 > select #3/B:276 #4/A:276 #10/D,A:276
    16804 
    16805 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16806 
    16807 > select #3/B:276-277 #4/A:276-277 #10/D,A:276-277
    16808 
    16809 76 atoms, 76 bonds, 8 residues, 3 models selected 
    16810 
    16811 > color sel #d1d4ffff
    16812 
    16813 > select #3/B:278-279 #4/A:278-279 #10/D,A:278-279
    16814 
    16815 76 atoms, 76 bonds, 8 residues, 3 models selected 
    16816 
    16817 > select #3/B:278-279 #4/A:278-279 #10/D,A:278-279
    16818 
    16819 76 atoms, 76 bonds, 8 residues, 3 models selected 
    16820 
    16821 > color sel #dddcffff
    16822 
    16823 > select #3/B:287-288 #4/A:287-288 #10/D,A:287-288
    16824 
    16825 56 atoms, 52 bonds, 8 residues, 3 models selected 
    16826 
    16827 > select #3/B:287-298 #4/A:287-298 #10/D,A:287-298
    16828 
    16829 340 atoms, 340 bonds, 48 residues, 3 models selected 
    16830 
    16831 > select #3/B:287-298 #4/A:287-298 #10/D,A:287-298
    16832 
    16833 340 atoms, 340 bonds, 48 residues, 3 models selected 
    16834 
    16835 > select #3/B:287-300 #4/A:287-300 #10/D,A:287-300
    16836 
    16837 412 atoms, 412 bonds, 56 residues, 3 models selected 
    16838 
    16839 > select #3/B:287-288 #4/A:287-288 #10/D,A:287-288
    16840 
    16841 56 atoms, 52 bonds, 8 residues, 3 models selected 
    16842 
    16843 > select #3/B:287-299 #4/A:287-299 #10/D,A:287-299
    16844 
    16845 384 atoms, 384 bonds, 52 residues, 3 models selected 
    16846 
    16847 > color sel #d3d2ffff
    16848 
    16849 > color sel #cbccffff
    16850 
    16851 > select #3/B:300 #4/A:300 #10/D,A:300
    16852 
    16853 28 atoms, 24 bonds, 4 residues, 3 models selected 
    16854 
    16855 > select #3/B:300-309 #4/A:300-309 #10/D,A:300-309
    16856 
    16857 272 atoms, 268 bonds, 40 residues, 3 models selected 
    16858 
    16859 > color sel #bfc3ffff
    16860 
    16861 > select #3/B:310 #4/A:310 #10/D,A:310
    16862 
    16863 36 atoms, 32 bonds, 4 residues, 3 models selected 
    16864 
    16865 > select #3/B:310 #4/A:310 #10/D,A:310
    16866 
    16867 36 atoms, 32 bonds, 4 residues, 3 models selected 
    16868 
    16869 > color sel #c8ceffff
    16870 
    16871 > select #3/B:311-312 #4/A:311-312 #10/D,A:311-312
    16872 
    16873 80 atoms, 84 bonds, 8 residues, 3 models selected 
    16874 
    16875 > select #3/B:311-333 #4/A:311-333 #10/D,A:311-333
    16876 
    16877 756 atoms, 784 bonds, 1 pseudobond, 92 residues, 4 models selected 
    16878 
    16879 > color (#3-4,10 & sel) #d2d3ffff
    16880 
    16881 > select #3/B:334 #4/A:334 #10/D,A:334
    16882 
    16883 36 atoms, 32 bonds, 4 residues, 3 models selected 
    16884 
    16885 > select #3/B:334 #4/A:334 #10/D,A:334
    16886 
    16887 36 atoms, 32 bonds, 4 residues, 3 models selected 
    16888 
    16889 > color sel #cbd5ffff
    16890 
    16891 > color sel #cbceffff
    16892 
    16893 > select #3/B:335 #4/A:335 #10/D,A:335
    16894 
    16895 32 atoms, 28 bonds, 4 residues, 3 models selected 
    16896 
    16897 > select #3/B:335-340 #4/A:335-340 #10/D,A:335-340
    16898 
    16899 208 atoms, 208 bonds, 24 residues, 3 models selected 
    16900 
    16901 > color sel #ceceffff
    16902 
    16903 > color sel #cfd1ffff
    16904 
    16905 > select #3/B:341 #4/A:341 #10/D,A:341
    16906 
    16907 36 atoms, 32 bonds, 4 residues, 3 models selected 
    16908 
    16909 > select #3/B:341-349 #4/A:341-349 #10/D,A:341-349
    16910 
    16911 288 atoms, 284 bonds, 36 residues, 3 models selected 
    16912 
    16913 > color sel #caceffff
    16914 
    16915 > color sel #c8ccffff
    16916 
    16917 > color sel #c3caffff
    16918 
    16919 > color sel #bdcbffff
    16920 
    16921 > select #3/B:350 #4/A:350 #10/D,A:350
    16922 
    16923 28 atoms, 24 bonds, 4 residues, 3 models selected 
    16924 
    16925 > select #3/B:350-352 #4/A:350-352 #10/D,A:350-352
    16926 
    16927 76 atoms, 72 bonds, 12 residues, 3 models selected 
    16928 
    16929 > color sel #ffebf3ff
    16930 
    16931 > color sel #ffe8efff
    16932 
    16933 > select #3/B:301-302 #4/A:301-302 #10/D,A:301-302
    16934 
    16935 56 atoms, 52 bonds, 8 residues, 3 models selected 
    16936 
    16937 > select #3/B:301-310 #4/A:301-310 #10/D,A:301-310
    16938 
    16939 280 atoms, 276 bonds, 40 residues, 3 models selected 
    16940 
    16941 > color sel #8c8cf7ff
    16942 
    16943 > color sel #8587ffff
    16944 
    16945 > color sel #8282ffff
    16946 
    16947 > color sel #7c83ffff
    16948 
    16949 > select add #3
    16950 
    16951 3011 atoms, 3079 bonds, 45 pseudobonds, 382 residues, 5 models selected 
    16952 
    16953 > select add #4
    16954 
    16955 5742 atoms, 5882 bonds, 90 pseudobonds, 724 residues, 5 models selected 
    16956 
    16957 > select subtract #3
    16958 
    16959 2941 atoms, 3010 bonds, 45 pseudobonds, 372 residues, 4 models selected 
    16960 
    16961 > select subtract #4
    16962 
    16963 140 atoms, 138 bonds, 20 residues, 1 model selected 
    16964 
    16965 > select add #12
    16966 
    16967 3541 atoms, 3631 bonds, 462 residues, 2 models selected 
    16968 
    16969 > select add #10
    16970 
    16971 12337 atoms, 12617 bonds, 1560 residues, 2 models selected 
    16972 
    16973 > select subtract #10
    16974 
    16975 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    16976 
    16977 > ui mousemode right "translate selected models"
    16978 
    16979 > view matrix models
    16980 > #12,0.82562,-0.34186,-0.44887,168.94,-0.52138,-0.76634,-0.37535,482.82,-0.21567,0.54392,-0.81094,284.87
    16981 
    16982 > view matrix models
    16983 > #12,0.82562,-0.34186,-0.44887,169.91,-0.52138,-0.76634,-0.37535,479.02,-0.21567,0.54392,-0.81094,283.58
    16984 
    16985 > view matrix models
    16986 > #12,0.82562,-0.34186,-0.44887,170.32,-0.52138,-0.76634,-0.37535,480.41,-0.21567,0.54392,-0.81094,282.28
    16987 
    16988 > view matrix models
    16989 > #12,0.82562,-0.34186,-0.44887,171.18,-0.52138,-0.76634,-0.37535,479.61,-0.21567,0.54392,-0.81094,282.22
    16990 
    16991 > ui mousemode right zoom
    16992 
    16993 > ui mousemode right "rotate selected models"
    16994 
    16995 > view matrix models
    16996 > #12,0.94747,-0.06803,0.31253,-40.388,-0.27852,-0.65592,0.70156,212.57,0.15727,-0.75175,-0.64041,392.6
    16997 
    16998 > view matrix models
    16999 > #12,0.65713,0.16685,-0.73508,171.79,0.09209,-0.98566,-0.1414,332.31,-0.74813,0.025227,-0.66307,473.05
    17000 
    17001 > view matrix models
    17002 > #12,0.95731,-0.18789,-0.21965,72.476,-0.15301,-0.97411,0.16641,333.66,-0.24523,-0.1257,-0.96128,433.82
    17003 
    17004 > view matrix models
    17005 > #12,0.96798,-0.24602,-0.049963,50.221,-0.17279,-0.7973,0.57833,234.35,-0.18211,-0.55117,-0.81427,467.97
    17006 
    17007 > ui mousemode right "translate selected models"
    17008 
    17009 > ui mousemode right zoom
    17010 
    17011 > show #!9 models
    17012 
    17013 > fitmap #12 inMap #9
    17014 
    17015 Fit molecule F562a.pdb (#12) to map sNS1wt-Fab562.mrc (#9) using 3401 atoms 
    17016 average map value = 0.09851, steps = 252 
    17017 shifted from previous position = 4.87 
    17018 rotated from previous position = 66.7 degrees 
    17019 atoms outside contour = 1988, contour level = 0.11015 
    17020  
    17021 Position of F562a.pdb (#12) relative to sNS1wt-Fab562.mrc (#9) coordinates: 
    17022 Matrix rotation and translation 
    17023 -0.10506635 -0.15760122 0.98189762 53.59780496 
    17024 -0.09254653 -0.98152811 -0.16744470 397.44466486 
    17025 0.99014960 -0.10846402 0.08854013 -3.70228919 
    17026 Axis 0.66872859 -0.09356170 0.73759629 
    17027 Axis point 22.53945284 199.32977295 0.00000000 
    17028 Rotation angle (degrees) 177.47248714 
    17029 Shift along axis -4.07401058 
    17030  
    17031 
    17032 > volume #9 level 0.08287
    17033 
    17034 > volume #9 level 0.06241
    17035 
    17036 > hide #10 models
    17037 
    17038 > show #10 models
    17039 
    17040 > hide #10 models
    17041 
    17042 > color #5 #7b137cff models
    17043 
    17044 > color #5 #7c0e7cff models
    17045 
    17046 > color #5 #fe1effff models
    17047 
    17048 > color #5 #ee1cefff models
    17049 
    17050 > hide #5 models
    17051 
    17052 > show #5 models
    17053 
    17054 > hide #6 models
    17055 
    17056 > show #6 models
    17057 
    17058 > hide #6 models
    17059 
    17060 > show #6 models
    17061 
    17062 > hide #6 models
    17063 
    17064 > show #6 models
    17065 
    17066 > show #7 models
    17067 
    17068 > hide #7 models
    17069 
    17070 > hide #4 models
    17071 
    17072 > show #4 models
    17073 
    17074 > hide #8 models
    17075 
    17076 > show #8 models
    17077 
    17078 > select add #2
    17079 
    17080 5068 atoms, 5183 bonds, 29 pseudobonds, 649 residues, 4 models selected 
    17081 
    17082 > select subtract #2
    17083 
    17084 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    17085 
    17086 > select add #2
    17087 
    17088 5068 atoms, 5183 bonds, 29 pseudobonds, 649 residues, 4 models selected 
    17089 
    17090 > select subtract #2
    17091 
    17092 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    17093 
    17094 > select subtract #12
    17095 
    17096 Nothing selected 
    17097 
    17098 > select add #2
    17099 
    17100 1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected 
    17101 
    17102 > select subtract #2
    17103 
    17104 Nothing selected 
    17105 
    17106 > select add #2
    17107 
    17108 1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected 
    17109 
    17110 > select add #1
    17111 
    17112 3334 atoms, 3380 bonds, 58 pseudobonds, 414 residues, 4 models selected 
    17113 
    17114 > select add #3
    17115 
    17116 6135 atoms, 6252 bonds, 103 pseudobonds, 766 residues, 6 models selected 
    17117 
    17118 > select add #4
    17119 
    17120 8936 atoms, 9124 bonds, 148 pseudobonds, 1118 residues, 7 models selected 
    17121 
    17122 > ui mousemode right "translate selected models"
    17123 
    17124 > view matrix models
    17125 > #1,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#2,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#3,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#4,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17126 
    17127 > view matrix models
    17128 > #1,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#2,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#3,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#4,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17129 
    17130 > view matrix models
    17131 > #1,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#2,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#3,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#4,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17132 
    17133 > ui mousemode right zoom
    17134 
    17135 > ui mousemode right "translate selected models"
    17136 
    17137 > ui mousemode right "rotate selected models"
    17138 
    17139 > view matrix models
    17140 > #1,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#2,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#3,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#4,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17141 
    17142 > view matrix models
    17143 > #1,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#2,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#3,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#4,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17144 
    17145 > view matrix models
    17146 > #1,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#2,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#3,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#4,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17147 
    17148 > view matrix models
    17149 > #1,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#2,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#3,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#4,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17150 
    17151 > view matrix models
    17152 > #1,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#2,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#3,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#4,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17153 
    17154 > ui mousemode right "translate selected models"
    17155 
    17156 > view matrix models
    17157 > #1,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#2,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#3,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#4,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17158 
    17159 > ui mousemode right zoom
    17160 
    17161 > ui mousemode right "rotate selected models"
    17162 
    17163 > view matrix models
    17164 > #1,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#2,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#3,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#4,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17165 
    17166 > view matrix models
    17167 > #1,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#2,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#3,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#4,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17168 
    17169 > ui mousemode right "translate selected models"
    17170 
    17171 > ui mousemode right "rotate selected models"
    17172 
    17173 > ui mousemode right zoom
    17174 
    17175 > ui mousemode right "rotate selected models"
    17176 
    17177 > view matrix models
    17178 > #1,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#2,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#3,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#4,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17179 
    17180 > view matrix models
    17181 > #1,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#2,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#3,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#4,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17182 
    17183 > view matrix models
    17184 > #1,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#2,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#3,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#4,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17185 
    17186 > ui mousemode right "translate selected models"
    17187 
    17188 > view matrix models
    17189 > #1,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#2,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#3,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#4,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17190 
    17191 > ui mousemode right zoom
    17192 
    17193 > select subtract #1
    17194 
    17195 7269 atoms, 7434 bonds, 119 pseudobonds, 911 residues, 6 models selected 
    17196 
    17197 > select subtract #2
    17198 
    17199 5602 atoms, 5744 bonds, 90 pseudobonds, 704 residues, 4 models selected 
    17200 
    17201 > select subtract #3
    17202 
    17203 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    17204 
    17205 > select subtract #4
    17206 
    17207 Nothing selected 
    17208 
    17209 > select add #12
    17210 
    17211 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    17212 
    17213 > ui tool show "Show Sequence Viewer"
    17214 
    17215 > sequence chain #12/C
    17216 
    17217 Alignment identifier is 12/C 
    17218 
    17219 > select subtract #12
    17220 
    17221 Nothing selected 
    17222 
    17223 > select #12/C:1
    17224 
    17225 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17226 
    17227 > select #12/C
    17228 
    17229 1769 atoms, 1825 bonds, 228 residues, 1 model selected 
    17230 
    17231 > hide #!9 models
    17232 
    17233 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    17234 > (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
    17235 > MS_recolored.cxs" includeMaps true
    17236 
    17237 > show #!9 models
    17238 
    17239 > select add #12
    17240 
    17241 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    17242 
    17243 > select subtract #12
    17244 
    17245 Nothing selected 
    17246 
    17247 > select add #2
    17248 
    17249 1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected 
    17250 
    17251 > select add #3
    17252 
    17253 4468 atoms, 4562 bonds, 74 pseudobonds, 559 residues, 5 models selected 
    17254 
    17255 > select add #4
    17256 
    17257 7269 atoms, 7434 bonds, 119 pseudobonds, 911 residues, 6 models selected 
    17258 
    17259 > select add #5
    17260 
    17261 7269 atoms, 7434 bonds, 173 pseudobonds, 911 residues, 6 models selected 
    17262 
    17263 > select subtract #5
    17264 
    17265 7269 atoms, 7434 bonds, 71 pseudobonds, 911 residues, 5 models selected 
    17266 
    17267 > select add #6
    17268 
    17269 7269 atoms, 7434 bonds, 142 pseudobonds, 911 residues, 5 models selected 
    17270 
    17271 > select subtract #6
    17272 
    17273 7269 atoms, 7434 bonds, 49 pseudobonds, 911 residues, 4 models selected 
    17274 
    17275 > select add #7
    17276 
    17277 7269 atoms, 7434 bonds, 97 pseudobonds, 911 residues, 4 models selected 
    17278 
    17279 > select subtract #7
    17280 
    17281 7269 atoms, 7434 bonds, 911 residues, 3 models selected 
    17282 
    17283 > select add #1
    17284 
    17285 8936 atoms, 9124 bonds, 29 pseudobonds, 1118 residues, 6 models selected 
    17286 
    17287 > select subtract #2
    17288 
    17289 7269 atoms, 7434 bonds, 29 pseudobonds, 911 residues, 5 models selected 
    17290 
    17291 > select add #2
    17292 
    17293 8936 atoms, 9124 bonds, 58 pseudobonds, 1118 residues, 6 models selected 
    17294 
    17295 > select subtract #3
    17296 
    17297 6135 atoms, 6252 bonds, 58 pseudobonds, 766 residues, 5 models selected 
    17298 
    17299 > select add #3
    17300 
    17301 8936 atoms, 9124 bonds, 103 pseudobonds, 1118 residues, 7 models selected 
    17302 
    17303 > select subtract #4
    17304 
    17305 6135 atoms, 6252 bonds, 103 pseudobonds, 766 residues, 6 models selected 
    17306 
    17307 > select add #4
    17308 
    17309 8936 atoms, 9124 bonds, 148 pseudobonds, 1118 residues, 7 models selected 
    17310 
    17311 > ui mousemode right "translate selected models"
    17312 
    17313 > view matrix models
    17314 > #1,0.9833,0.18192,0.0055417,-36.253,-0.18172,0.983,-0.026391,41.588,-0.010249,0.024943,0.99964,-2.0695,#2,0.9833,0.18192,0.0055417,-36.253,-0.18172,0.983,-0.026391,41.588,-0.010249,0.024943,0.99964,-2.0695,#3,0.9833,0.18192,0.0055417,-36.253,-0.18172,0.983,-0.026391,41.588,-0.010249,0.024943,0.99964,-2.0695,#4,0.9833,0.18192,0.0055417,-36.253,-0.18172,0.983,-0.026391,41.588,-0.010249,0.024943,0.99964,-2.0695,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17315 
    17316 > view matrix models
    17317 > #1,0.9833,0.18192,0.0055417,-36.847,-0.18172,0.983,-0.026391,41.972,-0.010249,0.024943,0.99964,-2.0445,#2,0.9833,0.18192,0.0055417,-36.847,-0.18172,0.983,-0.026391,41.972,-0.010249,0.024943,0.99964,-2.0445,#3,0.9833,0.18192,0.0055417,-36.847,-0.18172,0.983,-0.026391,41.972,-0.010249,0.024943,0.99964,-2.0445,#4,0.9833,0.18192,0.0055417,-36.847,-0.18172,0.983,-0.026391,41.972,-0.010249,0.024943,0.99964,-2.0445,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17318 
    17319 > volume #9 level 0.07332
    17320 
    17321 > volume #9 level 0.1102
    17322 
    17323 > view matrix models
    17324 > #1,0.9833,0.18192,0.0055417,-36.452,-0.18172,0.983,-0.026391,42.252,-0.010249,0.024943,0.99964,-1.3599,#2,0.9833,0.18192,0.0055417,-36.452,-0.18172,0.983,-0.026391,42.252,-0.010249,0.024943,0.99964,-1.3599,#3,0.9833,0.18192,0.0055417,-36.452,-0.18172,0.983,-0.026391,42.252,-0.010249,0.024943,0.99964,-1.3599,#4,0.9833,0.18192,0.0055417,-36.452,-0.18172,0.983,-0.026391,42.252,-0.010249,0.024943,0.99964,-1.3599,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17325 
    17326 > view matrix models
    17327 > #1,0.9833,0.18192,0.0055417,-36.881,-0.18172,0.983,-0.026391,42.629,-0.010249,0.024943,0.99964,-1.3368,#2,0.9833,0.18192,0.0055417,-36.881,-0.18172,0.983,-0.026391,42.629,-0.010249,0.024943,0.99964,-1.3368,#3,0.9833,0.18192,0.0055417,-36.881,-0.18172,0.983,-0.026391,42.629,-0.010249,0.024943,0.99964,-1.3368,#4,0.9833,0.18192,0.0055417,-36.881,-0.18172,0.983,-0.026391,42.629,-0.010249,0.024943,0.99964,-1.3368,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17328 
    17329 > ui mousemode right "rotate selected models"
    17330 
    17331 > view matrix models
    17332 > #1,0.98119,0.19216,-0.018632,-33.726,-0.19238,0.98126,-0.010945,41.781,0.016179,0.014324,0.99977,-3.9218,#2,0.98119,0.19216,-0.018632,-33.726,-0.19238,0.98126,-0.010945,41.781,0.016179,0.014324,0.99977,-3.9218,#3,0.98119,0.19216,-0.018632,-33.726,-0.19238,0.98126,-0.010945,41.781,0.016179,0.014324,0.99977,-3.9218,#4,0.98119,0.19216,-0.018632,-33.726,-0.19238,0.98126,-0.010945,41.781,0.016179,0.014324,0.99977,-3.9218,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17333 
    17334 > view matrix models
    17335 > #1,0.98027,0.19654,-0.021274,-33.885,-0.19691,0.98027,-0.017135,43.973,0.017487,0.020986,0.99963,-5.3968,#2,0.98027,0.19654,-0.021274,-33.885,-0.19691,0.98027,-0.017135,43.973,0.017487,0.020986,0.99963,-5.3968,#3,0.98027,0.19654,-0.021274,-33.885,-0.19691,0.98027,-0.017135,43.973,0.017487,0.020986,0.99963,-5.3968,#4,0.98027,0.19654,-0.021274,-33.885,-0.19691,0.98027,-0.017135,43.973,0.017487,0.020986,0.99963,-5.3968,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17336 
    17337 > ui mousemode right zoom
    17338 
    17339 > ui mousemode right "rotate selected models"
    17340 
    17341 > view matrix models
    17342 > #1,0.98134,0.18921,-0.034256,-30.12,-0.19038,0.98109,-0.034836,46.156,0.027017,0.040708,0.99881,-10.665,#2,0.98134,0.18921,-0.034256,-30.12,-0.19038,0.98109,-0.034836,46.156,0.027017,0.040708,0.99881,-10.665,#3,0.98134,0.18921,-0.034256,-30.12,-0.19038,0.98109,-0.034836,46.156,0.027017,0.040708,0.99881,-10.665,#4,0.98134,0.18921,-0.034256,-30.12,-0.19038,0.98109,-0.034836,46.156,0.027017,0.040708,0.99881,-10.665,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17343 
    17344 > view matrix models
    17345 > #1,0.98224,0.18112,-0.048941,-25.843,-0.18399,0.98094,-0.062517,50.521,0.036685,0.070412,0.99684,-17.635,#2,0.98224,0.18112,-0.048941,-25.843,-0.18399,0.98094,-0.062517,50.521,0.036685,0.070412,0.99684,-17.635,#3,0.98224,0.18112,-0.048941,-25.843,-0.18399,0.98094,-0.062517,50.521,0.036685,0.070412,0.99684,-17.635,#4,0.98224,0.18112,-0.048941,-25.843,-0.18399,0.98094,-0.062517,50.521,0.036685,0.070412,0.99684,-17.635,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17346 
    17347 > view matrix models
    17348 > #1,0.99655,0.077131,0.030705,-24.147,-0.074724,0.99453,-0.073036,31.058,-0.03617,0.070489,0.99686,-5.0238,#2,0.99655,0.077131,0.030705,-24.147,-0.074724,0.99453,-0.073036,31.058,-0.03617,0.070489,0.99686,-5.0238,#3,0.99655,0.077131,0.030705,-24.147,-0.074724,0.99453,-0.073036,31.058,-0.03617,0.070489,0.99686,-5.0238,#4,0.99655,0.077131,0.030705,-24.147,-0.074724,0.99453,-0.073036,31.058,-0.03617,0.070489,0.99686,-5.0238,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17349 
    17350 > view matrix models
    17351 > #1,0.98562,0.16498,-0.036586,-25.784,-0.16709,0.98381,-0.064738,47.47,0.025313,0.06992,0.99723,-15.64,#2,0.98562,0.16498,-0.036586,-25.784,-0.16709,0.98381,-0.064738,47.47,0.025313,0.06992,0.99723,-15.64,#3,0.98562,0.16498,-0.036586,-25.784,-0.16709,0.98381,-0.064738,47.47,0.025313,0.06992,0.99723,-15.64,#4,0.98562,0.16498,-0.036586,-25.784,-0.16709,0.98381,-0.064738,47.47,0.025313,0.06992,0.99723,-15.64,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17352 
    17353 > view matrix models
    17354 > #1,0.98733,0.14574,-0.062757,-17.252,-0.15017,0.98598,-0.072746,45.698,0.051275,0.081248,0.99537,-21.942,#2,0.98733,0.14574,-0.062757,-17.252,-0.15017,0.98598,-0.072746,45.698,0.051275,0.081248,0.99537,-21.942,#3,0.98733,0.14574,-0.062757,-17.252,-0.15017,0.98598,-0.072746,45.698,0.051275,0.081248,0.99537,-21.942,#4,0.98733,0.14574,-0.062757,-17.252,-0.15017,0.98598,-0.072746,45.698,0.051275,0.081248,0.99537,-21.942,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17355 
    17356 > view matrix models
    17357 > #1,0.98899,0.13015,-0.070408,-13.054,-0.13512,0.98828,-0.071057,42.311,0.060334,0.079788,0.99498,-23.16,#2,0.98899,0.13015,-0.070408,-13.054,-0.13512,0.98828,-0.071057,42.311,0.060334,0.079788,0.99498,-23.16,#3,0.98899,0.13015,-0.070408,-13.054,-0.13512,0.98828,-0.071057,42.311,0.060334,0.079788,0.99498,-23.16,#4,0.98899,0.13015,-0.070408,-13.054,-0.13512,0.98828,-0.071057,42.311,0.060334,0.079788,0.99498,-23.16,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17358 
    17359 > view matrix models
    17360 > #1,0.98612,0.15567,-0.057673,-19.94,-0.1595,0.98477,-0.069167,46.847,0.046028,0.077406,0.99594,-20.407,#2,0.98612,0.15567,-0.057673,-19.94,-0.1595,0.98477,-0.069167,46.847,0.046028,0.077406,0.99594,-20.407,#3,0.98612,0.15567,-0.057673,-19.94,-0.1595,0.98477,-0.069167,46.847,0.046028,0.077406,0.99594,-20.407,#4,0.98612,0.15567,-0.057673,-19.94,-0.1595,0.98477,-0.069167,46.847,0.046028,0.077406,0.99594,-20.407,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17361 
    17362 > view matrix models
    17363 > #1,0.97272,0.12606,-0.19474,14.958,-0.15151,0.98092,-0.12182,56.628,0.17567,0.148,0.97326,-52.111,#2,0.97272,0.12606,-0.19474,14.958,-0.15151,0.98092,-0.12182,56.628,0.17567,0.148,0.97326,-52.111,#3,0.97272,0.12606,-0.19474,14.958,-0.15151,0.98092,-0.12182,56.628,0.17567,0.148,0.97326,-52.111,#4,0.97272,0.12606,-0.19474,14.958,-0.15151,0.98092,-0.12182,56.628,0.17567,0.148,0.97326,-52.111,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17364 
    17365 > view matrix models
    17366 > #1,0.97391,0.04287,-0.22284,36.17,-0.072834,0.98909,-0.12804,42.459,0.21492,0.14093,0.96641,-56.313,#2,0.97391,0.04287,-0.22284,36.17,-0.072834,0.98909,-0.12804,42.459,0.21492,0.14093,0.96641,-56.313,#3,0.97391,0.04287,-0.22284,36.17,-0.072834,0.98909,-0.12804,42.459,0.21492,0.14093,0.96641,-56.313,#4,0.97391,0.04287,-0.22284,36.17,-0.072834,0.98909,-0.12804,42.459,0.21492,0.14093,0.96641,-56.313,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17367 
    17368 > view matrix models
    17369 > #1,0.97437,0.073896,-0.21246,28.12,-0.1022,0.98682,-0.12546,47.556,0.20039,0.14395,0.96908,-54.857,#2,0.97437,0.073896,-0.21246,28.12,-0.1022,0.98682,-0.12546,47.556,0.20039,0.14395,0.96908,-54.857,#3,0.97437,0.073896,-0.21246,28.12,-0.1022,0.98682,-0.12546,47.556,0.20039,0.14395,0.96908,-54.857,#4,0.97437,0.073896,-0.21246,28.12,-0.1022,0.98682,-0.12546,47.556,0.20039,0.14395,0.96908,-54.857,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17370 
    17371 > view matrix models
    17372 > #1,0.99279,0.030411,-0.11595,14.123,-0.049395,0.98513,-0.16456,46.325,0.10922,0.1691,0.97953,-45.703,#2,0.99279,0.030411,-0.11595,14.123,-0.049395,0.98513,-0.16456,46.325,0.10922,0.1691,0.97953,-45.703,#3,0.99279,0.030411,-0.11595,14.123,-0.049395,0.98513,-0.16456,46.325,0.10922,0.1691,0.97953,-45.703,#4,0.99279,0.030411,-0.11595,14.123,-0.049395,0.98513,-0.16456,46.325,0.10922,0.1691,0.97953,-45.703,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17373 
    17374 > view matrix models
    17375 > #1,0.99322,0.026282,-0.11323,14.297,-0.042299,0.98904,-0.14147,39.767,0.10827,0.1453,0.98345,-41.768,#2,0.99322,0.026282,-0.11323,14.297,-0.042299,0.98904,-0.14147,39.767,0.10827,0.1453,0.98345,-41.768,#3,0.99322,0.026282,-0.11323,14.297,-0.042299,0.98904,-0.14147,39.767,0.10827,0.1453,0.98345,-41.768,#4,0.99322,0.026282,-0.11323,14.297,-0.042299,0.98904,-0.14147,39.767,0.10827,0.1453,0.98345,-41.768,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17376 
    17377 > view matrix models
    17378 > #1,0.98565,0.068261,-0.15439,15.736,-0.087789,0.98846,-0.12342,44.288,0.14419,0.13521,0.98027,-45.509,#2,0.98565,0.068261,-0.15439,15.736,-0.087789,0.98846,-0.12342,44.288,0.14419,0.13521,0.98027,-45.509,#3,0.98565,0.068261,-0.15439,15.736,-0.087789,0.98846,-0.12342,44.288,0.14419,0.13521,0.98027,-45.509,#4,0.98565,0.068261,-0.15439,15.736,-0.087789,0.98846,-0.12342,44.288,0.14419,0.13521,0.98027,-45.509,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17379 
    17380 > view matrix models
    17381 > #1,0.98793,0.057456,-0.14382,15.313,-0.075925,0.98907,-0.12641,42.682,0.13499,0.13581,0.9815,-44.253,#2,0.98793,0.057456,-0.14382,15.313,-0.075925,0.98907,-0.12641,42.682,0.13499,0.13581,0.9815,-44.253,#3,0.98793,0.057456,-0.14382,15.313,-0.075925,0.98907,-0.12641,42.682,0.13499,0.13581,0.9815,-44.253,#4,0.98793,0.057456,-0.14382,15.313,-0.075925,0.98907,-0.12641,42.682,0.13499,0.13581,0.9815,-44.253,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17382 
    17383 > ui mousemode right zoom
    17384 
    17385 > ui mousemode right select
    17386 
    17387 > select clear
    17388 
    17389 > select #12/D:25
    17390 
    17391 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17392 
    17393 > select clear
    17394 
    17395 > select add #2
    17396 
    17397 1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected 
    17398 
    17399 > select subtract #2
    17400 
    17401 Nothing selected 
    17402 
    17403 > select add #3
    17404 
    17405 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    17406 
    17407 > select add #9
    17408 
    17409 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 5 models selected 
    17410 
    17411 > select subtract #9
    17412 
    17413 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    17414 
    17415 > select add #9
    17416 
    17417 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 5 models selected 
    17418 
    17419 > select subtract #9
    17420 
    17421 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    17422 
    17423 > select clear
    17424 
    17425 > select add #10
    17426 
    17427 8936 atoms, 9124 bonds, 1118 residues, 1 model selected 
    17428 
    17429 > select subtract #10
    17430 
    17431 Nothing selected 
    17432 
    17433 > select add #10
    17434 
    17435 8936 atoms, 9124 bonds, 1118 residues, 1 model selected 
    17436 
    17437 > select subtract #10
    17438 
    17439 Nothing selected 
    17440 
    17441 > select add #12
    17442 
    17443 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    17444 
    17445 > select clear
    17446 
    17447 > select add #12
    17448 
    17449 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    17450 
    17451 > ui mousemode right "translate selected models"
    17452 
    17453 > view matrix models
    17454 > #12,0.82559,-0.34194,-0.44887,169.92,-0.52142,-0.76637,-0.37524,483.13,-0.21569,0.54384,-0.811,285.08
    17455 
    17456 > view matrix models
    17457 > #12,0.82559,-0.34194,-0.44887,170.04,-0.52142,-0.76637,-0.37524,483.13,-0.21569,0.54384,-0.811,285.05
    17458 
    17459 > view matrix models
    17460 > #12,0.82559,-0.34194,-0.44887,170.05,-0.52142,-0.76637,-0.37524,482.88,-0.21569,0.54384,-0.811,285.15
    17461 
    17462 > view matrix models
    17463 > #12,0.82559,-0.34194,-0.44887,170.12,-0.52142,-0.76637,-0.37524,482.29,-0.21569,0.54384,-0.811,285.24
    17464 
    17465 > view matrix models
    17466 > #12,0.82559,-0.34194,-0.44887,170.68,-0.52142,-0.76637,-0.37524,482.21,-0.21569,0.54384,-0.811,285.02
    17467 
    17468 > view matrix models
    17469 > #12,0.82559,-0.34194,-0.44887,171.91,-0.52142,-0.76637,-0.37524,481.88,-0.21569,0.54384,-0.811,284.81
    17470 
    17471 > ui mousemode right zoom
    17472 
    17473 > ui mousemode right "translate selected models"
    17474 
    17475 > ui mousemode right "rotate selected models"
    17476 
    17477 > view matrix models
    17478 > #12,0.85565,-0.40349,-0.32413,153.63,-0.51632,-0.70873,-0.48074,489.16,-0.035744,0.5787,-0.81476,236.91
    17479 
    17480 > view matrix models
    17481 > #12,0.86103,-0.44709,-0.24235,145.6,-0.49595,-0.84364,-0.20569,459.53,-0.11249,0.29729,-0.94814,328.19
    17482 
    17483 > view matrix models
    17484 > #12,0.8588,-0.45952,-0.22652,145.52,-0.47641,-0.87891,-0.023255,428.91,-0.18841,0.12789,-0.97373,380.47
    17485 
    17486 > view matrix models
    17487 > #12,0.86899,-0.46074,-0.18049,135.2,-0.46357,-0.88559,0.028727,417.87,-0.17308,0.058707,-0.98316,390.72
    17488 
    17489 > view matrix models
    17490 > #12,0.65716,-0.59002,-0.46906,258.92,-0.69689,-0.71272,-0.079835,461.58,-0.2872,0.37935,-0.87955,342.79
    17491 
    17492 > view matrix models
    17493 > #12,0.68636,-0.55214,-0.47334,246.12,-0.67684,-0.72309,-0.13797,468.95,-0.26609,0.41507,-0.87001,329.82
    17494 
    17495 > ui mousemode right "translate selected models"
    17496 
    17497 > view matrix models
    17498 > #12,0.68636,-0.55214,-0.47334,247.09,-0.67684,-0.72309,-0.13797,468.4,-0.26609,0.41507,-0.87001,329.01
    17499 
    17500 > view matrix models
    17501 > #12,0.68636,-0.55214,-0.47334,245.66,-0.67684,-0.72309,-0.13797,466.52,-0.26609,0.41507,-0.87001,329.78
    17502 
    17503 > ui mousemode right "rotate selected models"
    17504 
    17505 > ui mousemode right zoom
    17506 
    17507 > ui mousemode right select
    17508 
    17509 > select clear
    17510 
    17511 > select add #3
    17512 
    17513 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    17514 
    17515 > ui mousemode right "rotate selected models"
    17516 
    17517 > select subtract #3
    17518 
    17519 Nothing selected 
    17520 
    17521 > select add #3
    17522 
    17523 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    17524 
    17525 > select subtract #3
    17526 
    17527 Nothing selected 
    17528 
    17529 > select add #3
    17530 
    17531 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    17532 
    17533 > select subtract #3
    17534 
    17535 Nothing selected 
    17536 
    17537 > select add #12
    17538 
    17539 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    17540 
    17541 > view matrix models
    17542 > #12,0.21516,0.9712,0.10233,-13.578,-0.81472,0.12074,0.56714,225.64,0.53845,-0.2054,0.81724,-48.675
    17543 
    17544 > view matrix models
    17545 > #12,0.43037,0.90252,0.01538,-36.834,-0.77438,0.3604,0.52005,182.2,0.46381,-0.23572,0.854,-32.23
    17546 
    17547 > view matrix models
    17548 > #12,0.29061,0.92832,-0.23189,35.263,-0.85384,0.36098,0.37503,226.45,0.43186,0.089009,0.89754,-89.643
    17549 
    17550 > view matrix models
    17551 > #12,0.19232,0.92899,-0.31622,73.22,-0.85462,0.31693,0.41132,227.99,0.48233,0.19114,0.85488,-112.01
    17552 
    17553 > view matrix models
    17554 > #12,0.16773,0.93259,-0.3196,78.977,-0.8501,0.30098,0.43213,226.06,0.49919,0.19921,0.84328,-115.36
    17555 
    17556 > view matrix models
    17557 > #12,-0.012017,0.94523,-0.32618,120.28,-0.79463,0.18898,0.57693,207.14,0.60697,0.26612,0.74884,-135.87
    17558 
    17559 > ui mousemode right zoom
    17560 
    17561 > ui mousemode right "rotate selected models"
    17562 
    17563 > view matrix models
    17564 > #12,0.21625,0.97297,0.080975,-10.373,-0.57946,0.061151,0.8127,137.29,0.78579,-0.22267,0.57703,-61.482
    17565 
    17566 > view matrix models
    17567 > #12,0.38482,0.92257,0.027751,-31.819,-0.62434,0.23804,0.744,128.82,0.67979,-0.30363,0.66761,-38.228
    17568 
    17569 > view matrix models
    17570 > #12,0.49592,0.83935,0.22263,-77.775,-0.58873,0.13653,0.79671,129.01,0.63832,-0.52617,0.56186,29.471
    17571 
    17572 > view matrix models
    17573 > #12,0.53883,0.71851,0.43979,-104.96,-0.52134,-0.12567,0.84405,150.98,0.66172,-0.68407,0.30687,96.857
    17574 
    17575 > view matrix models
    17576 > #12,0.58792,0.7378,0.33167,-100.83,-0.43616,-0.056188,0.89812,109.1,0.68127,-0.67268,0.28876,93.441
    17577 
    17578 > view matrix models
    17579 > #12,0.68026,0.64643,0.34551,-108.94,-0.39716,-0.071108,0.91499,99.553,0.61604,-0.75965,0.20837,138.36
    17580 
    17581 > view matrix models
    17582 > #12,0.69449,0.65973,0.28713,-104.32,-0.344,-0.046041,0.93784,78.561,0.63194,-0.75009,0.19497,135.3
    17583 
    17584 > ui mousemode right "translate selected models"
    17585 
    17586 > view matrix models
    17587 > #12,0.69449,0.65973,0.28713,-102.08,-0.344,-0.046041,0.93784,78.11,0.63194,-0.75009,0.19497,133.54
    17588 
    17589 > view matrix models
    17590 > #12,0.69449,0.65973,0.28713,-102.45,-0.344,-0.046041,0.93784,78.386,0.63194,-0.75009,0.19497,133.74
    17591 
    17592 > ui mousemode right "rotate selected models"
    17593 
    17594 > view matrix models
    17595 > #12,0.34284,0.899,0.27252,-59.156,-0.32401,-0.15913,0.93257,94.544,0.88175,-0.40802,0.23673,7.1605
    17596 
    17597 > view matrix models
    17598 > #12,0.30177,0.93844,0.16811,-37.978,-0.40954,-0.031635,0.91174,95.91,0.86093,-0.34399,0.37479,-23.623
    17599 
    17600 > view matrix models
    17601 > #12,0.34216,0.92298,0.17617,-46.197,-0.37936,-0.035844,0.92456,87.272,0.85966,-0.38318,0.33787,-9.8896
    17602 
    17603 > view matrix models
    17604 > #12,0.38667,0.91182,0.1381,-47.994,-0.31103,-0.012038,0.95032,62.414,0.86819,-0.41042,0.27895,3.3167
    17605 
    17606 > select subtract #12
    17607 
    17608 Nothing selected 
    17609 
    17610 > select add #3
    17611 
    17612 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    17613 
    17614 > ui mousemode right zoom
    17615 
    17616 > select add #2
    17617 
    17618 4468 atoms, 4562 bonds, 74 pseudobonds, 559 residues, 5 models selected 
    17619 
    17620 > select add #1
    17621 
    17622 6135 atoms, 6252 bonds, 103 pseudobonds, 766 residues, 6 models selected 
    17623 
    17624 > select add #4
    17625 
    17626 8936 atoms, 9124 bonds, 148 pseudobonds, 1118 residues, 7 models selected 
    17627 
    17628 > ui mousemode right "translate selected models"
    17629 
    17630 > view matrix models
    17631 > #1,0.98793,0.057456,-0.14382,14.056,-0.075925,0.98907,-0.12641,42.661,0.13499,0.13581,0.9815,-43.601,#2,0.98793,0.057456,-0.14382,14.056,-0.075925,0.98907,-0.12641,42.661,0.13499,0.13581,0.9815,-43.601,#3,0.98793,0.057456,-0.14382,14.056,-0.075925,0.98907,-0.12641,42.661,0.13499,0.13581,0.9815,-43.601,#4,0.98793,0.057456,-0.14382,14.056,-0.075925,0.98907,-0.12641,42.661,0.13499,0.13581,0.9815,-43.601,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17632 
    17633 > view matrix models
    17634 > #1,0.98793,0.057456,-0.14382,13.827,-0.075925,0.98907,-0.12641,42.608,0.13499,0.13581,0.9815,-43.292,#2,0.98793,0.057456,-0.14382,13.827,-0.075925,0.98907,-0.12641,42.608,0.13499,0.13581,0.9815,-43.292,#3,0.98793,0.057456,-0.14382,13.827,-0.075925,0.98907,-0.12641,42.608,0.13499,0.13581,0.9815,-43.292,#4,0.98793,0.057456,-0.14382,13.827,-0.075925,0.98907,-0.12641,42.608,0.13499,0.13581,0.9815,-43.292,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17635 
    17636 > volume #9 level 0.1033
    17637 
    17638 > view matrix models
    17639 > #1,0.98793,0.057456,-0.14382,13.882,-0.075925,0.98907,-0.12641,42.414,0.13499,0.13581,0.9815,-43.066,#2,0.98793,0.057456,-0.14382,13.882,-0.075925,0.98907,-0.12641,42.414,0.13499,0.13581,0.9815,-43.066,#3,0.98793,0.057456,-0.14382,13.882,-0.075925,0.98907,-0.12641,42.414,0.13499,0.13581,0.9815,-43.066,#4,0.98793,0.057456,-0.14382,13.882,-0.075925,0.98907,-0.12641,42.414,0.13499,0.13581,0.9815,-43.066,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17640 
    17641 > view matrix models
    17642 > #1,0.98793,0.057456,-0.14382,13.743,-0.075925,0.98907,-0.12641,41.91,0.13499,0.13581,0.9815,-42.398,#2,0.98793,0.057456,-0.14382,13.743,-0.075925,0.98907,-0.12641,41.91,0.13499,0.13581,0.9815,-42.398,#3,0.98793,0.057456,-0.14382,13.743,-0.075925,0.98907,-0.12641,41.91,0.13499,0.13581,0.9815,-42.398,#4,0.98793,0.057456,-0.14382,13.743,-0.075925,0.98907,-0.12641,41.91,0.13499,0.13581,0.9815,-42.398,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17643 
    17644 > ui mousemode right "rotate selected models"
    17645 
    17646 > view matrix models
    17647 > #1,0.98976,0.050761,-0.13341,12.648,-0.06712,0.99036,-0.12114,39.078,0.12598,0.12885,0.98363,-39.91,#2,0.98976,0.050761,-0.13341,12.648,-0.06712,0.99036,-0.12114,39.078,0.12598,0.12885,0.98363,-39.91,#3,0.98976,0.050761,-0.13341,12.648,-0.06712,0.99036,-0.12114,39.078,0.12598,0.12885,0.98363,-39.91,#4,0.98976,0.050761,-0.13341,12.648,-0.06712,0.99036,-0.12114,39.078,0.12598,0.12885,0.98363,-39.91,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17648 
    17649 > view matrix models
    17650 > #1,0.99033,0.070382,-0.11954,6.0597,-0.084892,0.98902,-0.12099,42.418,0.10971,0.12996,0.98543,-37.629,#2,0.99033,0.070382,-0.11954,6.0597,-0.084892,0.98902,-0.12099,42.418,0.10971,0.12996,0.98543,-37.629,#3,0.99033,0.070382,-0.11954,6.0597,-0.084892,0.98902,-0.12099,42.418,0.10971,0.12996,0.98543,-37.629,#4,0.99033,0.070382,-0.11954,6.0597,-0.084892,0.98902,-0.12099,42.418,0.10971,0.12996,0.98543,-37.629,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17651 
    17652 > view matrix models
    17653 > #1,0.9884,0.078396,-0.1301,6.9535,-0.093646,0.98887,-0.11557,42.908,0.11959,0.12642,0.98474,-38.545,#2,0.9884,0.078396,-0.1301,6.9535,-0.093646,0.98887,-0.11557,42.908,0.11959,0.12642,0.98474,-38.545,#3,0.9884,0.078396,-0.1301,6.9535,-0.093646,0.98887,-0.11557,42.908,0.11959,0.12642,0.98474,-38.545,#4,0.9884,0.078396,-0.1301,6.9535,-0.093646,0.98887,-0.11557,42.908,0.11959,0.12642,0.98474,-38.545,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17654 
    17655 > view matrix models
    17656 > #1,0.98395,0.11436,-0.13701,2.2264,-0.12871,0.98654,-0.10086,46.584,0.12364,0.11688,0.98542,-37.564,#2,0.98395,0.11436,-0.13701,2.2264,-0.12871,0.98654,-0.10086,46.584,0.12364,0.11688,0.98542,-37.564,#3,0.98395,0.11436,-0.13701,2.2264,-0.12871,0.98654,-0.10086,46.584,0.12364,0.11688,0.98542,-37.564,#4,0.98395,0.11436,-0.13701,2.2264,-0.12871,0.98654,-0.10086,46.584,0.12364,0.11688,0.98542,-37.564,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17657 
    17658 > ui mousemode right zoom
    17659 
    17660 > ui mousemode right "rotate selected models"
    17661 
    17662 > view matrix models
    17663 > #1,0.98197,0.14007,-0.12693,-4.3253,-0.15486,0.98119,-0.11524,55.01,0.10841,0.13282,0.98519,-37.901,#2,0.98197,0.14007,-0.12693,-4.3253,-0.15486,0.98119,-0.11524,55.01,0.10841,0.13282,0.98519,-37.901,#3,0.98197,0.14007,-0.12693,-4.3253,-0.15486,0.98119,-0.11524,55.01,0.10841,0.13282,0.98519,-37.901,#4,0.98197,0.14007,-0.12693,-4.3253,-0.15486,0.98119,-0.11524,55.01,0.10841,0.13282,0.98519,-37.901,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17664 
    17665 > view matrix models
    17666 > #1,0.98017,0.16776,-0.1055,-13.524,-0.17994,0.97645,-0.11899,61.028,0.083055,0.13561,0.98727,-34.425,#2,0.98017,0.16776,-0.1055,-13.524,-0.17994,0.97645,-0.11899,61.028,0.083055,0.13561,0.98727,-34.425,#3,0.98017,0.16776,-0.1055,-13.524,-0.17994,0.97645,-0.11899,61.028,0.083055,0.13561,0.98727,-34.425,#4,0.98017,0.16776,-0.1055,-13.524,-0.17994,0.97645,-0.11899,61.028,0.083055,0.13561,0.98727,-34.425,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17667 
    17668 > view matrix models
    17669 > #1,0.98125,0.15735,-0.11134,-10.574,-0.17036,0.97817,-0.11902,59.039,0.090181,0.13575,0.98663,-35.565,#2,0.98125,0.15735,-0.11134,-10.574,-0.17036,0.97817,-0.11902,59.039,0.090181,0.13575,0.98663,-35.565,#3,0.98125,0.15735,-0.11134,-10.574,-0.17036,0.97817,-0.11902,59.039,0.090181,0.13575,0.98663,-35.565,#4,0.98125,0.15735,-0.11134,-10.574,-0.17036,0.97817,-0.11902,59.039,0.090181,0.13575,0.98663,-35.565,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17670 
    17671 > ui mousemode right "translate selected models"
    17672 
    17673 > view matrix models
    17674 > #1,0.98125,0.15735,-0.11134,-11.563,-0.17036,0.97817,-0.11902,59.058,0.090181,0.13575,0.98663,-35.488,#2,0.98125,0.15735,-0.11134,-11.563,-0.17036,0.97817,-0.11902,59.058,0.090181,0.13575,0.98663,-35.488,#3,0.98125,0.15735,-0.11134,-11.563,-0.17036,0.97817,-0.11902,59.058,0.090181,0.13575,0.98663,-35.488,#4,0.98125,0.15735,-0.11134,-11.563,-0.17036,0.97817,-0.11902,59.058,0.090181,0.13575,0.98663,-35.488,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
    17675 
    17676 > ui mousemode right zoom
    17677 
    17678 > ui mousemode right select
    17679 
    17680 > select clear
    17681 
    17682 > ui tool show "Show Sequence Viewer"
    17683 
    17684 > sequence chain #12/D
    17685 
    17686 Alignment identifier is 12/D 
    17687 
    17688 > ui tool show "Renumber Residues"
    17689 
    17690 > renumber #12/D seqStart 229 relative false
    17691 
    17692 214 residues renumbered 
    17693 
    17694 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    17695 > (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/F562_1-442.pdb" models #12
    17696 
    17697 > combine #3 #4
    17698 
    17699 > rename #13 sNS1
    17700 
    17701 > hide #2 models
    17702 
    17703 > hide #3 models
    17704 
    17705 > hide #4 models
    17706 
    17707 > hide #5 models
    17708 
    17709 > hide #6 models
    17710 
    17711 > hide #8 models
    17712 
    17713 > hide #!9 models
    17714 
    17715 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    17716 > (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/D2NS1.pdb" models #13
    17717 
    17718 > select #12/D:229
    17719 
    17720 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17721 
    17722 > select #12/D
    17723 
    17724 1632 atoms, 1668 bonds, 214 residues, 1 model selected 
    17725 
    17726 > ui tool show "Show Sequence Viewer"
    17727 
    17728 > sequence chain #4/A
    17729 
    17730 Alignment identifier is 4/A 
    17731 
    17732 > select #4/A:1-2
    17733 
    17734 14 atoms, 13 bonds, 2 residues, 1 model selected 
    17735 
    17736 > select #4/A
    17737 
    17738 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    17739 
    17740 > show #3 models
    17741 
    17742 > show #4 models
    17743 
    17744 > select clear
    17745 
    17746 > ui mousemode right zoom
    17747 
    17748 > show #2 models
    17749 
    17750 > show #1 models
    17751 
    17752 > show #5 models
    17753 
    17754 > show #6 models
    17755 
    17756 > show #7 models
    17757 
    17758 > show #8 models
    17759 
    17760 > hide #8 models
    17761 
    17762 > show #8 models
    17763 
    17764 > hide #7 models
    17765 
    17766 > show #!9 models
    17767 
    17768 > color #9 #b4e3e620 models
    17769 
    17770 > color #9 #b4e3e61d models
    17771 
    17772 > color #9 #b4e3e61a models
    17773 
    17774 > color #9 #b4e3e60a models
    17775 
    17776 > color #9 #b4e3e60b models
    17777 
    17778 > color #9 #b4e3e60d models
    17779 
    17780 > ui tool show "Show Sequence Viewer"
    17781 
    17782 > sequence chain #12/C
    17783 
    17784 Alignment identifier is 12/C 
    17785 
    17786 > hide #!9 models
    17787 
    17788 > show #!9 models
    17789 
    17790 > hide #8 models
    17791 
    17792 > show #8 models
    17793 
    17794 > hide #12 models
    17795 
    17796 > show #12 models
    17797 
    17798 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    17799 > (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/view_top.png" width 978 height 807
    17800 > supersample 3 transparentBackground true
    17801 
    17802 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    17803 > (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/view_side.png" width 978 height 807
    17804 > supersample 3
    17805 
    17806 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    17807 > (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/view_side.png" width 978 height 807
    17808 > supersample 3 transparentBackground true
    17809 
    17810 > select add #12
    17811 
    17812 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    17813 
    17814 > ui mousemode right "translate selected models"
    17815 
    17816 > view matrix models
    17817 > #12,0.38667,0.91182,0.1381,-47.42,-0.31103,-0.012038,0.95032,62.146,0.86819,-0.41042,0.27895,3.0647
    17818 
    17819 > view matrix models
    17820 > #12,0.38667,0.91182,0.1381,-47.326,-0.31103,-0.012038,0.95032,61.501,0.86819,-0.41042,0.27895,2.9386
    17821 
    17822 > view matrix models
    17823 > #12,0.38667,0.91182,0.1381,-47.268,-0.31103,-0.012038,0.95032,61.611,0.86819,-0.41042,0.27895,2.923
    17824 
    17825 > view matrix models
    17826 > #12,0.38667,0.91182,0.1381,-47.161,-0.31103,-0.012038,0.95032,61.629,0.86819,-0.41042,0.27895,2.8732
    17827 
    17828 > view matrix models
    17829 > #12,0.38667,0.91182,0.1381,-47.025,-0.31103,-0.012038,0.95032,61.858,0.86819,-0.41042,0.27895,2.61
    17830 
    17831 > ui mousemode right "rotate selected models"
    17832 
    17833 > view matrix models
    17834 > #12,0.40207,0.90968,0.10404,-44.258,-0.30079,0.023902,0.95339,52.565,0.86479,-0.41462,0.28323,3.394
    17835 
    17836 > view matrix models
    17837 > #12,0.43588,0.8998,0.019269,-35.504,-0.22748,0.089432,0.96967,20.855,0.87078,-0.42704,0.24367,11.163
    17838 
    17839 > view matrix models
    17840 > #12,0.44682,0.88805,0.10825,-51.738,-0.30462,0.037257,0.95175,51.403,0.84116,-0.45824,0.28716,15.96
    17841 
    17842 > view matrix models
    17843 > #12,0.4731,0.86918,0.14391,-60.908,-0.27044,-0.012188,0.96266,50.135,0.83848,-0.49435,0.22929,33.188
    17844 
    17845 > select subtract #12
    17846 
    17847 Nothing selected 
    17848 
    17849 > select #12/C:101-103
    17850 
    17851 32 atoms, 33 bonds, 3 residues, 1 model selected 
    17852 
    17853 > select #12/C:101-105
    17854 
    17855 50 atoms, 52 bonds, 5 residues, 1 model selected 
    17856 
    17857 > ui mousemode right "translate selected models"
    17858 
    17859 > ui mousemode right zoom
    17860 
    17861 > select #12/C:102-103
    17862 
    17863 24 atoms, 25 bonds, 2 residues, 1 model selected 
    17864 
    17865 > select #12/C:102-108
    17866 
    17867 61 atoms, 64 bonds, 7 residues, 1 model selected 
    17868 
    17869 > select #12/C:102-105
    17870 
    17871 42 atoms, 44 bonds, 4 residues, 1 model selected 
    17872 
    17873 > select #12/C:102-109
    17874 
    17875 65 atoms, 68 bonds, 8 residues, 1 model selected 
    17876 
    17877 > color sel #3b3bffff
    17878 
    17879 > select #12/C:15-30
    17880 
    17881 126 atoms, 130 bonds, 16 residues, 1 model selected 
    17882 
    17883 > select #12/C:31-34
    17884 
    17885 25 atoms, 24 bonds, 4 residues, 1 model selected 
    17886 
    17887 > select #12/C:35
    17888 
    17889 12 atoms, 12 bonds, 1 residue, 1 model selected 
    17890 
    17891 > select #12/C:30-35
    17892 
    17893 43 atoms, 43 bonds, 6 residues, 1 model selected 
    17894 
    17895 > color sel #5d62ffff
    17896 
    17897 > select add #12
    17898 
    17899 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    17900 
    17901 > ui mousemode right "rotate selected models"
    17902 
    17903 > view matrix models
    17904 > #12,0.48862,0.86407,0.12095,-59.608,-0.26178,0.012952,0.96504,43.24,0.8323,-0.5032,0.23252,35.632
    17905 
    17906 > view matrix models
    17907 > #12,0.54523,0.80683,0.2275,-81.692,-0.25523,-0.098725,0.96183,61.956,0.79849,-0.58248,0.1521,71.795
    17908 
    17909 > view matrix models
    17910 > #12,0.56505,0.79487,0.22115,-83.133,-0.25139,-0.089428,0.96375,59.071,0.78583,-0.60016,0.14929,78.392
    17911 
    17912 > view matrix models
    17913 > #12,0.61857,0.76623,0.17398,-82.364,-0.21294,-0.049666,0.9758,40.865,0.75633,-0.64065,0.13244,95.463
    17914 
    17915 > view matrix models
    17916 > #12,0.61335,0.74396,0.26517,-93.325,-0.25312,-0.13287,0.95827,68.106,0.74815,-0.65488,0.10682,104.43
    17917 
    17918 > ui mousemode right select
    17919 
    17920 > select clear
    17921 
    17922 > ui mousemode right zoom
    17923 
    17924 > color #9 #e4ebc20d models
    17925 
    17926 > color #9 #e7ebbd0d models
    17927 
    17928 > color #9 #e9eb960d models
    17929 
    17930 > color #9 #ebe98e0d models
    17931 
    17932 > color #9 #ebe7900d models
    17933 
    17934 > color #9 #ebe79017 models
    17935 
    17936 > select add #5
    17937 
    17938 102 pseudobonds, 1 model selected 
    17939 
    17940 
    17941 ===== Log before crash end =====
    17942 
    17943 Log:
    17944 UCSF ChimeraX version: 1.5 (2022-11-24) 
    17945 © 2016-2022 Regents of the University of California. All rights reserved. 
    17946 
    17947 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    17948 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
    17949 > MS_recolored.cxs
    17950 
    17951 Opened sNS1wt-Fab562.mrc as #9, grid size 416,416,416, pixel 0.85, shown at
    17952 level 0.0624, step 1, values float32 
    17953 Opened map 8 as #11, grid size 416,416,416, pixel 0.85, shown at level 0.0375,
    17954 step 1, values float32 
    17955 Log from Wed Apr 19 17:03:52 2023UCSF ChimeraX version: 1.5 (2022-11-24) 
    17956 © 2016-2022 Regents of the University of California. All rights reserved. 
    17957 
    17958 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    17959 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
    17960 > MS_recolored.cxs
    17961 
    17962 Opened sNS1wt-Fab562.mrc as #9, grid size 416,416,416, pixel 0.85, shown at
    17963 level 0.11, step 1, values float32 
    17964 Opened map 8 as #11, grid size 416,416,416, pixel 0.85, shown at level 0.0375,
    17965 step 1, values float32 
    17966 Log from Wed Apr 19 14:11:57 2023UCSF ChimeraX version: 1.5 (2022-11-24) 
    17967 © 2016-2022 Regents of the University of California. All rights reserved. 
    17968 
    17969 > open "/Users/alvinchew/Library/CloudStorage/OneDrive-
    17970 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_MS_Wint/XMAS
    17971 > files/NS1-apoAI_models-forwint_forAlvin.cxs"
    17972 
    17973 Log from Mon Apr 3 16:43:31 2023UCSF ChimeraX version: 1.5 (2022-11-24) 
    17974 © 2016-2022 Regents of the University of California. All rights reserved. 
    17975 
    17976 > open /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    17977 
    17978 Log from Mon Apr 3 15:19:20 2023UCSF ChimeraX version: 1.5 (2022-11-24) 
    17979 © 2016-2022 Regents of the University of California. All rights reserved. 
    17980 
    17981 > open /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint.cxs
    17982 
    17983 Log from Sat Apr 1 16:55:32 2023UCSF ChimeraX version: 1.5 (2022-11-24) 
    17984 © 2016-2022 Regents of the University of California. All rights reserved. 
    17985 
    17986 > set bgColor #ffffff00
    17987 
    17988 Log from Thu Mar 30 23:52:24 2023UCSF ChimeraX version: 1.5 (2022-11-24) 
    17989 © 2016-2022 Regents of the University of California. All rights reserved. 
    17990 
    17991 > open "/Users/alvinchew/Library/CloudStorage/OneDrive-
    17992 > NanyangTechnologicalUniversity/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM
    17993 > Maps_docked structures/EDEN2 sNS1wt-Fab562/sNS1wt-Fab-
    17994 > ApoAI_Ab562_compare.cxs"
    17995 
    17996 Opened sNS1wt-Ab562.mrc as #2, grid size 352,352,352, pixel 0.85, shown at
    17997 level 0.17, step 1, values float32 
    17998 Opened sNS1wt-Fab562.mrc as #8, grid size 416,416,416, pixel 0.85, shown at
    17999 level 0.0754, step 1, values float32 
    18000 Log from Sat Nov 19 10:30:44 2022UCSF ChimeraX version: 1.4 (2022-06-03) 
    18001 © 2016-2022 Regents of the University of California. All rights reserved. 
    18002 
    18003 > open "/Users/alvinchew/Library/CloudStorage/OneDrive-
    18004 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM
    18005 > Maps_docked structures/EDEN2 sNS1wt-Fab562/20220323_NS1wt-Ab-Fab-
    18006 > ApoAI_hdl.cxs"
    18007 
    18008 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18009 416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32 
    18010 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18011 352,352,352, pixel 0.85, shown at level 0.17, step 1, values float32 
    18012 Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
    18013 416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32 
    18014 Opened cryosparc_P39_J166_002_volume_map_sharp (1).mrc as #6, grid size
    18015 416,416,416, pixel 0.85, shown at level 0.0687, step 1, values float32 
    18016 Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
    18017 416,416,416, pixel 0.85, shown at level 0.0754, step 1, values float32 
    18018 Log from Thu Mar 24 12:02:48 2022UCSF ChimeraX version: 1.3 (2021-12-08) 
    18019 © 2016-2021 Regents of the University of California. All rights reserved. 
    18020 
    18021 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    18022 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-
    18023 > Fab-ApoAI_hdl.cxs
    18024 
    18025 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18026 416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32 
    18027 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18028 352,352,352, pixel 0.85, shown at level 0.169, step 1, values float32 
    18029 Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
    18030 416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32 
    18031 Log from Sat Mar 12 14:58:51 2022UCSF ChimeraX version: 1.3 (2021-12-08) 
    18032 © 2016-2021 Regents of the University of California. All rights reserved. 
    18033 
    18034 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    18035 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-
    18036 > Fab-ApoAI_hdl_Compare-NS1ts.cxs
    18037 
    18038 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18039 416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32 
    18040 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18041 352,352,352, pixel 0.85, shown at level 0.169, step 1, values float32 
    18042 Opened cryosparc_P35_J90_005_volume_map_sharp.mrc as #6, grid size
    18043 416,416,416, pixel 0.858, shown at level 0.135, step 1, values float32 
    18044 Opened cryosparc_P35_J141_class_00_final_volume.mrc as #8, grid size
    18045 128,128,128, pixel 2.79, shown at level 0.318, step 1, values float32 
    18046 Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
    18047 416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32 
    18048 Log from Fri Mar 11 18:14:28 2022UCSF ChimeraX version: 1.3 (2021-12-08) 
    18049 © 2016-2021 Regents of the University of California. All rights reserved. 
    18050 
    18051 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    18052 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-
    18053 > Fab-ApoAI_hdl.cxs
    18054 
    18055 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18056 416,416,416, pixel 0.858, shown at level 0.127, step 1, values float32 
    18057 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18058 352,352,352, pixel 0.85, shown at level 0.191, step 1, values float32 
    18059 Log from Thu Mar 3 21:24:07 2022UCSF ChimeraX version: 1.2.2 (2021-05-08) 
    18060 © 2016-2021 Regents of the University of California. All rights reserved. 
    18061 
    18062 > open "/Users/alvinchew/OneDrive - Nanyang Technological
    18063 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    18064 
    18065 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18066 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 
    18067 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18068 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18069 Opened cryosparc_P47_J128_002_volume_map_sharp.mrc resampled as #7, grid size
    18070 352,352,352, pixel 0.85, shown at level 0.0969, step 1, values float32 
    18071 Log from Thu Mar 3 19:50:19 2022UCSF ChimeraX version: 1.2.2 (2021-05-08) 
    18072 © 2016-2021 Regents of the University of California. All rights reserved. 
    18073 
    18074 > open "/Users/alvinchew/OneDrive - Nanyang Technological
    18075 > University/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-Fab5-DL.cxs"
    18076 > format session
    18077 
    18078 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18079 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 
    18080 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18081 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18082 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
    18083 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18084 Opened cryosparc_P35_J100_005_volume_map_sharp (1).mrc as #11, grid size
    18085 416,416,416, pixel 0.858, shown at level 0.05, step 1, values float32 
    18086 Log from Thu Mar 3 12:01:46 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    18087 © 2016-2021 Regents of the University of California. All rights reserved. 
    18088 
    18089 > open "C:\\\Users\\\dahailuo\\\OneDrive - Nanyang Technological
    18090 > University\\\Temporal\\\202112_FlaviNS1\\\Data_EM_Alvin\\\20220302_D2NS1ts-
    18091 > Ab56-apoa1.cxs"
    18092 
    18093 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18094 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 
    18095 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18096 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18097 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
    18098 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18099 Log from Wed Mar 2 00:18:18 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    18100 © 2016-2021 Regents of the University of California. All rights reserved. 
    18101 
    18102 > open "D:\OneDrive - Nanyang Technological
    18103 > University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220302_D2NS1ts-
    18104 > Ab56-apoa1.cxs" format session
    18105 
    18106 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18107 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 
    18108 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18109 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18110 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
    18111 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18112 Log from Wed Mar 2 00:08:07 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    18113 © 2016-2021 Regents of the University of California. All rights reserved. 
    18114 
    18115 > open "D:/OneDrive - Nanyang Technological
    18116 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
    18117 
    18118 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18119 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 
    18120 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18121 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18122 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
    18123 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18124 Log from Tue Feb 22 22:03:06 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    18125 © 2016-2021 Regents of the University of California. All rights reserved. 
    18126 
    18127 > open "D:\OneDrive - Nanyang Technological
    18128 > University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220222_D2NS1-Ab56-AA1.cxs"
    18129 > format session
    18130 
    18131 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18132 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 
    18133 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18134 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18135 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
    18136 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18137 Log from Tue Feb 22 21:54:19 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    18138 © 2016-2021 Regents of the University of California. All rights reserved. 
    18139 
    18140 > open "D:\OneDrive - Nanyang Technological
    18141 > University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220222_D2NS1-Ab56.cxs"
    18142 > format session
    18143 
    18144 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18145 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 
    18146 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18147 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18148 Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc as #8, grid size
    18149 352,352,352, pixel 0.85, shown at level 0.421, step 2, values float32 
    18150 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
    18151 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 
    18152 Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy as #11, grid size
    18153 352,352,352, pixel 0.85, shown at level 0.471, step 1, values float32 
    18154 Log from Tue Feb 22 21:05:12 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) 
    18155 © 2016-2021 Regents of the University of California. All rights reserved. 
    18156 How to cite UCSF ChimeraX 
    18157 
    18158 > open "D:/OneDrive - Nanyang Technological
    18159 > University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
    18160 > sNS1-Fab56-2/cryosparc_P35_J91_006_volume_map_sharp.mrc"
    18161 
    18162 Opened cryosparc_P35_J91_006_volume_map_sharp.mrc as #1, grid size
    18163 416,416,416, pixel 0.858, shown at level 0.0468, step 2, values float32 
    18164 
    18165 > surface dust #1 size 8.58
    18166 
    18167 > open "D:/OneDrive - Nanyang Technological
    18168 > University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
    18169 > sNS1-Fab56-2/cryosparc_P35_J96_006_volume_map_sharp.mrc"
    18170 
    18171 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #2, grid size
    18172 416,416,416, pixel 0.858, shown at level 0.0481, step 2, values float32 
    18173 
    18174 > surface dust #1 size 8.58
    18175 
    18176 > surface dust #2 size 8.58
    18177 
    18178 > close #2
    18179 
    18180 > close #1
    18181 
    18182 > open "D:/OneDrive - Nanyang Technological
    18183 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    18184 > sNS1-Fab56-2/cryosparc_P35_J96_006_volume_map_sharp.mrc"
    18185 
    18186 Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
    18187 416,416,416, pixel 0.858, shown at level 0.0481, step 2, values float32 
    18188 
    18189 > open "D:/OneDrive - Nanyang Technological
    18190 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J20_004_volume_map_sharp.mrc"
    18191 
    18192 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
    18193 352,352,352, pixel 0.85, shown at level 0.142, step 2, values float32 
    18194 
    18195 > surface dust #1 size 8.58
    18196 
    18197 > surface dust #2 size 8.5
    18198 
    18199 > open "D:/OneDrive - Nanyang Technological
    18200 > University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
    18201 > sNS1-Fab56-2/D2NS1.pdb"
    18202 
    18203 Summary of feedback from opening D:/OneDrive - Nanyang Technological
    18204 University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
    18205 sNS1-Fab56-2/D2NS1.pdb 
    18206 --- 
    18207 warning | Ignored bad PDB record found on line 5732 
    18208 END 
    18209  
    18210 Chain information for D2NS1.pdb #3 
    18211 --- 
    18212 Chain | Description 
    18213 B C | No description available 
    18214  
    18215 
    18216 > hide #!2 models
    18217 
    18218 > volume #1 level 0.07524
    18219 
    18220 > volume #1 level 0.07
    18221 
    18222 > volume #1 level 0.072
    18223 
    18224 > select #3
    18225 
    18226 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    18227 
    18228 > ui mousemode right "rotate selected models"
    18229 
    18230 > view matrix models
    18231 > #3,0.89628,-0.44038,-0.052381,101.61,0.096778,0.078954,0.99217,-38.919,-0.43279,-0.89433,0.11338,384.44
    18232 
    18233 > view matrix models
    18234 > #3,0.99109,-0.12056,-0.056551,31.91,0.0080432,0.4781,-0.87827,242.8,0.13292,0.86999,0.47482,-76.088
    18235 
    18236 > view matrix models
    18237 > #3,0.79841,-0.57175,0.18879,97.95,-0.1953,0.050686,0.97943,19.471,-0.56956,-0.81886,-0.071196,428.68
    18238 
    18239 > view matrix models
    18240 > #3,0.82022,-0.53629,0.19907,86.322,-0.4792,-0.8342,-0.2729,441.29,0.31242,0.12845,-0.94122,269.29
    18241 
    18242 > view matrix models
    18243 > #3,0.33094,0.34033,0.88014,-96.351,-0.87516,0.45954,0.15137,217.82,-0.35295,-0.82036,0.44993,298
    18244 
    18245 > view matrix models
    18246 > #3,0.12486,-0.10929,0.98614,-3.3941,-0.98525,0.10355,0.13622,299.73,-0.117,-0.9886,-0.094748,381.83
    18247 
    18248 > view matrix models
    18249 > #3,-0.013734,0.34293,0.93926,-46.701,0.87722,0.45496,-0.15328,-35.332,-0.47989,0.82183,-0.30707,179.08
    18250 
    18251 > view matrix models
    18252 > #3,-0.024741,-0.048477,0.99852,10.486,0.22627,0.97263,0.052827,-44.605,-0.97375,0.22725,-0.013095,313.53
    18253 
    18254 > view matrix models
    18255 > #3,0.22803,-0.14862,0.96224,-10.67,-0.86757,-0.4796,0.13152,377.92,0.44195,-0.86481,-0.23831,288.28
    18256 
    18257 > view matrix models
    18258 > #3,-0.090598,0.23885,0.96682,-20.594,-0.90644,0.38234,-0.1794,295.23,-0.4125,-0.89262,0.18187,368.38
    18259 
    18260 > ui mousemode right "translate selected models"
    18261 
    18262 > view matrix models
    18263 > #3,-0.090598,0.23885,0.96682,-20.895,-0.90644,0.38234,-0.1794,305.2,-0.4125,-0.89262,0.18187,368.62
    18264 
    18265 > view matrix models
    18266 > #3,-0.090598,0.23885,0.96682,-18.453,-0.90644,0.38234,-0.1794,307.34,-0.4125,-0.89262,0.18187,380.09
    18267 
    18268 > ui tool show "Fit in Map"
    18269 
    18270 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18271 (#1) using 5602 atoms 
    18272 average map value = 0.09223, steps = 72 
    18273 shifted from previous position = 2.04 
    18274 rotated from previous position = 4.6 degrees 
    18275 atoms outside contour = 3319, contour level = 0.072 
    18276  
    18277 Position of D2NS1.pdb (#3) relative to
    18278 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18279 Matrix rotation and translation 
    18280 -0.06802577 0.24460859 0.96723274 -24.08767794 
    18281 -0.87342564 0.45395004 -0.17623011 287.61942533 
    18282 -0.48218273 -0.85679405 0.18276711 387.90605974 
    18283 Axis -0.34848182 0.74217118 -0.57248788 
    18284 Axis point 265.32854097 -0.00000000 317.95880744 
    18285 Rotation angle (degrees) 102.45391693 
    18286 Shift along axis -0.21455122 
    18287  
    18288 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18289 (#1) using 5602 atoms 
    18290 average map value = 0.09223, steps = 40 
    18291 shifted from previous position = 0.0168 
    18292 rotated from previous position = 0.017 degrees 
    18293 atoms outside contour = 3323, contour level = 0.072 
    18294  
    18295 Position of D2NS1.pdb (#3) relative to
    18296 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18297 Matrix rotation and translation 
    18298 -0.06800908 0.24437415 0.96729317 -24.07786550 
    18299 -0.87335170 0.45412951 -0.17613415 287.55836847 
    18300 -0.48231900 -0.85676584 0.18253965 387.96533381 
    18301 Axis -0.34851775 0.74227452 -0.57233199 
    18302 Axis point 265.31869899 0.00000000 317.91033718 
    18303 Rotation angle (degrees) 102.45483514 
    18304 Shift along axis -0.20615891 
    18305  
    18306 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18307 (#1) using 5602 atoms 
    18308 average map value = 0.09224, steps = 44 
    18309 shifted from previous position = 0.00415 
    18310 rotated from previous position = 0.0128 degrees 
    18311 atoms outside contour = 3322, contour level = 0.072 
    18312  
    18313 Position of D2NS1.pdb (#3) relative to
    18314 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18315 Matrix rotation and translation 
    18316 -0.06778785 0.24439903 0.96730241 -24.12733834 
    18317 -0.87337367 0.45415748 -0.17595301 287.52563608 
    18318 -0.48231036 -0.85674392 0.18266531 387.93712068 
    18319 Axis -0.34858450 0.74224338 -0.57233173 
    18320 Axis point 265.33740374 0.00000000 317.91776063 
    18321 Rotation angle (degrees) 102.44383763 
    18322 Shift along axis -0.20430725 
    18323  
    18324 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18325 (#1) using 5602 atoms 
    18326 average map value = 0.09223, steps = 44 
    18327 shifted from previous position = 0.0152 
    18328 rotated from previous position = 0.013 degrees 
    18329 atoms outside contour = 3321, contour level = 0.072 
    18330  
    18331 Position of D2NS1.pdb (#3) relative to
    18332 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18333 Matrix rotation and translation 
    18334 -0.06797653 0.24451862 0.96725895 -24.09141306 
    18335 -0.87335854 0.45410159 -0.17617224 287.57257739 
    18336 -0.48231121 -0.85673942 0.18268417 387.93432608 
    18337 Axis -0.34847884 0.74224049 -0.57239982 
    18338 Axis point 265.31882258 -0.00000000 317.92823841 
    18339 Rotation angle (degrees) 102.45045928 
    18340 Shift along axis -0.21017795 
    18341  
    18342 
    18343 > transparency #1.1 50
    18344 
    18345 > open "D:/OneDrive - Nanyang Technological
    18346 > University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
    18347 > sNS1-Fab56-2/F562a.pdb"
    18348 
    18349 Chain information for F562a.pdb #4 
    18350 --- 
    18351 Chain | Description 
    18352 B | No description available 
    18353 C | No description available 
    18354  
    18355 
    18356 > ui tool show "Color Actions"
    18357 
    18358 > color sel bychain
    18359 
    18360 > color sel bychain
    18361 
    18362 > select #4
    18363 
    18364 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    18365 
    18366 > color sel bychain
    18367 
    18368 > color sel bychain
    18369 
    18370 > color sel bychain
    18371 
    18372 > open "D:/OneDrive - Nanyang Technological
    18373 > University/Temporal/202109_zvNS1/3_Structures/7bsc_DEN2 NS1c.pdb"
    18374 
    18375 7bsc_DEN2 NS1c.pdb title: 
    18376 Complex structure of 1G5.3 fab bound to DENV2 NS1C [more info...] 
    18377  
    18378 Chain information for 7bsc_DEN2 NS1c.pdb #5 
    18379 --- 
    18380 Chain | Description 
    18381 A | non-structural protein 1 
    18382 H | 1G5.3 fab heavy chain 
    18383 L | 1G5.3 fab light chain 
    18384  
    18385 
    18386 > mmaker #5 to #3
    18387 
    18388 Parameters 
    18389 --- 
    18390 Chain pairing | bb 
    18391 Alignment algorithm | Needleman-Wunsch 
    18392 Similarity matrix | BLOSUM-62 
    18393 SS fraction | 0.3 
    18394 Gap open (HH/SS/other) | 18/18/6 
    18395 Gap extend | 1 
    18396 SS matrix |  |  | H | S | O 
    18397 ---|---|---|--- 
    18398 H | 6 | -9 | -6 
    18399 S |  | 6 | -6 
    18400 O |  |  | 4 
    18401 Iteration cutoff | 2 
    18402  
    18403 Matchmaker D2NS1.pdb, chain B (#3) with 7bsc_DEN2 NS1c.pdb, chain A (#5),
    18404 sequence alignment score = 896.9 
    18405 RMSD between 162 pruned atom pairs is 0.535 angstroms; (across all 177 pairs:
    18406 2.714) 
    18407  
    18408 
    18409 > mmaker #4 to #5
    18410 
    18411 Parameters 
    18412 --- 
    18413 Chain pairing | bb 
    18414 Alignment algorithm | Needleman-Wunsch 
    18415 Similarity matrix | BLOSUM-62 
    18416 SS fraction | 0.3 
    18417 Gap open (HH/SS/other) | 18/18/6 
    18418 Gap extend | 1 
    18419 SS matrix |  |  | H | S | O 
    18420 ---|---|---|--- 
    18421 H | 6 | -9 | -6 
    18422 S |  | 6 | -6 
    18423 O |  |  | 4 
    18424 Iteration cutoff | 2 
    18425  
    18426 Matchmaker 7bsc_DEN2 NS1c.pdb, chain H (#5) with F562a.pdb, chain B (#4),
    18427 sequence alignment score = 1028.9 
    18428 RMSD between 105 pruned atom pairs is 0.627 angstroms; (across all 215 pairs:
    18429 11.308) 
    18430  
    18431 
    18432 > ~select #4
    18433 
    18434 Nothing selected 
    18435 
    18436 > hide #!5 models
    18437 
    18438 > select #4
    18439 
    18440 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    18441 
    18442 > view matrix models
    18443 > #4,0.59089,-0.15644,-0.79144,253.32,0.26071,0.96541,0.0038114,-36.876,0.76347,-0.20859,0.61123,8.3612
    18444 
    18445 > view matrix models
    18446 > #4,0.59089,-0.15644,-0.79144,249.54,0.26071,0.96541,0.0038114,-38.171,0.76347,-0.20859,0.61123,-6.5674
    18447 
    18448 > view matrix models
    18449 > #4,0.59089,-0.15644,-0.79144,250.18,0.26071,0.96541,0.0038114,-52.258,0.76347,-0.20859,0.61123,-8.7931
    18450 
    18451 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18452 (#1) using 3401 atoms 
    18453 average map value = 0.08302, steps = 284 
    18454 shifted from previous position = 3.86 
    18455 rotated from previous position = 9.32 degrees 
    18456 atoms outside contour = 2026, contour level = 0.072 
    18457  
    18458 Position of F562a.pdb (#4) relative to
    18459 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18460 Matrix rotation and translation 
    18461 0.70756240 -0.18104725 -0.68306467 216.74116501 
    18462 0.24257753 0.97011437 -0.00585274 -48.06381473 
    18463 0.66371047 -0.16155497 0.73033445 -11.10097449 
    18464 Axis -0.10961944 -0.94817357 0.29824565 
    18465 Axis point 132.17662306 0.00000000 263.68811665 
    18466 Rotation angle (degrees) 45.25073566 
    18467 Shift along axis 18.50297639 
    18468  
    18469 
    18470 > transparency #1.1 0
    18471 
    18472 > view matrix models
    18473 > #4,0.70756,-0.18105,-0.68306,218.9,0.24258,0.97011,-0.0058527,-47.556,0.66371,-0.16155,0.73033,-11.137
    18474 
    18475 > ui mousemode right "rotate selected models"
    18476 
    18477 > view matrix models
    18478 > #4,0.60929,0.056492,-0.79093,206.86,0.79214,-0.088481,0.60389,-30.096,-0.035867,-0.99447,-0.09866,369.53
    18479 
    18480 > view matrix models
    18481 > #4,0.13536,-0.077461,-0.98776,343.37,0.97999,0.15727,0.12197,-53.095,0.1459,-0.98451,0.097201,310.49
    18482 
    18483 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18484 (#1) using 3401 atoms 
    18485 average map value = 0.1078, steps = 96 
    18486 shifted from previous position = 8.35 
    18487 rotated from previous position = 5.73 degrees 
    18488 atoms outside contour = 1603, contour level = 0.072 
    18489  
    18490 Position of F562a.pdb (#4) relative to
    18491 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18492 Matrix rotation and translation 
    18493 0.18515527 -0.12030538 -0.97531746 334.84540290 
    18494 0.98054878 0.08839233 0.17524520 -44.47549541 
    18495 0.06512764 -0.98879392 0.13433160 327.48525231 
    18496 Axis -0.60933659 -0.54463915 0.57626133 
    18497 Axis point 0.00000000 23.05515362 346.04002443 
    18498 Rotation angle (degrees) 107.22113422 
    18499 Shift along axis 8.90662490 
    18500  
    18501 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18502 (#1) using 3401 atoms 
    18503 average map value = 0.1078, steps = 28 
    18504 shifted from previous position = 0.017 
    18505 rotated from previous position = 0.0169 degrees 
    18506 atoms outside contour = 1608, contour level = 0.072 
    18507  
    18508 Position of F562a.pdb (#4) relative to
    18509 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18510 Matrix rotation and translation 
    18511 0.18543237 -0.12023134 -0.97527394 334.76776945 
    18512 0.98049261 0.08847529 0.17551742 -44.49851310 
    18513 0.06518495 -0.98879550 0.13429212 327.47372226 
    18514 Axis -0.60944823 -0.54461805 0.57616320 
    18515 Axis point 0.00000000 23.10963968 345.96113737 
    18516 Rotation angle (degrees) 107.21151966 
    18517 Shift along axis 8.88937821 
    18518  
    18519 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18520 (#1) using 3401 atoms 
    18521 average map value = 0.1078, steps = 44 
    18522 shifted from previous position = 0.0205 
    18523 rotated from previous position = 0.0218 degrees 
    18524 atoms outside contour = 1604, contour level = 0.072 
    18525  
    18526 Position of F562a.pdb (#4) relative to
    18527 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18528 Matrix rotation and translation 
    18529 0.18554107 -0.12011878 -0.97526714 334.73699226 
    18530 0.98049338 0.08814571 0.17567888 -44.47566373 
    18531 0.06486328 -0.98883862 0.13413032 327.56427605 
    18532 Axis -0.60959315 -0.54447990 0.57614045 
    18533 Axis point 0.00000000 23.17721063 345.92539580 
    18534 Rotation angle (degrees) 107.22299700 
    18535 Shift along axis 8.88575635 
    18536  
    18537 
    18538 > transparency #1.1 50
    18539 
    18540 > view matrix models
    18541 > #4,0.95986,-0.22484,0.16768,73.526,0.27579,0.64758,-0.71034,90.606,0.051126,0.72807,0.68359,-47.104
    18542 
    18543 > view matrix models
    18544 > #4,0.75847,0.64831,0.066474,-35.582,0.26049,-0.20809,-0.94278,276.59,-0.59738,0.73239,-0.32671,193.1
    18545 
    18546 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18547 (#1) using 3401 atoms 
    18548 average map value = 0.09049, steps = 88 
    18549 shifted from previous position = 2.42 
    18550 rotated from previous position = 6.19 degrees 
    18551 atoms outside contour = 1911, contour level = 0.072 
    18552  
    18553 Position of F562a.pdb (#4) relative to
    18554 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18555 Matrix rotation and translation 
    18556 0.72637414 0.68694818 -0.02197301 -24.03798979 
    18557 0.18664733 -0.22792648 -0.95562142 294.38643021 
    18558 -0.66147062 0.69003748 -0.29377694 209.53189487 
    18559 Axis 0.89678670 0.34848835 -0.27263435 
    18560 Axis point 0.00000000 72.78629578 205.81231454 
    18561 Rotation angle (degrees) 113.43226483 
    18562 Shift along axis 23.90769923 
    18563  
    18564 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18565 (#1) using 3401 atoms 
    18566 average map value = 0.0905, steps = 44 
    18567 shifted from previous position = 0.0137 
    18568 rotated from previous position = 0.0204 degrees 
    18569 atoms outside contour = 1906, contour level = 0.072 
    18570  
    18571 Position of F562a.pdb (#4) relative to
    18572 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18573 Matrix rotation and translation 
    18574 0.72623985 0.68709241 -0.02190190 -24.03578291 
    18575 0.18654834 -0.22764140 -0.95570869 294.36480593 
    18576 -0.66164597 0.68998798 -0.29349821 209.53312556 
    18577 Axis 0.89671635 0.34858730 -0.27273923 
    18578 Axis point 0.00000000 72.74870511 205.83733915 
    18579 Rotation angle (degrees) 113.41885466 
    18580 Shift along axis 23.91065009 
    18581  
    18582 
    18583 > view matrix models
    18584 > #4,0.4777,0.81916,-0.31746,33.473,0.28288,-0.48553,-0.82719,308.03,-0.83173,0.30535,-0.46366,331.51
    18585 
    18586 > view matrix models
    18587 > #4,0.53443,0.7221,-0.43927,54.882,0.15416,-0.59427,-0.78935,347.48,-0.83104,0.35413,-0.42891,318.4
    18588 
    18589 > view matrix models
    18590 > #4,0.55861,0.65321,-0.51116,71.372,0.070767,-0.65156,-0.75529,369.52,-0.82641,0.38574,-0.41019,309.57
    18591 
    18592 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18593 (#1) using 3401 atoms 
    18594 average map value = 0.0972, steps = 104 
    18595 shifted from previous position = 3.1 
    18596 rotated from previous position = 2.07 degrees 
    18597 atoms outside contour = 1844, contour level = 0.072 
    18598  
    18599 Position of F562a.pdb (#4) relative to
    18600 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18601 Matrix rotation and translation 
    18602 0.58731938 0.63730986 -0.49889086 69.51709433 
    18603 0.06189895 -0.64996950 -0.75743526 371.85473470 
    18604 -0.80698480 0.41397558 -0.42118849 304.38816914 
    18605 Axis 0.87354940 0.22975311 -0.42909784 
    18606 Axis point 0.00000000 108.25389938 250.40641939 
    18607 Rotation angle (degrees) 137.89516888 
    18608 Shift along axis 15.54909083 
    18609  
    18610 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18611 (#1) using 3401 atoms 
    18612 average map value = 0.0972, steps = 100 
    18613 shifted from previous position = 0.0102 
    18614 rotated from previous position = 0.0178 degrees 
    18615 atoms outside contour = 1844, contour level = 0.072 
    18616  
    18617 Position of F562a.pdb (#4) relative to
    18618 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18619 Matrix rotation and translation 
    18620 0.58732049 0.63712467 -0.49912604 69.58840441 
    18621 0.06165901 -0.65012663 -0.75731997 371.91413492 
    18622 -0.80700236 0.41401391 -0.42111716 304.37603978 
    18623 Axis 0.87355306 0.22960687 -0.42916866 
    18624 Axis point 0.00000000 108.28874120 250.42594564 
    18625 Rotation angle (degrees) 137.89878759 
    18626 Shift along axis 15.55454641 
    18627  
    18628 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18629 (#1) using 3401 atoms 
    18630 average map value = 0.0972, steps = 84 
    18631 shifted from previous position = 0.011 
    18632 rotated from previous position = 0.0172 degrees 
    18633 atoms outside contour = 1844, contour level = 0.072 
    18634  
    18635 Position of F562a.pdb (#4) relative to
    18636 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18637 Matrix rotation and translation 
    18638 0.58733885 0.63729229 -0.49889038 69.51578518 
    18639 0.06188954 -0.64997620 -0.75743028 371.85701767 
    18640 -0.80697135 0.41399213 -0.42119800 304.38350057 
    18641 Axis 0.87355567 0.22974281 -0.42909059 
    18642 Axis point 0.00000000 108.25696578 250.40359329 
    18643 Rotation angle (degrees) 137.89502914 
    18644 Shift along axis 15.54928904 
    18645  
    18646 
    18647 > view matrix models
    18648 > #4,0.65819,-0.32045,-0.68124,252,0.74547,0.15105,0.6492,-68.256,-0.10513,-0.93515,0.3383,328.44
    18649 
    18650 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18651 (#1) using 3401 atoms 
    18652 average map value = 0.102, steps = 172 
    18653 shifted from previous position = 4.22 
    18654 rotated from previous position = 10.1 degrees 
    18655 atoms outside contour = 1745, contour level = 0.072 
    18656  
    18657 Position of F562a.pdb (#4) relative to
    18658 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18659 Matrix rotation and translation 
    18660 0.62980729 -0.32213914 -0.70680207 259.21419516 
    18661 0.77615676 0.29659722 0.55642680 -86.34491343 
    18662 0.03038868 -0.89903085 0.43682956 282.25072430 
    18663 Axis -0.74003611 -0.37482903 0.55843509 
    18664 Axis point 0.00000000 121.16366768 309.58820660 
    18665 Rotation angle (degrees) 79.53603811 
    18666 Shift along axis -1.84457671 
    18667  
    18668 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18669 (#1) using 3401 atoms 
    18670 average map value = 0.1019, steps = 48 
    18671 shifted from previous position = 0.0802 
    18672 rotated from previous position = 0.389 degrees 
    18673 atoms outside contour = 1748, contour level = 0.072 
    18674  
    18675 Position of F562a.pdb (#4) relative to
    18676 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18677 Matrix rotation and translation 
    18678 0.62493642 -0.32416938 -0.71018919 260.92042942 
    18679 0.78000765 0.29690303 0.55085085 -86.37873091 
    18680 0.03228835 -0.89819976 0.43840012 281.55642716 
    18681 Axis -0.73657217 -0.37741145 0.56126823 
    18682 Axis point 0.00000000 119.97837519 311.01534570 
    18683 Rotation angle (degrees) 79.62326298 
    18684 Shift along axis -1.55772605 
    18685  
    18686 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18687 (#1) using 3401 atoms 
    18688 average map value = 0.1019, steps = 44 
    18689 shifted from previous position = 0.00561 
    18690 rotated from previous position = 0.0322 degrees 
    18691 atoms outside contour = 1746, contour level = 0.072 
    18692  
    18693 Position of F562a.pdb (#4) relative to
    18694 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18695 Matrix rotation and translation 
    18696 0.62451536 -0.32441238 -0.71044858 261.07250560 
    18697 0.78034368 0.29682398 0.55041736 -86.36985039 
    18698 0.03231597 -0.89813815 0.43852428 281.52393140 
    18699 Axis -0.73629476 -0.37754414 0.56154292 
    18700 Axis point 0.00000000 119.89834457 311.14057931 
    18701 Rotation angle (degrees) 79.63421202 
    18702 Shift along axis -1.53011648 
    18703  
    18704 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18705 (#1) using 3401 atoms 
    18706 average map value = 0.1019, steps = 80 
    18707 shifted from previous position = 0.189 
    18708 rotated from previous position = 1.07 degrees 
    18709 atoms outside contour = 1750, contour level = 0.072 
    18710  
    18711 Position of F562a.pdb (#4) relative to
    18712 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18713 Matrix rotation and translation 
    18714 0.61106207 -0.33151468 -0.71881930 265.86650256 
    18715 0.79073980 0.29753498 0.53497991 -86.41685086 
    18716 0.03652019 -0.89530496 0.44395419 279.51480621 
    18717 Axis -0.72651910 -0.38367781 0.57005380 
    18718 Axis point 0.00000000 116.77430340 315.34054751 
    18719 Rotation angle (degrees) 79.84710044 
    18720 Shift along axis -0.66238880 
    18721  
    18722 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18723 (#1) using 3401 atoms 
    18724 average map value = 0.1019, steps = 60 
    18725 shifted from previous position = 0.014 
    18726 rotated from previous position = 0.0403 degrees 
    18727 atoms outside contour = 1749, contour level = 0.072 
    18728  
    18729 Position of F562a.pdb (#4) relative to
    18730 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18731 Matrix rotation and translation 
    18732 0.61056528 -0.33194773 -0.71904155 266.05161554 
    18733 0.79112724 0.29741686 0.53447255 -86.39981112 
    18734 0.03643813 -0.89518374 0.44420530 279.47442312 
    18735 Axis -0.72617579 -0.38373633 0.57045170 
    18736 Axis point 0.00000000 116.70216550 315.50779421 
    18737 Rotation angle (degrees) 79.85768786 
    18738 Shift along axis -0.61883651 
    18739  
    18740 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18741 (#1) using 3401 atoms 
    18742 average map value = 0.1019, steps = 56 
    18743 shifted from previous position = 0.00922 
    18744 rotated from previous position = 0.0302 degrees 
    18745 atoms outside contour = 1747, contour level = 0.072 
    18746  
    18747 Position of F562a.pdb (#4) relative to
    18748 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18749 Matrix rotation and translation 
    18750 0.61096453 -0.33178461 -0.71877766 265.91505542 
    18751 0.79082389 0.29745317 0.53490111 -86.40973158 
    18752 0.03633074 -0.89523215 0.44411653 279.51627475 
    18753 Axis -0.72644097 -0.38355984 0.57023274 
    18754 Axis point -0.00000000 116.79213793 315.39803173 
    18755 Rotation angle (degrees) 79.84759520 
    18756 Shift along axis -0.63895706 
    18757  
    18758 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18759 (#1) using 3401 atoms 
    18760 average map value = 0.1019, steps = 60 
    18761 shifted from previous position = 0.0112 
    18762 rotated from previous position = 0.0392 degrees 
    18763 atoms outside contour = 1755, contour level = 0.072 
    18764  
    18765 Position of F562a.pdb (#4) relative to
    18766 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18767 Matrix rotation and translation 
    18768 0.61092141 -0.33119723 -0.71908514 265.86201413 
    18769 0.79084444 0.29729954 0.53495614 -86.39268360 
    18770 0.03660768 -0.89550063 0.44355214 279.58799940 
    18771 Axis -0.72655505 -0.38383015 0.56990540 
    18772 Axis point 0.00000000 116.72048670 315.29183470 
    18773 Rotation angle (degrees) 79.86974659 
    18774 Shift along axis -0.66456157 
    18775  
    18776 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18777 (#1) using 3401 atoms 
    18778 average map value = 0.1019, steps = 48 
    18779 shifted from previous position = 0.0123 
    18780 rotated from previous position = 0.0779 degrees 
    18781 atoms outside contour = 1747, contour level = 0.072 
    18782  
    18783 Position of F562a.pdb (#4) relative to
    18784 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18785 Matrix rotation and translation 
    18786 0.61046660 -0.33218219 -0.71901706 266.11491018 
    18787 0.79119095 0.29782655 0.53415002 -86.45092816 
    18788 0.03670725 -0.89496053 0.44463270 279.33262127 
    18789 Axis -0.72594735 -0.38388637 0.57064148 
    18790 Axis point 0.00000000 116.64464322 315.61501173 
    18791 Rotation angle (degrees) 79.83619740 
    18792 Shift along axis -0.59930216 
    18793  
    18794 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18795 (#1) using 3401 atoms 
    18796 average map value = 0.1019, steps = 36 
    18797 shifted from previous position = 0.00553 
    18798 rotated from previous position = 0.0185 degrees 
    18799 atoms outside contour = 1746, contour level = 0.072 
    18800  
    18801 Position of F562a.pdb (#4) relative to
    18802 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18803 Matrix rotation and translation 
    18804 0.61052405 -0.33197184 -0.71906543 266.07628678 
    18805 0.79114928 0.29764543 0.53431266 -86.42628442 
    18806 0.03664978 -0.89509882 0.44435898 279.40085187 
    18807 Axis -0.72607396 -0.38386786 0.57049283 
    18808 Axis point 0.00000000 116.66062451 315.54721201 
    18809 Rotation angle (degrees) 79.84776315 
    18810 Shift along axis -0.61860883 
    18811  
    18812 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18813 (#1) using 3401 atoms 
    18814 average map value = 0.1019, steps = 48 
    18815 shifted from previous position = 0.0181 
    18816 rotated from previous position = 0.0284 degrees 
    18817 atoms outside contour = 1749, contour level = 0.072 
    18818  
    18819 Position of F562a.pdb (#4) relative to
    18820 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18821 Matrix rotation and translation 
    18822 0.61082613 -0.33169276 -0.71893766 265.95113585 
    18823 0.79091989 0.29755592 0.53470198 -86.43037190 
    18824 0.03656738 -0.89523203 0.44409733 279.47798684 
    18825 Axis -0.72633614 -0.38375939 0.57023200 
    18826 Axis point -0.00000000 116.71858763 315.43181746 
    18827 Rotation angle (degrees) 79.84919126 
    18828 Shift along axis -0.63416214 
    18829  
    18830 
    18831 > view matrix models
    18832 > #4,0.4439,-0.28201,-0.85054,303.77,0.88884,0.018251,0.45784,-44.907,-0.11359,-0.95924,0.25876,341.18
    18833 
    18834 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18835 (#1) using 3401 atoms 
    18836 average map value = 0.1055, steps = 424 
    18837 shifted from previous position = 2.2 
    18838 rotated from previous position = 6.39 degrees 
    18839 atoms outside contour = 1635, contour level = 0.072 
    18840  
    18841 Position of F562a.pdb (#4) relative to
    18842 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18843 Matrix rotation and translation 
    18844 0.47014986 -0.27680804 -0.83805515 296.29282889 
    18845 0.88242695 0.12936746 0.45231266 -60.98673857 
    18846 -0.01678672 -0.95217718 0.30508496 317.15529629 
    18847 Axis -0.70304515 -0.41110215 0.58027799 
    18848 Axis point 0.00000000 97.60706796 321.98215187 
    18849 Rotation angle (degrees) 92.73398070 
    18850 Shift along axis 0.80277942 
    18851  
    18852 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18853 (#1) using 3401 atoms 
    18854 average map value = 0.1055, steps = 44 
    18855 shifted from previous position = 0.0281 
    18856 rotated from previous position = 0.296 degrees 
    18857 atoms outside contour = 1634, contour level = 0.072 
    18858  
    18859 Position of F562a.pdb (#4) relative to
    18860 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18861 Matrix rotation and translation 
    18862 0.47131282 -0.27849458 -0.83684228 296.21168106 
    18863 0.88186020 0.13410185 0.45203904 -61.71403302 
    18864 -0.01366832 -0.95102969 0.30879721 315.93242787 
    18865 Axis -0.70218063 -0.41196614 0.58071186 
    18866 Axis point 0.00000000 97.40904882 322.29816415 
    18867 Rotation angle (degrees) 92.45840264 
    18868 Shift along axis 0.89569574 
    18869  
    18870 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18871 (#1) using 3401 atoms 
    18872 average map value = 0.1055, steps = 40 
    18873 shifted from previous position = 0.0165 
    18874 rotated from previous position = 0.16 degrees 
    18875 atoms outside contour = 1637, contour level = 0.072 
    18876  
    18877 Position of F562a.pdb (#4) relative to
    18878 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18879 Matrix rotation and translation 
    18880 0.47202347 -0.27915399 -0.83622180 296.12646474 
    18881 0.88150690 0.13674791 0.45193539 -62.12511633 
    18882 -0.01180798 -0.95045940 0.31062439 315.27843547 
    18883 Axis -0.70176755 -0.41254208 0.58080232 
    18884 Axis point 0.00000000 97.28028496 322.43137386 
    18885 Rotation angle (degrees) 92.30976635 
    18886 Shift along axis 0.93172962 
    18887  
    18888 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18889 (#1) using 3401 atoms 
    18890 average map value = 0.1055, steps = 40 
    18891 shifted from previous position = 0.0221 
    18892 rotated from previous position = 0.193 degrees 
    18893 atoms outside contour = 1638, contour level = 0.072 
    18894  
    18895 Position of F562a.pdb (#4) relative to
    18896 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18897 Matrix rotation and translation 
    18898 0.47308077 -0.28050864 -0.83517034 296.03384583 
    18899 0.88096007 0.13964438 0.45211592 -62.58112928 
    18900 -0.01019558 -0.94963907 0.31317998 314.52160203 
    18901 Axis -0.70135897 -0.41277074 0.58113330 
    18902 Axis point 0.00000000 97.26838533 322.61659552 
    18903 Rotation angle (degrees) 92.12314752 
    18904 Shift along axis 0.98464198 
    18905  
    18906 
    18907 > transparency #1.1 0
    18908 
    18909 > view matrix models
    18910 > #4,0.84021,-0.0035817,-0.54224,142.19,-0.39021,0.69038,-0.60919,201.03,0.37654,0.72344,0.57867,-93.731
    18911 
    18912 > view matrix models
    18913 > #4,0.79315,-0.11192,-0.59866,177.39,0.50761,-0.42168,0.75135,74.2,-0.33653,-0.89981,-0.27764,436.47
    18914 
    18915 > view matrix models
    18916 > #4,0.7358,0.3335,-0.58938,106.02,-0.64815,0.094684,-0.7556,375.07,-0.19619,0.93798,0.28583,9.2542
    18917 
    18918 > view matrix models
    18919 > #4,0.79115,-0.59673,-0.13416,211.08,0.60994,0.75351,0.24535,-98.992,-0.045318,-0.27593,0.96011,122.12
    18920 
    18921 > view matrix models
    18922 > #4,0.66555,-0.4336,-0.60749,260.88,0.69641,0.65352,0.29652,-103.07,0.26843,-0.62041,0.73691,152.31
    18923 
    18924 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18925 (#1) using 3401 atoms 
    18926 average map value = 0.1, steps = 416 
    18927 shifted from previous position = 2.7 
    18928 rotated from previous position = 17.5 degrees 
    18929 atoms outside contour = 1774, contour level = 0.072 
    18930  
    18931 Position of F562a.pdb (#4) relative to
    18932 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18933 Matrix rotation and translation 
    18934 0.67732915 -0.28469604 -0.67836083 239.91883502 
    18935 0.71088577 0.49065254 0.50388643 -103.74543128 
    18936 0.18938499 -0.82353401 0.53471962 227.48787848 
    18937 Axis -0.70890735 -0.46341865 0.53168931 
    18938 Axis point 0.00000000 101.86597662 309.82596584 
    18939 Rotation angle (degrees) 69.43005060 
    18940 Shift along axis -1.04978373 
    18941  
    18942 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18943 (#1) using 3401 atoms 
    18944 average map value = 0.1, steps = 44 
    18945 shifted from previous position = 0.00594 
    18946 rotated from previous position = 0.0194 degrees 
    18947 atoms outside contour = 1776, contour level = 0.072 
    18948  
    18949 Position of F562a.pdb (#4) relative to
    18950 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18951 Matrix rotation and translation 
    18952 0.67756361 -0.28454385 -0.67819052 239.83133941 
    18953 0.71064745 0.49081816 0.50406126 -103.75597407 
    18954 0.18944069 -0.82348792 0.53477088 227.46549023 
    18955 Axis -0.70904026 -0.46339937 0.53152886 
    18956 Axis point 0.00000000 101.90886125 309.76335536 
    18957 Rotation angle (degrees) 69.41623953 
    18958 Shift along axis -1.06514982 
    18959  
    18960 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18961 (#1) using 3401 atoms 
    18962 average map value = 0.09997, steps = 40 
    18963 shifted from previous position = 0.0133 
    18964 rotated from previous position = 0.00996 degrees 
    18965 atoms outside contour = 1778, contour level = 0.072 
    18966  
    18967 Position of F562a.pdb (#4) relative to
    18968 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18969 Matrix rotation and translation 
    18970 0.67763562 -0.28462709 -0.67808363 239.81516361 
    18971 0.71058849 0.49090368 0.50406111 -103.75178064 
    18972 0.18940430 -0.82340817 0.53490655 227.43306000 
    18973 Axis -0.70903930 -0.46335011 0.53157309 
    18974 Axis point 0.00000000 101.93201901 309.76345143 
    18975 Rotation angle (degrees) 69.40726713 
    18976 Shift along axis -1.06768104 
    18977  
    18978 
    18979 > view matrix models
    18980 > #4,0.67386,0.21665,-0.70638,152.68,-0.73712,0.13162,-0.66282,370.99,-0.050625,0.96733,0.2484,-19.457
    18981 
    18982 > view matrix models
    18983 > #4,0.26977,0.74198,-0.61375,121.96,-0.64983,-0.33008,-0.68467,441.19,-0.7106,0.58353,0.39312,157.04
    18984 
    18985 > view matrix models
    18986 > #4,0.83537,0.35405,-0.42048,63.612,-0.53507,0.34852,-0.76957,306.25,-0.12592,0.86786,0.48059,-14.673
    18987 
    18988 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    18989 (#1) using 3401 atoms 
    18990 average map value = 0.1062, steps = 108 
    18991 shifted from previous position = 1.02 
    18992 rotated from previous position = 11.1 degrees 
    18993 atoms outside contour = 1639, contour level = 0.072 
    18994  
    18995 Position of F562a.pdb (#4) relative to
    18996 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    18997 Matrix rotation and translation 
    18998 0.88907475 0.29063713 -0.35366111 56.95234558 
    18999 -0.45699328 0.51877555 -0.72251581 256.52548266 
    19000 -0.02651919 0.80399130 0.59404945 -35.16228912 
    19001 Axis 0.88188843 -0.18899530 -0.43191847 
    19002 Axis point 0.00000000 161.74872048 251.74241852 
    19003 Rotation angle (degrees) 59.93713751 
    19004 Shift along axis 16.93074519 
    19005  
    19006 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19007 (#1) using 3401 atoms 
    19008 average map value = 0.1062, steps = 44 
    19009 shifted from previous position = 0.0122 
    19010 rotated from previous position = 0.077 degrees 
    19011 atoms outside contour = 1637, contour level = 0.072 
    19012  
    19013 Position of F562a.pdb (#4) relative to
    19014 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19015 Matrix rotation and translation 
    19016 0.88924092 0.29042756 -0.35341541 56.93133633 
    19017 -0.45670512 0.51991995 -0.72187513 256.18534624 
    19018 -0.02590471 0.80332752 0.59497383 -35.27785394 
    19019 Axis 0.88179482 -0.18935008 -0.43195422 
    19020 Axis point -0.00000000 161.74523741 251.76190662 
    19021 Rotation angle (degrees) 59.86313127 
    19022 Shift along axis 16.93146051 
    19023  
    19024 
    19025 > view matrix models
    19026 > #4,0.83879,0.21495,-0.50022,97.467,-0.52296,0.062549,-0.85006,366.96,-0.15144,0.97462,0.16488,7.9202
    19027 
    19028 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19029 (#1) using 3401 atoms 
    19030 average map value = 0.1097, steps = 264 
    19031 shifted from previous position = 0.803 
    19032 rotated from previous position = 13.4 degrees 
    19033 atoms outside contour = 1566, contour level = 0.072 
    19034  
    19035 Position of F562a.pdb (#4) relative to
    19036 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19037 Matrix rotation and translation 
    19038 0.90125965 0.23249395 -0.36561951 66.81826163 
    19039 -0.42074684 0.26813163 -0.86664730 312.38684742 
    19040 -0.10345610 0.93490749 0.33947732 -14.03685609 
    19041 Axis 0.93143071 -0.13554240 -0.33773523 
    19042 Axis point 0.00000000 165.03559591 224.93775063 
    19043 Rotation angle (degrees) 75.25993272 
    19044 Shift along axis 24.63566001 
    19045  
    19046 
    19047 > view matrix models
    19048 > #4,0.85035,0.35218,-0.39099,57.593,-0.48265,0.22596,-0.84616,329.25,-0.20965,0.90825,0.36212,8.0544
    19049 
    19050 > ui mousemode right "translate selected models"
    19051 
    19052 > view matrix models
    19053 > #4,0.85035,0.35218,-0.39099,60.231,-0.48265,0.22596,-0.84616,326.26,-0.20965,0.90825,0.36212,12.759
    19054 
    19055 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19056 (#1) using 3401 atoms 
    19057 average map value = 0.1101, steps = 168 
    19058 shifted from previous position = 2.33 
    19059 rotated from previous position = 5.98 degrees 
    19060 atoms outside contour = 1596, contour level = 0.072 
    19061  
    19062 Position of F562a.pdb (#4) relative to
    19063 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19064 Matrix rotation and translation 
    19065 0.88028089 0.25385290 -0.40082949 74.19694561 
    19066 -0.45618497 0.22068248 -0.86208731 322.45385437 
    19067 -0.13038732 0.94173137 0.31006645 -3.17418883 
    19068 Axis 0.92158142 -0.13817047 -0.36276246 
    19069 Axis point 0.00000000 162.85511452 230.82234394 
    19070 Rotation angle (degrees) 78.14035717 
    19071 Shift along axis 24.97640109 
    19072  
    19073 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19074 (#1) using 3401 atoms 
    19075 average map value = 0.1101, steps = 64 
    19076 shifted from previous position = 0.011 
    19077 rotated from previous position = 0.0221 degrees 
    19078 atoms outside contour = 1600, contour level = 0.072 
    19079  
    19080 Position of F562a.pdb (#4) relative to
    19081 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19082 Matrix rotation and translation 
    19083 0.88011312 0.25412437 -0.40102585 74.19170998 
    19084 -0.45646647 0.22069435 -0.86193525 322.48434036 
    19085 -0.13053461 0.94165537 0.31023525 -3.15440043 
    19086 Axis 0.92146618 -0.13819573 -0.36304548 
    19087 Axis point 0.00000000 162.86097718 230.89097488 
    19088 Rotation angle (degrees) 78.13997962 
    19089 Shift along axis 24.94438268 
    19090  
    19091 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19092 (#1) using 3401 atoms 
    19093 average map value = 0.1101, steps = 64 
    19094 shifted from previous position = 0.00421 
    19095 rotated from previous position = 0.0136 degrees 
    19096 atoms outside contour = 1600, contour level = 0.072 
    19097  
    19098 Position of F562a.pdb (#4) relative to
    19099 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19100 Matrix rotation and translation 
    19101 0.88018838 0.25419012 -0.40081894 74.13944294 
    19102 -0.45629950 0.22079847 -0.86199700 322.44263683 
    19103 -0.13061091 0.94161321 0.31033107 -3.14778151 
    19104 Axis 0.92150340 -0.13805512 -0.36300449 
    19105 Axis point 0.00000000 162.82540766 230.87431985 
    19106 Rotation angle (degrees) 78.13192347 
    19107 Shift along axis 24.94755119 
    19108  
    19109 
    19110 > view matrix models
    19111 > #4,0.88019,0.25419,-0.40082,73.448,-0.4563,0.2208,-0.862,321.07,-0.13061,0.94161,0.31033,-5.8994
    19112 
    19113 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19114 (#1) using 3401 atoms 
    19115 average map value = 0.1115, steps = 160 
    19116 shifted from previous position = 2.99 
    19117 rotated from previous position = 8.44 degrees 
    19118 atoms outside contour = 1603, contour level = 0.072 
    19119  
    19120 Position of F562a.pdb (#4) relative to
    19121 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19122 Matrix rotation and translation 
    19123 0.87327534 0.17162879 -0.45599755 97.28727310 
    19124 -0.48720393 0.31672140 -0.81383039 304.58441441 
    19125 0.00474745 0.93286180 0.36020320 -32.68286674 
    19126 Axis 0.90839597 -0.23961801 -0.34263678 
    19127 Axis point 0.00000000 182.33141527 229.00675692 
    19128 Rotation angle (degrees) 74.03202850 
    19129 Shift along axis 26.58980844 
    19130  
    19131 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19132 (#1) using 3401 atoms 
    19133 average map value = 0.1115, steps = 80 
    19134 shifted from previous position = 0.0187 
    19135 rotated from previous position = 0.0503 degrees 
    19136 atoms outside contour = 1606, contour level = 0.072 
    19137  
    19138 Position of F562a.pdb (#4) relative to
    19139 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19140 Matrix rotation and translation 
    19141 0.87307788 0.17102576 -0.45660182 97.51562460 
    19142 -0.48755025 0.31670719 -0.81362849 304.62173537 
    19143 0.00545764 0.93297736 0.35989370 -32.78455753 
    19144 Axis 0.90828067 -0.24028299 -0.34247673 
    19145 Axis point 0.00000000 182.48861826 229.00019788 
    19146 Rotation angle (degrees) 74.04755731 
    19147 Shift along axis 26.60408358 
    19148  
    19149 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19150 (#1) using 3401 atoms 
    19151 average map value = 0.1115, steps = 64 
    19152 shifted from previous position = 0.00983 
    19153 rotated from previous position = 0.00562 degrees 
    19154 atoms outside contour = 1605, contour level = 0.072 
    19155  
    19156 Position of F562a.pdb (#4) relative to
    19157 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19158 Matrix rotation and translation 
    19159 0.87308357 0.17093159 -0.45662622 97.52642834 
    19160 -0.48753906 0.31671935 -0.81363046 304.61327140 
    19161 0.00554721 0.93299049 0.35985828 -32.79571036 
    19162 Axis 0.90828615 -0.24034163 -0.34242104 
    19163 Axis point 0.00000000 182.49871036 228.98437979 
    19164 Rotation angle (degrees) 74.04808080 
    19165 Shift along axis 26.60059602 
    19166  
    19167 
    19168 > ui mousemode right "rotate selected models"
    19169 
    19170 > transparency #1.1 50
    19171 
    19172 > ui mousemode right "translate selected models"
    19173 
    19174 > view matrix models
    19175 > #4,0.87308,0.17093,-0.45663,98.781,-0.48754,0.31672,-0.81363,307.95,0.0055472,0.93299,0.35986,-31.624
    19176 
    19177 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19178 (#1) using 3401 atoms 
    19179 average map value = 0.1045, steps = 152 
    19180 shifted from previous position = 1.66 
    19181 rotated from previous position = 10.1 degrees 
    19182 atoms outside contour = 1670, contour level = 0.072 
    19183  
    19184 Position of F562a.pdb (#4) relative to
    19185 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19186 Matrix rotation and translation 
    19187 0.85430945 0.22816829 -0.46700601 94.00588935 
    19188 -0.50530889 0.15416741 -0.84905556 345.08239658 
    19189 -0.12173045 0.96133847 0.24700214 -1.12292161 
    19190 Axis 0.91267386 -0.17406375 -0.36976782 
    19191 Axis point 0.00000000 176.18270876 236.27702715 
    19192 Rotation angle (degrees) 82.66101368 
    19193 Shift along axis 26.14560144 
    19194  
    19195 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19196 (#1) using 3401 atoms 
    19197 average map value = 0.1045, steps = 60 
    19198 shifted from previous position = 0.00837 
    19199 rotated from previous position = 0.0183 degrees 
    19200 atoms outside contour = 1667, contour level = 0.072 
    19201  
    19202 Position of F562a.pdb (#4) relative to
    19203 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19204 Matrix rotation and translation 
    19205 0.85416080 0.22824487 -0.46724044 94.04888675 
    19206 -0.50553655 0.15397090 -0.84895570 345.14108146 
    19207 -0.12182835 0.96135179 0.24690203 -1.09962552 
    19208 Axis 0.91260386 -0.17412755 -0.36991051 
    19209 Axis point 0.00000000 176.20594034 236.31033169 
    19210 Rotation angle (degrees) 82.67387511 
    19211 Shift along axis 26.13756946 
    19212  
    19213 
    19214 > view matrix models
    19215 > #4,0.85416,0.22824,-0.46724,92.304,-0.50554,0.15397,-0.84896,343.85,-0.12183,0.96135,0.2469,-1.3966
    19216 
    19217 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19218 (#1) using 3401 atoms 
    19219 average map value = 0.1115, steps = 132 
    19220 shifted from previous position = 2.46 
    19221 rotated from previous position = 10.1 degrees 
    19222 atoms outside contour = 1603, contour level = 0.072 
    19223  
    19224 Position of F562a.pdb (#4) relative to
    19225 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19226 Matrix rotation and translation 
    19227 0.87327321 0.17148581 -0.45605541 97.32164807 
    19228 -0.48720576 0.31684479 -0.81378127 304.55640572 
    19229 0.00494684 0.93284619 0.36024093 -32.71905415 
    19230 Axis 0.90838381 -0.23975747 -0.34257148 
    19231 Axis point 0.00000000 182.35784967 228.99751317 
    19232 Rotation angle (degrees) 74.02729082 
    19233 Shift along axis 26.59434986 
    19234  
    19235 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19236 (#1) using 3401 atoms 
    19237 average map value = 0.1115, steps = 100 
    19238 shifted from previous position = 0.0199 
    19239 rotated from previous position = 0.0492 degrees 
    19240 atoms outside contour = 1607, contour level = 0.072 
    19241  
    19242 Position of F562a.pdb (#4) relative to
    19243 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19244 Matrix rotation and translation 
    19245 0.87291436 0.17135958 -0.45678926 97.50396396 
    19246 -0.48784609 0.31650499 -0.81352984 304.69020219 
    19247 0.00516995 0.93298473 0.35987885 -32.73221582 
    19248 Axis 0.90818184 -0.24021727 -0.34278478 
    19249 Axis point 0.00000000 182.47945606 229.06508608 
    19250 Rotation angle (degrees) 74.05889597 
    19251 Shift along axis 26.57958591 
    19252  
    19253 
    19254 > volume #1 step 1
    19255 
    19256 > volume #1 level 0.08
    19257 
    19258 > volume #2 step 1
    19259 
    19260 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19261 (#1) using 3401 atoms 
    19262 average map value = 0.1115, steps = 96 
    19263 shifted from previous position = 0.0269 
    19264 rotated from previous position = 0.0588 degrees 
    19265 atoms outside contour = 1705, contour level = 0.08 
    19266  
    19267 Position of F562a.pdb (#4) relative to
    19268 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19269 Matrix rotation and translation 
    19270 0.87339018 0.17133657 -0.45588748 97.30726750 
    19271 -0.48699588 0.31678456 -0.81393032 304.55388891 
    19272 0.00496208 0.93289407 0.36011672 -32.71648369 
    19273 Axis 0.90847710 -0.23967565 -0.34238127 
    19274 Axis point 0.00000000 182.34480224 228.95151912 
    19275 Rotation angle (degrees) 74.02930115 
    19276 Shift along axis 26.60878416 
    19277  
    19278 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19279 (#1) using 3401 atoms 
    19280 average map value = 0.1115, steps = 60 
    19281 shifted from previous position = 0.0234 
    19282 rotated from previous position = 0.0504 degrees 
    19283 atoms outside contour = 1711, contour level = 0.08 
    19284  
    19285 Position of F562a.pdb (#4) relative to
    19286 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19287 Matrix rotation and translation 
    19288 0.87307658 0.17097372 -0.45662380 97.51998587 
    19289 -0.48755237 0.31664803 -0.81365025 304.63116274 
    19290 0.00547621 0.93300698 0.35981662 -32.78056504 
    19291 Axis 0.90828882 -0.24029916 -0.34244377 
    19292 Axis point 0.00000000 182.49216804 228.98849803 
    19293 Rotation angle (degrees) 74.05165523 
    19294 Shift along axis 26.59919907 
    19295  
    19296 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19297 (#1) using 3401 atoms 
    19298 average map value = 0.1115, steps = 84 
    19299 shifted from previous position = 0.0236 
    19300 rotated from previous position = 0.0512 degrees 
    19301 atoms outside contour = 1709, contour level = 0.08 
    19302  
    19303 Position of F562a.pdb (#4) relative to
    19304 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19305 Matrix rotation and translation 
    19306 0.87330072 0.17150987 -0.45599367 97.31366850 
    19307 -0.48715626 0.31696366 -0.81376461 304.52650710 
    19308 0.00496476 0.93280138 0.36035670 -32.73218629 
    19309 Axis 0.90838730 -0.23974404 -0.34257162 
    19310 Axis point 0.00000000 182.35082823 229.00016180 
    19311 Rotation angle (degrees) 74.01947881 
    19312 Shift along axis 26.60320358 
    19313  
    19314 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19315 (#1) using 5602 atoms 
    19316 average map value = 0.09224, steps = 36 
    19317 shifted from previous position = 0.0101 
    19318 rotated from previous position = 0.0146 degrees 
    19319 atoms outside contour = 3383, contour level = 0.08 
    19320  
    19321 Position of D2NS1.pdb (#3) relative to
    19322 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19323 Matrix rotation and translation 
    19324 -0.06781116 0.24433459 0.96731706 -24.10970616 
    19325 -0.87336663 0.45417416 -0.17594486 287.52120019 
    19326 -0.48231982 -0.85675345 0.18259559 387.95373087 
    19327 Axis -0.34859656 0.74226213 -0.57230007 
    19328 Axis point 265.34079550 0.00000000 317.90521257 
    19329 Rotation angle (degrees) 102.44607735 
    19330 Shift along axis -0.20528738 
    19331  
    19332 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19333 (#1) using 5602 atoms 
    19334 average map value = 0.09224, steps = 40 
    19335 shifted from previous position = 0.00617 
    19336 rotated from previous position = 0.0174 degrees 
    19337 atoms outside contour = 3388, contour level = 0.08 
    19338  
    19339 Position of D2NS1.pdb (#3) relative to
    19340 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19341 Matrix rotation and translation 
    19342 -0.06800223 0.24456045 0.96724657 -24.09574276 
    19343 -0.87334229 0.45411451 -0.17621946 287.57652794 
    19344 -0.48233700 -0.85672063 0.18270418 387.93151574 
    19345 Axis -0.34844475 0.74224675 -0.57241245 
    19346 Axis point 265.30857487 0.00000000 317.93174566 
    19347 Rotation angle (degrees) 102.45024724 
    19348 Shift along axis -0.20805003 
    19349  
    19350 
    19351 > ui mousemode right "rotate selected models"
    19352 
    19353 > view matrix models
    19354 > #4,0.8783,0.21948,-0.42476,83.959,-0.47606,0.31931,-0.81939,302.68,-0.044211,0.92188,0.38494,-24.427
    19355 
    19356 > view matrix models
    19357 > #4,0.88185,0.18737,-0.43271,90.075,-0.47057,0.40846,-0.78213,281.03,0.030198,0.89334,0.44837,-40.684
    19358 
    19359 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19360 (#1) using 3401 atoms 
    19361 average map value = 0.1115, steps = 108 
    19362 shifted from previous position = 0.192 
    19363 rotated from previous position = 5.8 degrees 
    19364 atoms outside contour = 1706, contour level = 0.08 
    19365  
    19366 Position of F562a.pdb (#4) relative to
    19367 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19368 Matrix rotation and translation 
    19369 0.87316782 0.17153805 -0.45623751 97.35347505 
    19370 -0.48739404 0.31688450 -0.81365305 304.56284709 
    19371 0.00500214 0.93282310 0.36029997 -32.73417130 
    19372 Axis 0.90830421 -0.23988070 -0.34269623 
    19373 Axis point 0.00000000 182.38522859 229.02890887 
    19374 Rotation angle (degrees) 74.02748836 
    19375 Shift along axis 26.58569939 
    19376  
    19377 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19378 (#1) using 3401 atoms 
    19379 average map value = 0.1115, steps = 100 
    19380 shifted from previous position = 0.0157 
    19381 rotated from previous position = 0.0308 degrees 
    19382 atoms outside contour = 1714, contour level = 0.08 
    19383  
    19384 Position of F562a.pdb (#4) relative to
    19385 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19386 Matrix rotation and translation 
    19387 0.87319228 0.17106442 -0.45636852 97.46138911 
    19388 -0.48734683 0.31669009 -0.81375701 304.60534678 
    19389 0.00532251 0.93297608 0.35989904 -32.76360108 
    19390 Axis 0.90836070 -0.24009506 -0.34239627 
    19391 Axis point 0.00000000 182.44525999 228.97324319 
    19392 Rotation angle (degrees) 74.04449916 
    19393 Shift along axis 26.61399150 
    19394  
    19395 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19396 (#1) using 3401 atoms 
    19397 average map value = 0.1115, steps = 76 
    19398 shifted from previous position = 0.0215 
    19399 rotated from previous position = 0.0496 degrees 
    19400 atoms outside contour = 1707, contour level = 0.08 
    19401  
    19402 Position of F562a.pdb (#4) relative to
    19403 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19404 Matrix rotation and translation 
    19405 0.87344661 0.17154945 -0.45569927 97.23463453 
    19406 -0.48689717 0.31676739 -0.81399606 304.54231699 
    19407 0.00471009 0.93286078 0.36020634 -32.68225206 
    19408 Axis 0.90851141 -0.23945131 -0.34244721 
    19409 Axis point 0.00000000 182.29150588 228.95203805 
    19410 Rotation angle (degrees) 74.02546087 
    19411 Shift along axis 26.60766517 
    19412  
    19413 
    19414 > close #5
    19415 
    19416 > open "D:/OneDrive - Nanyang Technological
    19417 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562b.pdb"
    19418 
    19419 Chain information for F562b.pdb #5 
    19420 --- 
    19421 Chain | Description 
    19422 B | No description available 
    19423 C | No description available 
    19424  
    19425 
    19426 > select #5
    19427 
    19428 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    19429 
    19430 > view matrix models
    19431 > #5,0.88246,-0.46571,0.066244,91.139,0.4452,0.87234,0.20206,-101.84,-0.15189,-0.14881,0.97713,59.494
    19432 
    19433 > ui mousemode right "translate selected models"
    19434 
    19435 > view matrix models
    19436 > #5,0.88246,-0.46571,0.066244,31.321,0.4452,0.87234,0.20206,-110.9,-0.15189,-0.14881,0.97713,2.868
    19437 
    19438 > view matrix models
    19439 > #5,0.88246,-0.46571,0.066244,29.937,0.4452,0.87234,0.20206,-111.7,-0.15189,-0.14881,0.97713,-4.3706
    19440 
    19441 > view matrix models
    19442 > #5,0.91945,-0.24365,-0.30863,71.496,-0.34812,-0.86933,-0.35081,481.22,-0.18283,0.42999,-0.88413,336.53
    19443 
    19444 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19445 (#1) using 3401 atoms 
    19446 average map value = 0.1014, steps = 252 
    19447 shifted from previous position = 4.97 
    19448 rotated from previous position = 12.4 degrees 
    19449 atoms outside contour = 1810, contour level = 0.08 
    19450  
    19451 Position of F562b.pdb (#5) relative to
    19452 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19453 Matrix rotation and translation 
    19454 0.96186420 -0.19777272 -0.18895294 31.32789418 
    19455 -0.26901427 -0.80896731 -0.52268846 497.86596548 
    19456 -0.04948323 0.55358635 -0.83132038 280.55853441 
    19457 Axis 0.98957826 -0.12823509 -0.06550286 
    19458 Axis point 0.00000000 209.55045747 214.71270936 
    19459 Rotation angle (degrees) 147.05697484 
    19460 Shift along axis -51.21986933 
    19461  
    19462 
    19463 > view matrix models
    19464 > #5,0.96186,-0.19777,-0.18895,31.586,-0.26901,-0.80897,-0.52269,497.84,-0.049483,0.55359,-0.83132,280.45
    19465 
    19466 > view matrix models
    19467 > #5,0.96186,-0.19777,-0.18895,30.409,-0.26901,-0.80897,-0.52269,498.49,-0.049483,0.55359,-0.83132,281.14
    19468 
    19469 > view matrix models
    19470 > #5,0.88111,-0.30725,-0.35949,105.37,-0.46365,-0.71093,-0.52878,515.6,-0.093104,0.63259,-0.76887,259.2
    19471 
    19472 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19473 (#1) using 3401 atoms 
    19474 average map value = 0.1109, steps = 80 
    19475 shifted from previous position = 3.4 
    19476 rotated from previous position = 5.08 degrees 
    19477 atoms outside contour = 1772, contour level = 0.08 
    19478  
    19479 Position of F562b.pdb (#5) relative to
    19480 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19481 Matrix rotation and translation 
    19482 0.88807867 -0.23238898 -0.39662534 101.69393944 
    19483 -0.43540490 -0.70196949 -0.56361460 519.59851714 
    19484 -0.14744106 0.67322671 -0.72458742 250.51818794 
    19485 Axis 0.96785351 -0.19499177 -0.15886409 
    19486 Axis point 0.00000000 224.56879044 228.99496698 
    19487 Rotation angle (degrees) 140.28561169 
    19488 Shift along axis -42.69094177 
    19489  
    19490 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19491 (#1) using 3401 atoms 
    19492 average map value = 0.1109, steps = 40 
    19493 shifted from previous position = 0.0247 
    19494 rotated from previous position = 0.0823 degrees 
    19495 atoms outside contour = 1771, contour level = 0.08 
    19496  
    19497 Position of F562b.pdb (#5) relative to
    19498 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19499 Matrix rotation and translation 
    19500 0.88749875 -0.23316934 -0.39746451 102.13143422 
    19501 -0.43663025 -0.70123937 -0.56357554 519.69347155 
    19502 -0.14730923 0.67371761 -0.72415784 250.30786189 
    19503 Axis 0.96767878 -0.19564479 -0.15912543 
    19504 Axis point 0.00000000 224.69705024 229.03906748 
    19505 Rotation angle (degrees) 140.25962425 
    19506 Shift along axis -42.67524524 
    19507  
    19508 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19509 (#1) using 3401 atoms 
    19510 average map value = 0.1109, steps = 40 
    19511 shifted from previous position = 0.0089 
    19512 rotated from previous position = 0.0313 degrees 
    19513 atoms outside contour = 1770, contour level = 0.08 
    19514  
    19515 Position of F562b.pdb (#5) relative to
    19516 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19517 Matrix rotation and translation 
    19518 0.88726809 -0.23348649 -0.39779316 102.30830437 
    19519 -0.43710961 -0.70099140 -0.56351243 519.72597500 
    19520 -0.14727705 0.67386581 -0.72402648 250.24321586 
    19521 Axis 0.96761002 -0.19589960 -0.15923003 
    19522 Axis point 0.00000000 224.74651301 229.05595353 
    19523 Rotation angle (degrees) 140.25296234 
    19524 Shift along axis -42.66580653 
    19525  
    19526 
    19527 > view matrix models
    19528 > #5,0.90434,-0.19289,-0.38074,87.744,-0.3816,-0.76498,-0.51883,511.31,-0.19118,0.61449,-0.76541,278.75
    19529 
    19530 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19531 (#1) using 3401 atoms 
    19532 average map value = 0.1109, steps = 100 
    19533 shifted from previous position = 0.228 
    19534 rotated from previous position = 5.49 degrees 
    19535 atoms outside contour = 1772, contour level = 0.08 
    19536  
    19537 Position of F562b.pdb (#5) relative to
    19538 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19539 Matrix rotation and translation 
    19540 0.88741151 -0.23323538 -0.39762052 102.19303295 
    19541 -0.43675670 -0.70132020 -0.56337694 519.68635289 
    19542 -0.14745987 0.67361061 -0.72422672 250.37123988 
    19543 Axis 0.96765550 -0.19569262 -0.15920817 
    19544 Axis point 0.00000000 224.70331960 229.05340664 
    19545 Rotation angle (degrees) 140.27024302 
    19546 Shift along axis -42.67227987 
    19547  
    19548 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19549 (#1) using 3401 atoms 
    19550 average map value = 0.1109, steps = 80 
    19551 shifted from previous position = 0.0119 
    19552 rotated from previous position = 0.0244 degrees 
    19553 atoms outside contour = 1769, contour level = 0.08 
    19554  
    19555 Position of F562b.pdb (#5) relative to
    19556 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19557 Matrix rotation and translation 
    19558 0.88757691 -0.23309386 -0.39733424 102.06718757 
    19559 -0.43649500 -0.70124393 -0.56367462 519.68560309 
    19560 -0.14723913 0.67373898 -0.72415222 250.29116827 
    19561 Axis 0.96770087 -0.19558315 -0.15906683 
    19562 Axis point 0.00000000 224.68268474 229.02792313 
    19563 Rotation angle (degrees) 140.25607412 
    19564 Shift along axis -42.68426633 
    19565  
    19566 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19567 (#1) using 3401 atoms 
    19568 average map value = 0.1109, steps = 64 
    19569 shifted from previous position = 0.0443 
    19570 rotated from previous position = 0.146 degrees 
    19571 atoms outside contour = 1761, contour level = 0.08 
    19572  
    19573 Position of F562b.pdb (#5) relative to
    19574 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19575 Matrix rotation and translation 
    19576 0.88644690 -0.23468134 -0.39891925 102.92117215 
    19577 -0.43878232 -0.70033958 -0.56302270 519.80857088 
    19578 -0.14724801 0.67412844 -0.72378787 250.13865633 
    19579 Axis 0.96736944 -0.19679007 -0.15959331 
    19580 Axis point 0.00000000 224.90663730 229.11626097 
    19581 Rotation angle (degrees) 140.24985998 
    19582 Shift along axis -42.65082531 
    19583  
    19584 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19585 (#1) using 3401 atoms 
    19586 average map value = 0.1109, steps = 28 
    19587 shifted from previous position = 0.0228 
    19588 rotated from previous position = 0.0509 degrees 
    19589 atoms outside contour = 1770, contour level = 0.08 
    19590  
    19591 Position of F562b.pdb (#5) relative to
    19592 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19593 Matrix rotation and translation 
    19594 0.88682818 -0.23410569 -0.39840974 102.63155782 
    19595 -0.43798841 -0.70069517 -0.56319841 519.75407402 
    19596 -0.14731582 0.67395906 -0.72393179 250.21245718 
    19597 Axis 0.96748195 -0.19636048 -0.15944037 
    19598 Axis point 0.00000000 224.82302925 229.08819200 
    19599 Rotation angle (degrees) 140.25515764 
    19600 Shift along axis -42.65894548 
    19601  
    19602 Average map value = 0.1109 for 3401 atoms, 1770 outside contour 
    19603 Average map value = 0.1109 for 3401 atoms, 1770 outside contour 
    19604 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19605 (#1) using 3401 atoms 
    19606 average map value = 0.1109, steps = 40 
    19607 shifted from previous position = 0.0277 
    19608 rotated from previous position = 0.119 degrees 
    19609 atoms outside contour = 1770, contour level = 0.08 
    19610  
    19611 Position of F562b.pdb (#5) relative to
    19612 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19613 Matrix rotation and translation 
    19614 0.88773516 -0.23286893 -0.39711253 101.94821925 
    19615 -0.43614356 -0.70150514 -0.56362163 519.65415902 
    19616 -0.14732651 0.67354481 -0.72431506 250.37946507 
    19617 Axis 0.96774956 -0.19539029 -0.15900765 
    19618 Axis point 0.00000000 224.64447067 229.01845950 
    19619 Rotation angle (degrees) 140.26798555 
    19620 Shift along axis -42.68728231 
    19621  
    19622 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    19623 (#1) using 3401 atoms 
    19624 average map value = 0.1109, steps = 36 
    19625 shifted from previous position = 0.0101 
    19626 rotated from previous position = 0.0384 degrees 
    19627 atoms outside contour = 1772, contour level = 0.08 
    19628  
    19629 Position of F562b.pdb (#5) relative to
    19630 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19631 Matrix rotation and translation 
    19632 0.88743039 -0.23323831 -0.39757668 102.17484111 
    19633 -0.43673470 -0.70130263 -0.56341586 519.68061974 
    19634 -0.14741140 0.67362788 -0.72422052 250.35767544 
    19635 Axis 0.96766061 -0.19568838 -0.15918228 
    19636 Axis point 0.00000000 224.69868010 229.04697101 
    19637 Rotation angle (degrees) 140.26833165 
    19638 Shift along axis -42.67739283 
    19639  
    19640 
    19641 > ~select #5
    19642 
    19643 Nothing selected 
    19644 
    19645 > show #!2 models
    19646 
    19647 > select #2
    19648 
    19649 2 models selected 
    19650 
    19651 > view matrix models
    19652 > #2,0.19536,0.75362,0.62761,-85.152,-0.79186,-0.25635,0.5543,213.6,0.57862,-0.60527,0.54668,70.661
    19653 
    19654 > view matrix models
    19655 > #2,0.11282,0.94881,0.29501,-45.954,-0.85716,-0.057225,0.51186,202.13,0.50254,-0.31062,0.80683,-2.2981
    19656 
    19657 > view matrix models
    19658 > #2,0.11282,0.94881,0.29501,-10.942,-0.85716,-0.057225,0.51186,230.24,0.50254,-0.31062,0.80683,26.411
    19659 
    19660 > view matrix models
    19661 > #2,-0.3673,0.80202,0.47101,56.376,-0.91933,-0.38991,-0.052965,380.04,0.14117,-0.45246,0.88054,91.186
    19662 
    19663 > view matrix models
    19664 > #2,-0.37949,0.87152,0.31056,74.515,-0.81999,-0.16136,-0.54916,412.77,-0.42849,-0.46305,0.77587,198.78
    19665 
    19666 > view matrix models
    19667 > #2,-0.37949,0.87152,0.31056,77.692,-0.81999,-0.16136,-0.54916,412.77,-0.42849,-0.46305,0.77587,195.9
    19668 
    19669 > view matrix models
    19670 > #2,-0.4416,0.17153,0.88066,94.799,-0.84825,0.23999,-0.47209,346.93,-0.29232,-0.9555,0.039518,365.71
    19671 
    19672 > view matrix models
    19673 > #2,-0.16701,0.27438,0.94701,26.293,-0.9691,-0.22254,-0.10643,372.5,0.18155,-0.93552,0.30307,245.76
    19674 
    19675 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
    19676 cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points 
    19677 correlation = 0.3616, correlation about mean = 0.238, overlap = 5797 
    19678 steps = 816, shift = 17.1, angle = 92.5 degrees 
    19679  
    19680 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
    19681 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19682 Matrix rotation and translation 
    19683 -0.23884246 0.36253629 0.90084502 32.04958536 
    19684 -0.12095024 0.90936326 -0.39803210 133.21868643 
    19685 -0.96349643 -0.20402438 -0.17334571 390.21884814 
    19686 Axis 0.10022302 0.96310562 -0.24976572 
    19687 Axis point 169.19260085 0.00000000 200.88498104 
    19688 Rotation angle (degrees) 104.56110947 
    19689 Shift along axis 34.05247827 
    19690  
    19691 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
    19692 cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points 
    19693 correlation = 0.3616, correlation about mean = 0.238, overlap = 5797 
    19694 steps = 40, shift = 0.000646, angle = 0.0027 degrees 
    19695  
    19696 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
    19697 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19698 Matrix rotation and translation 
    19699 -0.23884389 0.36253338 0.90084582 32.04982504 
    19700 -0.12099611 0.90935469 -0.39803771 133.22769414 
    19701 -0.96349031 -0.20406771 -0.17332869 390.22127920 
    19702 Axis 0.10020344 0.96310196 -0.24978768 
    19703 Axis point 169.19590472 0.00000000 200.88843406 
    19704 Rotation angle (degrees) 104.56090162 
    19705 Shift along axis 34.05088824 
    19706  
    19707 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
    19708 cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points 
    19709 correlation = 0.3616, correlation about mean = 0.238, overlap = 5797 
    19710 steps = 40, shift = 2.75e-05, angle = 5.91e-05 degrees 
    19711  
    19712 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
    19713 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19714 Matrix rotation and translation 
    19715 -0.23884450 0.36253261 0.90084597 32.05002579 
    19716 -0.12099600 0.90935500 -0.39803705 133.22750949 
    19717 -0.96349017 -0.20406771 -0.17332945 390.22138385 
    19718 Axis 0.10020311 0.96310210 -0.24978726 
    19719 Axis point 169.19595961 -0.00000000 200.88835343 
    19720 Rotation angle (degrees) 104.56093288 
    19721 Shift along axis 34.05087684 
    19722  
    19723 
    19724 > hide #!1 models
    19725 
    19726 > ui mousemode right "rotate selected models"
    19727 
    19728 > view matrix models
    19729 > #2,-0.24143,0.39089,0.88821,30.445,-0.11992,0.89625,-0.42703,139.68,-0.96298,-0.20961,-0.16951,390.31
    19730 
    19731 > view matrix models
    19732 > #2,-0.24371,0.41583,0.87618,29.184,-0.11889,0.8838,-0.45252,145.47,-0.96253,-0.21445,-0.16596,390.36
    19733 
    19734 > view matrix models
    19735 > #2,-0.23248,0.44368,0.86551,25.173,-0.098419,0.87459,-0.47477,147.23,-0.96761,-0.19556,-0.15966,387.41
    19736 
    19737 > view matrix models
    19738 > #2,-0.015904,0.29362,0.95579,-1.8481,0.11672,0.94992,-0.28987,72.596,-0.99304,0.10695,-0.049378,329.9
    19739 
    19740 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
    19741 cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points 
    19742 correlation = 0.3636, correlation about mean = 0.2345, overlap = 5800 
    19743 steps = 160, shift = 4.43, angle = 14.2 degrees 
    19744  
    19745 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
    19746 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19747 Matrix rotation and translation 
    19748 -0.23589350 0.38613188 0.89177153 30.30521757 
    19749 0.14116968 0.92155092 -0.36168365 84.35973344 
    19750 -0.96147045 0.04057228 -0.27189798 372.10342069 
    19751 Axis 0.21036827 0.96919218 -0.12810818 
    19752 Axis point 149.90554609 -0.00000000 183.31483684 
    19753 Rotation angle (degrees) 107.04485499 
    19754 Shift along axis 40.46655914 
    19755  
    19756 
    19757 > transparency sel 50
    19758 
    19759 > view matrix models
    19760 > #2,-0.32117,0.35848,0.87655,50.083,0.35637,0.9033,-0.23885,33.297,-0.87741,0.23567,-0.41786,354.8
    19761 
    19762 > view matrix models
    19763 > #2,-0.25849,0.33315,0.90675,38.999,0.20781,0.93585,-0.2846,59.301,-0.9434,0.11486,-0.31114,365.02
    19764 
    19765 > hide #3 models
    19766 
    19767 > hide #4 models
    19768 
    19769 > hide #5 models
    19770 
    19771 > show #5 models
    19772 
    19773 > show #4 models
    19774 
    19775 > show #3 models
    19776 
    19777 > open "D:/OneDrive - Nanyang Technological
    19778 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
    19779 
    19780 Chain information for D2NS1-F562.pdb #6 
    19781 --- 
    19782 Chain | Description 
    19783 B | No description available 
    19784 C E | No description available 
    19785 D | No description available 
    19786 F | No description available 
    19787  
    19788 
    19789 > close #6
    19790 
    19791 > save "D:/OneDrive - Nanyang Technological
    19792 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1.pdb" models #3
    19793 > relModel #1
    19794 
    19795 > save "D:/OneDrive - Nanyang Technological
    19796 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562a.pdb" models #4
    19797 > relModel #1
    19798 
    19799 > save "D:/OneDrive - Nanyang Technological
    19800 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562b.pdb" models #5
    19801 > relModel #1
    19802 
    19803 > open "D:/OneDrive - Nanyang Technological
    19804 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
    19805 
    19806 Chain information for D2NS1-F562.pdb #6 
    19807 --- 
    19808 Chain | Description 
    19809 B | No description available 
    19810 C | No description available 
    19811  
    19812 
    19813 > close #6
    19814 
    19815 > open "D:/OneDrive - Nanyang Technological
    19816 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
    19817 
    19818 Chain information for D2NS1-F562.pdb #6 
    19819 --- 
    19820 Chain | Description 
    19821 A B | No description available 
    19822 C E | No description available 
    19823 D F | No description available 
    19824  
    19825 
    19826 > hide atoms
    19827 
    19828 > show cartoons
    19829 
    19830 > hide #3 models
    19831 
    19832 > hide #5 models
    19833 
    19834 > hide #4 models
    19835 
    19836 Fit molecule D2NS1-F562.pdb (#6) to map
    19837 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    19838 average map value = 0.1026, steps = 40 
    19839 shifted from previous position = 0.0103 
    19840 rotated from previous position = 0.00699 degrees 
    19841 atoms outside contour = 6863, contour level = 0.08 
    19842  
    19843 Position of D2NS1-F562.pdb (#6) relative to
    19844 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19845 Matrix rotation and translation 
    19846 1.00000000 -0.00007640 -0.00005950 0.01644925 
    19847 0.00007639 0.99999999 -0.00007418 0.00540007 
    19848 0.00005950 0.00007417 1.00000000 -0.02042262 
    19849 Axis 0.60809281 -0.48779755 0.62631995 
    19850 Axis point -36.04322257 258.47150214 0.00000000 
    19851 Rotation angle (degrees) 0.00698874 
    19852 Shift along axis -0.00542257 
    19853  
    19854 Fit molecule D2NS1-F562.pdb (#6) to map
    19855 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 12404 atoms 
    19856 average map value = 0.1322, steps = 204 
    19857 shifted from previous position = 3.17 
    19858 rotated from previous position = 16.9 degrees 
    19859 atoms outside contour = 7037, contour level = 0.14151 
    19860  
    19861 Position of D2NS1-F562.pdb (#6) relative to
    19862 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    19863 Matrix rotation and translation 
    19864 -0.15126719 0.47107682 -0.86902521 263.21094843 
    19865 0.40313494 0.83210747 0.38089281 -155.24920226 
    19866 0.90255217 -0.29271785 -0.31577809 100.07490639 
    19867 Axis -0.35517923 -0.93411153 -0.03582417 
    19868 Axis point 121.90346818 0.00000000 160.98219047 
    19869 Rotation angle (degrees) 108.50992410 
    19870 Shift along axis 47.94790735 
    19871  
    19872 
    19873 > show #3 models
    19874 
    19875 > mmaker #6 to #3
    19876 
    19877 Parameters 
    19878 --- 
    19879 Chain pairing | bb 
    19880 Alignment algorithm | Needleman-Wunsch 
    19881 Similarity matrix | BLOSUM-62 
    19882 SS fraction | 0.3 
    19883 Gap open (HH/SS/other) | 18/18/6 
    19884 Gap extend | 1 
    19885 SS matrix |  |  | H | S | O 
    19886 ---|---|---|--- 
    19887 H | 6 | -9 | -6 
    19888 S |  | 6 | -6 
    19889 O |  |  | 4 
    19890 Iteration cutoff | 2 
    19891  
    19892 Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
    19893 alignment score = 1871.9 
    19894 RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
    19895 0.023) 
    19896  
    19897 
    19898 > hide #6 models
    19899 
    19900 > hide #3 models
    19901 
    19902 > ui mousemode right "map eraser"
    19903 
    19904 > open "D:/OneDrive - Nanyang Technological
    19905 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J59_004_volume_map_sharp
    19906 > (3).mrc"
    19907 
    19908 Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc as #8, grid size
    19909 352,352,352, pixel 0.85, shown at level 0.366, step 2, values float32 
    19910 
    19911 > close #7
    19912 
    19913 > hide #!2 models
    19914 
    19915 > surface dust #8 size 8.5
    19916 
    19917 > select #8
    19918 
    19919 2 models selected 
    19920 
    19921 > close #7
    19922 
    19923 > ui mousemode right "translate selected models"
    19924 
    19925 > view matrix models #8,1,0,0,35.396,0,1,0,60.903,0,0,1,32.921
    19926 
    19927 > ui mousemode right "rotate selected models"
    19928 
    19929 > view matrix models
    19930 > #8,-0.3457,-0.50036,0.79381,208.17,-0.017535,0.84927,0.52767,14.154,-0.93818,0.1685,-0.30237,329.15
    19931 
    19932 > view matrix models
    19933 > #8,-0.51948,-0.14515,0.84206,178.05,0.63577,0.59277,0.49439,-45.989,-0.57091,0.79219,-0.21565,171.93
    19934 
    19935 > view matrix models
    19936 > #8,-0.55842,-0.30769,0.77039,216.83,0.59819,0.49406,0.63093,-44.478,-0.57475,0.81316,-0.09184,152.9
    19937 
    19938 > view matrix models
    19939 > #8,-0.55842,-0.30769,0.77039,191.12,0.59819,0.49406,0.63093,-46.563,-0.57475,0.81316,-0.09184,158.22
    19940 
    19941 > show #6 models
    19942 
    19943 > ~select #8
    19944 
    19945 Nothing selected 
    19946 Fit molecule D2NS1-F562.pdb (#6) to map
    19947 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    19948 average map value = 0.1026, steps = 168 
    19949 shifted from previous position = 1.67 
    19950 rotated from previous position = 11.8 degrees 
    19951 atoms outside contour = 6854, contour level = 0.08 
    19952  
    19953 Position of D2NS1-F562.pdb (#6) relative to
    19954 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19955 Matrix rotation and translation 
    19956 -1.00000000 0.00007634 0.00003096 356.91445101 
    19957 -0.00007636 -0.99999975 -0.00069729 357.06728170 
    19958 0.00003091 -0.00069729 0.99999976 0.11956672 
    19959 Axis -0.00001547 0.00034864 -0.99999994 
    19960 Axis point 178.46403997 178.52684922 0.00000000 
    19961 Rotation angle (degrees) 179.99562555 
    19962 Shift along axis -0.00059852 
    19963  
    19964 Fit molecule D2NS1-F562.pdb (#6) to map
    19965 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    19966 average map value = 0.1026, steps = 40 
    19967 shifted from previous position = 0.00373 
    19968 rotated from previous position = 0.0435 degrees 
    19969 atoms outside contour = 6861, contour level = 0.08 
    19970  
    19971 Position of D2NS1-F562.pdb (#6) relative to
    19972 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    19973 Matrix rotation and translation 
    19974 -1.00000000 0.00004453 0.00006393 356.91507698 
    19975 -0.00004452 -1.00000000 0.00006135 356.92005524 
    19976 0.00006393 0.00006135 1.00000000 -0.02104448 
    19977 Axis -0.00003196 -0.00003068 -1.00000000 
    19978 Axis point 178.46151168 178.45605515 0.00000000 
    19979 Rotation angle (degrees) 179.99744898 
    19980 Shift along axis -0.00131278 
    19981  
    19982 
    19983 > select #8
    19984 
    19985 2 models selected 
    19986 
    19987 > view matrix models
    19988 > #8,-0.55842,-0.30769,0.77039,144.53,0.59819,0.49406,0.63093,-60.652,-0.57475,0.81316,-0.09184,256.77
    19989 
    19990 > view matrix models
    19991 > #8,-0.55842,-0.30769,0.77039,188.5,0.59819,0.49406,0.63093,-43.585,-0.57475,0.81316,-0.09184,207.1
    19992 
    19993 > view matrix models
    19994 > #8,0.20416,-0.32979,0.92171,53.292,0.8306,0.55667,0.015197,-5.7187,-0.5181,0.76247,0.38758,141.12
    19995 
    19996 > view matrix models
    19997 > #8,-0.17775,-0.55408,0.81327,158.88,0.42359,0.70287,0.57144,-38.275,-0.88824,0.44606,0.10977,280.75
    19998 
    19999 > view matrix models
    20000 > #8,-0.44365,-0.53212,0.72113,209.28,0.54415,0.47941,0.68853,-40.877,-0.71209,0.69787,0.076868,222.08
    20001 
    20002 > view matrix models
    20003 > #8,-0.44365,-0.53212,0.72113,201.21,0.54415,0.47941,0.68853,-58.258,-0.71209,0.69787,0.076868,191.6
    20004 
    20005 > view matrix models
    20006 > #8,-0.44365,-0.53212,0.72113,198.44,0.54415,0.47941,0.68853,-54.781,-0.71209,0.69787,0.076868,186.46
    20007 
    20008 > view matrix models
    20009 > #8,-0.078986,-0.30105,0.95033,78.334,0.99624,-0.057911,0.064456,35.555,0.03563,0.95185,0.30449,4.0251
    20010 
    20011 > view matrix models
    20012 > #8,-0.078986,-0.30105,0.95033,83.821,0.99624,-0.057911,0.064456,34.166,0.03563,0.95185,0.30449,22.679
    20013 
    20014 > view matrix models
    20015 > #8,-0.13528,-0.37298,0.91792,107.12,0.9291,0.27408,0.24829,-27.377,-0.34419,0.88644,0.30946,90.098
    20016 
    20017 > view matrix models
    20018 > #8,-0.13528,-0.37298,0.91792,107.41,0.9291,0.27408,0.24829,-25.4,-0.34419,0.88644,0.30946,74.434
    20019 
    20020 > view matrix models
    20021 > #8,0.021026,-0.64563,0.76336,142.78,0.95068,0.24925,0.18463,-16.653,-0.30947,0.72183,0.61903,50.881
    20022 
    20023 > view matrix models
    20024 > #8,0.18242,-0.5728,0.79914,102.63,0.95907,0.28269,-0.016302,4.2907,-0.21658,0.76941,0.60092,32.168
    20025 
    20026 > view matrix models
    20027 > #8,0.18242,-0.5728,0.79914,103.51,0.95907,0.28269,-0.016302,-14.792,-0.21658,0.76941,0.60092,29.021
    20028 
    20029 > view matrix models
    20030 > #8,0.18242,-0.5728,0.79914,103.75,0.95907,0.28269,-0.016302,-13.773,-0.21658,0.76941,0.60092,25.236
    20031 
    20032 > view matrix models
    20033 > #8,0.19689,-0.59123,0.7821,106.42,0.95308,0.30251,-0.011255,-16.342,-0.22993,0.74762,0.62305,27.429
    20034 
    20035 > view matrix models
    20036 > #8,0.16349,-0.53138,0.83121,96.478,0.91695,0.39269,0.070685,-34.591,-0.36397,0.75062,0.55145,57.366
    20037 
    20038 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    20039 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    20040 correlation = 0.2099, correlation about mean = -0.0466, overlap = 1148 
    20041 steps = 220, shift = 8.88, angle = 20.7 degrees 
    20042  
    20043 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    20044 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20045 Matrix rotation and translation 
    20046 0.16970377 -0.22411591 0.95967322 38.04053966 
    20047 0.82808228 0.56039048 -0.01556391 -26.95927500 
    20048 -0.53430362 0.79732965 0.28068680 115.40605181 
    20049 Axis 0.40645268 0.74699927 0.52610674 
    20050 Axis point 84.17805896 0.00000000 56.92499809 
    20051 Rotation angle (degrees) 89.69114416 
    20052 Shift along axis 56.03902271 
    20053  
    20054 
    20055 > hide #!8 models
    20056 
    20057 > hide #7 models
    20058 
    20059 > show #!8 models
    20060 
    20061 > hide #!8 models
    20062 
    20063 > show #!8 models
    20064 
    20065 > view matrix models
    20066 > #8,0.17985,-0.20944,0.96114,34.185,0.82577,0.56311,-0.031812,-24.805,-0.53457,0.7994,0.27422,116.02
    20067 
    20068 > view matrix models
    20069 > #8,-0.19365,-0.33381,0.92253,114.87,-0.70512,-0.60645,-0.36745,423.6,0.68213,-0.72166,-0.11794,196.81
    20070 
    20071 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    20072 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    20073 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    20074 steps = 196, shift = 4.16, angle = 13 degrees 
    20075  
    20076 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    20077 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20078 Matrix rotation and translation 
    20079 -0.07683115 -0.17561277 0.98145662 66.44166832 
    20080 -0.66408769 -0.72522667 -0.18175198 411.16957530 
    20081 0.74369650 -0.66573749 -0.06090228 170.05104945 
    20082 Axis -0.66519466 0.32677996 -0.67136497 
    20083 Axis point 7.75299271 239.88960504 0.00000000 
    20084 Rotation angle (degrees) 158.66671698 
    20085 Shift along axis -24.00098327 
    20086  
    20087 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    20088 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    20089 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    20090 steps = 44, shift = 0.00106, angle = 0.00247 degrees 
    20091  
    20092 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    20093 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20094 Matrix rotation and translation 
    20095 -0.07685176 -0.17562808 0.98145227 66.44848746 
    20096 -0.66411122 -0.72519937 -0.18177500 411.17240045 
    20097 0.74367337 -0.66576320 -0.06090373 170.05786271 
    20098 Axis -0.66518608 0.32679973 -0.67136385 
    20099 Axis point 7.75566835 239.89404572 0.00000000 
    20100 Rotation angle (degrees) 158.66630362 
    20101 Shift along axis -24.00027887 
    20102  
    20103 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    20104 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    20105 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    20106 steps = 44, shift = 0.00214, angle = 0.00428 degrees 
    20107  
    20108 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    20109 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20110 Matrix rotation and translation 
    20111 -0.07680221 -0.17565442 0.98145143 66.44396733 
    20112 -0.66407552 -0.72523465 -0.18176462 411.17025225 
    20113 0.74371036 -0.66571781 -0.06094818 170.05404481 
    20114 Axis -0.66520863 0.32678246 -0.67134991 
    20115 Axis point 7.74491366 239.89221167 -0.00000000 
    20116 Rotation angle (degrees) 158.66868085 
    20117 Shift along axis -24.00164195 
    20118  
    20119 
    20120 > select up
    20121 
    20122 24808 atoms, 25460 bonds, 3176 residues, 11 models selected 
    20123 
    20124 > select up
    20125 
    20126 24808 atoms, 25460 bonds, 3176 residues, 11 models selected 
    20127 
    20128 > select up
    20129 
    20130 24808 atoms, 25460 bonds, 3176 residues, 11 models selected 
    20131 
    20132 > select down
    20133 
    20134 2 models selected 
    20135 
    20136 > volume flip #8
    20137 
    20138 Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip as #9, grid size
    20139 352,352,352, pixel 0.85, shown at step 1, values float32 
    20140 
    20141 > hide #!9 models
    20142 
    20143 > show #!9 models
    20144 
    20145 > select #9
    20146 
    20147 2 models selected 
    20148 
    20149 > view matrix models
    20150 > #9,0.04932,0.5784,-0.81426,225.85,0.77832,-0.53317,-0.33159,193.54,-0.62593,-0.6174,-0.47647,432.54
    20151 
    20152 > view matrix models
    20153 > #9,0.49864,0.44515,-0.74377,167.72,0.18866,-0.89322,-0.40812,346.38,-0.84603,0.063187,-0.52938,372.95
    20154 
    20155 > view matrix models
    20156 > #9,0.41566,0.19473,-0.88843,240.37,-0.83603,-0.30285,-0.45753,418.6,-0.35815,0.93293,0.036921,80.781
    20157 
    20158 > view matrix models
    20159 > #9,0.18699,-0.28999,-0.93858,354,0.30934,-0.88945,0.33644,207.89,-0.93239,-0.35325,-0.076615,374.31
    20160 
    20161 > view matrix models
    20162 > #9,0.12166,-0.27135,-0.95476,363.51,0.35041,-0.88823,0.29709,207.97,-0.92866,-0.37071,-0.01298,366.08
    20163 
    20164 > ui mousemode right "translate selected models"
    20165 
    20166 > view matrix models
    20167 > #9,0.12166,-0.27135,-0.95476,343.55,0.35041,-0.88823,0.29709,204.63,-0.92866,-0.37071,-0.01298,384.14
    20168 
    20169 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    20170 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    20171 correlation = 0.2626, correlation about mean = -0.03988, overlap = 1580 
    20172 steps = 48, shift = 0.0161, angle = 0.00778 degrees 
    20173  
    20174 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    20175 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20176 Matrix rotation and translation 
    20177 -0.07667600 -0.17562499 0.98146657 66.40220937 
    20178 -0.66405605 -0.72527845 -0.18166098 411.15872420 
    20179 0.74374077 -0.66567786 -0.06101339 170.05477366 
    20180 Axis -0.66525588 0.32674168 -0.67132294 
    20181 Axis point 7.71835621 239.88762888 0.00000000 
    20182 Rotation angle (degrees) 158.66732589 
    20183 Shift along axis -23.99344049 
    20184  
    20185 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    20186 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    20187 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    20188 steps = 84, shift = 0.0157, angle = 0.009 degrees 
    20189  
    20190 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    20191 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20192 Matrix rotation and translation 
    20193 -0.07682622 -0.17562423 0.98145496 66.44206918 
    20194 -0.66408132 -0.72523107 -0.18175771 411.17012882 
    20195 0.74370270 -0.66572968 -0.06091201 170.05004664 
    20196 Axis -0.66519758 0.32677973 -0.67136219 
    20197 Axis point 7.75121505 239.88987802 0.00000000 
    20198 Rotation angle (degrees) 158.66744100 
    20199 Shift along axis -24.00021217 
    20200  
    20201 
    20202 > view matrix models
    20203 > #9,0.12166,-0.27135,-0.95476,338.02,0.35041,-0.88823,0.29709,203.08,-0.92866,-0.37071,-0.01298,379.52
    20204 
    20205 > ui mousemode right "rotate selected models"
    20206 
    20207 > view matrix models
    20208 > #9,0.30016,-0.86169,-0.40914,310.95,-0.62921,-0.50123,0.59402,242.86,-0.71693,0.079138,-0.69264,391.26
    20209 
    20210 > view matrix models
    20211 > #9,0.079463,-0.47579,-0.87596,361.79,-0.033015,-0.87952,0.47472,229.87,-0.99629,-0.0088031,-0.085597,347.7
    20212 
    20213 > view matrix models
    20214 > #9,0.41919,-0.72698,-0.54387,295.14,-0.54116,-0.68106,0.49326,272.69,-0.729,0.087548,-0.6789,389.59
    20215 
    20216 > view matrix models
    20217 > #9,-0.24911,-0.67335,-0.6961,410.62,-0.72999,-0.34178,0.59185,234.54,-0.63644,0.65558,-0.4064,247.91
    20218 
    20219 > view matrix models
    20220 > #9,0.38176,-0.48586,-0.78626,304.1,-0.52937,-0.81227,0.24491,330.41,-0.75764,0.32273,-0.56729,341.04
    20221 
    20222 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    20223 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    20224 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    20225 steps = 40, shift = 0.000846, angle = 0.00177 degrees 
    20226  
    20227 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    20228 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20229 Matrix rotation and translation 
    20230 -0.07680654 -0.17560484 0.98145997 66.43537485 
    20231 -0.66409320 -0.72522729 -0.18172939 411.16781129 
    20232 0.74369413 -0.66573891 -0.06091578 170.05270073 
    20233 Axis -0.66520310 0.32677576 -0.67135865 
    20234 Axis point 7.74972828 239.88942606 0.00000000 
    20235 Rotation angle (degrees) 158.66589087 
    20236 Shift along axis -23.99969612 
    20237  
    20238 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    20239 cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points 
    20240 correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580 
    20241 steps = 40, shift = 0.00125, angle = 0.00125 degrees 
    20242  
    20243 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    20244 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20245 Matrix rotation and translation 
    20246 -0.07681767 -0.17562278 0.98145589 66.43984164 
    20247 -0.66408848 -0.72522635 -0.18175040 411.16938528 
    20248 0.74369719 -0.66573520 -0.06091887 170.05309874 
    20249 Axis -0.66520021 0.32678120 -0.67135886 
    20250 Axis point 7.74944501 239.89073787 0.00000000 
    20251 Rotation angle (degrees) 158.66693629 
    20252 Shift along axis -24.00002709 
    20253  
    20254 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip in map
    20255 cryosparc_P35_J96_006_volume_map_sharp.mrc using 435032 points 
    20256 correlation = 0.2522, correlation about mean = -0.0372, overlap = 1.179e+04 
    20257 steps = 324, shift = 5.58, angle = 29.2 degrees 
    20258  
    20259 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip (#9)
    20260 relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20261 Matrix rotation and translation 
    20262 0.07209466 -0.25700523 -0.96371709 344.01508219 
    20263 -0.25749943 -0.93827144 0.23095609 315.15876008 
    20264 -0.96358516 0.23150590 -0.13382306 321.33072132 
    20265 Axis 0.73215596 -0.17567940 -0.65809148 
    20266 Axis point 0.00000000 198.81231893 315.31278484 
    20267 Rotation angle (degrees) 179.97848683 
    20268 Shift along axis -14.95921604 
    20269  
    20270 
    20271 > hide #!9 models
    20272 
    20273 > show #!9 models
    20274 
    20275 > hide #!9 models
    20276 
    20277 > show #!8 models
    20278 
    20279 > show #!9 models
    20280 
    20281 > hide #!8 models
    20282 
    20283 > save "D:/OneDrive - Nanyang Technological
    20284 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
    20285 
    20286 > save "D:/OneDrive - Nanyang Technological
    20287 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
    20288 > includeMaps true
    20289 
    20290 > show #!8 models
    20291 
    20292 > hide #!8 models
    20293 
    20294 > hide #!9 models
    20295 
    20296 > show #!8 models
    20297 
    20298 > hide #!8 models
    20299 
    20300 > show #!2 models
    20301 
    20302 > ~select #9
    20303 
    20304 Nothing selected 
    20305 
    20306 > show #7 models
    20307 
    20308 > hide #6 models
    20309 
    20310 > hide #!1 models
    20311 
    20312 > select #7
    20313 
    20314 1 model selected 
    20315 
    20316 > view matrix models
    20317 > #7,0.28314,0.80804,0.51663,178.11,-0.89657,0.0317,0.44178,178.55,0.34059,-0.58828,0.73343,173.27
    20318 
    20319 > view matrix models
    20320 > #7,-0.85167,0.44193,-0.28171,178.2,0.13709,-0.33096,-0.93363,178.47,-0.50584,-0.83376,0.22128,173.34
    20321 
    20322 > view matrix models
    20323 > #7,-0.052894,0.17656,-0.98287,178.14,0.95344,0.30156,0.0028629,178.4,0.2969,-0.93695,-0.18429,173.28
    20324 
    20325 > ui mousemode right "translate selected models"
    20326 
    20327 > view matrix models
    20328 > #7,-0.052894,0.17656,-0.98287,123.75,0.95344,0.30156,0.0028629,168.98,0.2969,-0.93695,-0.18429,135.65
    20329 
    20330 > view matrix models
    20331 > #7,-0.052894,0.17656,-0.98287,171.65,0.95344,0.30156,0.0028629,239.46,0.2969,-0.93695,-0.18429,240.81
    20332 
    20333 > view matrix models
    20334 > #7,-0.052894,0.17656,-0.98287,168.29,0.95344,0.30156,0.0028629,214.9,0.2969,-0.93695,-0.18429,234.8
    20335 
    20336 > transparency #2.1 0
    20337 
    20338 > volume erase #2 center 168.29,214.9,234.8 radius 57.895
    20339 
    20340 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
    20341 352,352,352, pixel 0.85, shown at step 1, values float32 
    20342 
    20343 > view matrix models
    20344 > #7,-0.052894,0.17656,-0.98287,158.31,0.95344,0.30156,0.0028629,232.11,0.2969,-0.93695,-0.18429,231.78
    20345 
    20346 > volume erase #10 center 158.31,232.11,231.78 radius 57.895
    20347 
    20348 > view matrix models
    20349 > #7,-0.052894,0.17656,-0.98287,179.95,0.95344,0.30156,0.0028629,219.57,0.2969,-0.93695,-0.18429,237.28
    20350 
    20351 > view matrix models
    20352 > #7,-0.052894,0.17656,-0.98287,196.31,0.95344,0.30156,0.0028629,220.25,0.2969,-0.93695,-0.18429,246.32
    20353 
    20354 > volume erase #10 center 196.31,220.25,246.32 radius 57.895
    20355 
    20356 > view matrix models
    20357 > #7,-0.052894,0.17656,-0.98287,185.48,0.95344,0.30156,0.0028629,234.46,0.2969,-0.93695,-0.18429,244.14
    20358 
    20359 > view matrix models
    20360 > #7,-0.052894,0.17656,-0.98287,151.71,0.95344,0.30156,0.0028629,160.15,0.2969,-0.93695,-0.18429,262.05
    20361 
    20362 > view matrix models
    20363 > #7,-0.052894,0.17656,-0.98287,147.93,0.95344,0.30156,0.0028629,158.34,0.2969,-0.93695,-0.18429,267.59
    20364 
    20365 > view matrix models
    20366 > #7,-0.052894,0.17656,-0.98287,139.18,0.95344,0.30156,0.0028629,153.5,0.2969,-0.93695,-0.18429,267
    20367 
    20368 > volume erase #10 center 139.18,153.5,267 radius 57.895
    20369 
    20370 > view matrix models
    20371 > #7,-0.052894,0.17656,-0.98287,140,0.95344,0.30156,0.0028629,152.53,0.2969,-0.93695,-0.18429,263.01
    20372 
    20373 > view matrix models
    20374 > #7,-0.052894,0.17656,-0.98287,156.67,0.95344,0.30156,0.0028629,178.21,0.2969,-0.93695,-0.18429,266.42
    20375 
    20376 > volume erase #10 center 156.67,178.21,266.42 radius 57.895
    20377 
    20378 > view matrix models
    20379 > #7,-0.052894,0.17656,-0.98287,158.47,0.95344,0.30156,0.0028629,179.86,0.2969,-0.93695,-0.18429,260.63
    20380 
    20381 > view matrix models
    20382 > #7,-0.052894,0.17656,-0.98287,146.27,0.95344,0.30156,0.0028629,179.75,0.2969,-0.93695,-0.18429,264.96
    20383 
    20384 > view matrix models
    20385 > #7,-0.052894,0.17656,-0.98287,136.73,0.95344,0.30156,0.0028629,165.7,0.2969,-0.93695,-0.18429,256.45
    20386 
    20387 > volume erase #10 center 136.73,165.7,256.45 radius 57.895
    20388 
    20389 > view matrix models
    20390 > #7,-0.052894,0.17656,-0.98287,170.65,0.95344,0.30156,0.0028629,257.57,0.2969,-0.93695,-0.18429,281.54
    20391 
    20392 > view matrix models
    20393 > #7,-0.052894,0.17656,-0.98287,198.12,0.95344,0.30156,0.0028629,237.97,0.2969,-0.93695,-0.18429,234.34
    20394 
    20395 > volume erase #10 center 198.12,237.97,234.34 radius 57.895
    20396 
    20397 > close #7
    20398 
    20399 > show #!1 models
    20400 
    20401 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc copy in map
    20402 cryosparc_P35_J96_006_volume_map_sharp.mrc using 252601 points 
    20403 correlation = 0.4197, correlation about mean = 0.1732, overlap = 5606 
    20404 steps = 100, shift = 2.13, angle = 5.64 degrees 
    20405  
    20406 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) relative to
    20407 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20408 Matrix rotation and translation 
    20409 -0.26232817 0.42310640 0.86727444 32.84932501 
    20410 0.23389320 0.89982892 -0.36824168 75.35914970 
    20411 -0.93620401 0.10624943 -0.33501218 371.04180450 
    20412 Axis 0.25313923 0.96214902 -0.10094453 
    20413 Axis point 142.07695422 0.00000000 181.57625532 
    20414 Rotation angle (degrees) 110.41122784 
    20415 Shift along axis 43.36754334 
    20416  
    20417 
    20418 > select #10
    20419 
    20420 2 models selected 
    20421 
    20422 > view matrix models
    20423 > #10,-0.26233,0.42311,0.86727,32.251,0.23389,0.89983,-0.36824,72.484,-0.9362,0.10625,-0.33501,370.49
    20424 
    20425 > ui mousemode right "rotate selected models"
    20426 
    20427 > view matrix models
    20428 > #10,-0.13878,0.40417,0.9041,8.8226,0.22067,0.9026,-0.36963,74.459,-0.96543,0.14821,-0.21445,349.11
    20429 
    20430 > view matrix models
    20431 > #10,0.081829,0.24713,0.96552,-14.455,0.27881,0.92441,-0.26024,43.68,-0.95685,0.29049,0.0067426,290.35
    20432 
    20433 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc copy in map
    20434 cryosparc_P35_J96_006_volume_map_sharp.mrc using 252601 points 
    20435 correlation = 0.4197, correlation about mean = 0.1733, overlap = 5606 
    20436 steps = 228, shift = 2.88, angle = 23.2 degrees 
    20437  
    20438 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) relative to
    20439 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20440 Matrix rotation and translation 
    20441 -0.26246485 0.42303734 0.86726677 32.87464761 
    20442 0.23392580 0.89986112 -0.36814227 75.32527217 
    20443 -0.93615756 0.10625167 -0.33514125 371.06459232 
    20444 Axis 0.25309913 0.96216476 -0.10089498 
    20445 Axis point 142.08264269 0.00000000 181.57434136 
    20446 Rotation angle (degrees) 110.41836671 
    20447 Shift along axis 43.35731307 
    20448  
    20449 
    20450 > show #6 models
    20451 
    20452 > save "D:/OneDrive - Nanyang Technological
    20453 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
    20454 > includeMaps true
    20455 
    20456 > hide #!10 models
    20457 
    20458 > show #!8 models
    20459 
    20460 > hide #!1 models
    20461 
    20462 > ~select #10
    20463 
    20464 Nothing selected 
    20465 
    20466 > hide #6 models
    20467 
    20468 > select #7
    20469 
    20470 1 model selected 
    20471 
    20472 > view matrix models
    20473 > #7,0.92464,0.25458,-0.28325,178.06,0.04684,0.66208,0.74796,178.47,0.37795,-0.70486,0.60026,173.27
    20474 
    20475 > ui mousemode right "translate selected models"
    20476 
    20477 > view matrix models
    20478 > #7,0.92464,0.25458,-0.28325,204.47,0.04684,0.66208,0.74796,168.78,0.37795,-0.70486,0.60026,117.92
    20479 
    20480 > view matrix models
    20481 > #7,0.92464,0.25458,-0.28325,205.35,0.04684,0.66208,0.74796,172.6,0.37795,-0.70486,0.60026,132.71
    20482 
    20483 > view matrix models
    20484 > #7,0.92464,0.25458,-0.28325,202.38,0.04684,0.66208,0.74796,170.72,0.37795,-0.70486,0.60026,135.25
    20485 
    20486 > view matrix models
    20487 > #7,0.92464,0.25458,-0.28325,208.14,0.04684,0.66208,0.74796,169.1,0.37795,-0.70486,0.60026,122.9
    20488 
    20489 > volume #8 level 0.8304
    20490 
    20491 > view matrix models
    20492 > #7,0.92464,0.25458,-0.28325,209.46,0.04684,0.66208,0.74796,167.64,0.37795,-0.70486,0.60026,121.48
    20493 
    20494 > volume erase #8 center 209.46,167.64,121.48 radius 64.178
    20495 
    20496 Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy as #11, grid size
    20497 352,352,352, pixel 0.85, shown at step 1, values float32 
    20498 
    20499 > view matrix models
    20500 > #7,0.92464,0.25458,-0.28325,202.68,0.04684,0.66208,0.74796,128.68,0.37795,-0.70486,0.60026,117.72
    20501 
    20502 > volume erase #11 center 202.68,128.68,117.72 radius 64.178
    20503 
    20504 > view matrix models
    20505 > #7,0.92464,0.25458,-0.28325,183.78,0.04684,0.66208,0.74796,136.58,0.37795,-0.70486,0.60026,112.38
    20506 
    20507 > volume erase #11 center 183.78,136.58,112.38 radius 64.178
    20508 
    20509 > view matrix models
    20510 > #7,0.92464,0.25458,-0.28325,262.78,0.04684,0.66208,0.74796,132.37,0.37795,-0.70486,0.60026,184.94
    20511 
    20512 > view matrix models
    20513 > #7,0.92464,0.25458,-0.28325,269.47,0.04684,0.66208,0.74796,136.95,0.37795,-0.70486,0.60026,179.85
    20514 
    20515 > view matrix models
    20516 > #7,0.92464,0.25458,-0.28325,267.59,0.04684,0.66208,0.74796,127.26,0.37795,-0.70486,0.60026,154.16
    20517 
    20518 > view matrix models
    20519 > #7,0.92464,0.25458,-0.28325,261.44,0.04684,0.66208,0.74796,136.21,0.37795,-0.70486,0.60026,158.39
    20520 
    20521 > volume erase #11 center 261.44,136.21,158.39 radius 64.178
    20522 
    20523 > view matrix models
    20524 > #7,0.92464,0.25458,-0.28325,234.76,0.04684,0.66208,0.74796,204.63,0.37795,-0.70486,0.60026,115.7
    20525 
    20526 > view matrix models
    20527 > #7,0.92464,0.25458,-0.28325,232.48,0.04684,0.66208,0.74796,207.24,0.37795,-0.70486,0.60026,119.09
    20528 
    20529 > volume erase #11 center 232.48,207.24,119.09 radius 64.178
    20530 
    20531 > view matrix models
    20532 > #7,0.92464,0.25458,-0.28325,211.86,0.04684,0.66208,0.74796,185.05,0.37795,-0.70486,0.60026,105.87
    20533 
    20534 > view matrix models
    20535 > #7,0.92464,0.25458,-0.28325,195.04,0.04684,0.66208,0.74796,187.39,0.37795,-0.70486,0.60026,114.92
    20536 
    20537 > view matrix models
    20538 > #7,0.92464,0.25458,-0.28325,201.04,0.04684,0.66208,0.74796,190.35,0.37795,-0.70486,0.60026,113.3
    20539 
    20540 > volume erase #11 center 201.04,190.35,113.3 radius 64.178
    20541 
    20542 > show #!1 models
    20543 
    20544 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
    20545 cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points 
    20546 correlation = 0.3648, correlation about mean = -0.1049, overlap = 2621 
    20547 steps = 72, shift = 2.57, angle = 2.92 degrees 
    20548  
    20549 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
    20550 to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20551 Matrix rotation and translation 
    20552 -0.05111081 -0.21510165 0.97525327 67.52834138 
    20553 -0.64952035 -0.73462917 -0.19606954 411.11615250 
    20554 0.75862440 -0.64346813 -0.10216541 168.35220279 
    20555 Axis -0.67771084 0.32814528 -0.65804915 
    20556 Axis point 0.00000000 241.21252430 -1.00026216 
    20557 Rotation angle (degrees) 160.72632370 
    20558 Shift along axis -21.64288928 
    20559  
    20560 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
    20561 cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points 
    20562 correlation = 0.3649, correlation about mean = -0.1049, overlap = 2621 
    20563 steps = 40, shift = 0.0141, angle = 0.00956 degrees 
    20564  
    20565 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
    20566 to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20567 Matrix rotation and translation 
    20568 -0.05107225 -0.21496635 0.97528512 67.48907810 
    20569 -0.64946346 -0.73471119 -0.19595064 411.10839498 
    20570 0.75867570 -0.64341970 -0.10208944 168.33302170 
    20571 Axis -0.67772214 0.32806961 -0.65807524 
    20572 Axis point 0.00000000 241.19521972 -0.99729201 
    20573 Rotation angle (degrees) 160.72350203 
    20574 Shift along axis -21.64246440 
    20575  
    20576 Correlation = 0.3649, Correlation about mean = -0.1049, Overlap = 2621 
    20577  
    20578 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
    20579 cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points 
    20580 correlation = 0.3649, correlation about mean = -0.1049, overlap = 2621 
    20581 steps = 28, shift = 0.011, angle = 0.00422 degrees 
    20582  
    20583 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
    20584 to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20585 Matrix rotation and translation 
    20586 -0.05110002 -0.21502631 0.97527045 67.51163904 
    20587 -0.64943800 -0.73471600 -0.19601698 411.10850225 
    20588 0.75869563 -0.64339417 -0.10210226 168.32377829 
    20589 Axis -0.67771626 0.32808172 -0.65807526 
    20590 Axis point 0.00000000 241.19615320 -1.00289431 
    20591 Rotation angle (degrees) 160.72744238 
    20592 Shift along axis -21.64626553 
    20593  
    20594 
    20595 > close #7
    20596 
    20597 > volume #8 level 0.4211
    20598 
    20599 > hide #!8 models
    20600 
    20601 > volume #11 level 0.6377
    20602 
    20603 > volume #11 level 0.4713
    20604 
    20605 > show #!10 models
    20606 
    20607 > hide #!10 models
    20608 
    20609 > show #!10 models
    20610 
    20611 > select #11
    20612 
    20613 2 models selected 
    20614 
    20615 > ui mousemode right "rotate selected models"
    20616 
    20617 > view matrix models
    20618 > #11,-0.14971,0.63965,-0.75394,191.13,-0.95888,-0.2799,-0.047058,377.99,-0.24113,0.71589,0.65525,40.47
    20619 
    20620 > view matrix models
    20621 > #11,-0.069022,0.30969,-0.94833,249.55,0.96027,0.27828,0.020987,-16.584,0.2704,-0.9092,-0.3166,311.78
    20622 
    20623 > ui mousemode right "translate selected models"
    20624 
    20625 > view matrix models
    20626 > #11,-0.069022,0.30969,-0.94833,292.24,0.96027,0.27828,0.020987,-16.748,0.2704,-0.9092,-0.3166,306.11
    20627 
    20628 > view matrix models
    20629 > #11,-0.069022,0.30969,-0.94833,288.83,0.96027,0.27828,0.020987,-15.141,0.2704,-0.9092,-0.3166,305.54
    20630 
    20631 > ui mousemode right "rotate selected models"
    20632 
    20633 > view matrix models
    20634 > #11,-0.12042,0.37081,-0.92087,284.98,0.89214,0.44729,0.063446,-33.276,0.43542,-0.8139,-0.38467,274.73
    20635 
    20636 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
    20637 cryosparc_P35_J96_006_volume_map_sharp.mrc using 185886 points 
    20638 correlation = 0.3705, correlation about mean = -0.01342, overlap = 9885 
    20639 steps = 84, shift = 3.3, angle = 7.24 degrees 
    20640  
    20641 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
    20642 to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20643 Matrix rotation and translation 
    20644 -0.08967779 0.29999028 -0.94971770 295.49237204 
    20645 0.84493489 0.52775912 0.08692132 -41.96570345 
    20646 0.52729773 -0.79465472 -0.30080053 248.18221209 
    20647 Axis -0.48858097 -0.81858128 0.30201543 
    20648 Axis point 60.64458577 -0.00000000 223.51625228 
    20649 Rotation angle (degrees) 115.55387500 
    20650 Shift along axis -35.06475327 
    20651  
    20652 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
    20653 cryosparc_P35_J96_006_volume_map_sharp.mrc using 185886 points 
    20654 correlation = 0.3706, correlation about mean = -0.01331, overlap = 9885 
    20655 steps = 40, shift = 0.0143, angle = 0.0103 degrees 
    20656  
    20657 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
    20658 to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    20659 Matrix rotation and translation 
    20660 -0.08981970 0.29998685 -0.94970537 295.52003565 
    20661 0.84486634 0.52788229 0.08683967 -41.94876855 
    20662 0.52738342 -0.79457419 -0.30086302 248.17026594 
    20663 Axis -0.48850161 -0.81863956 0.30198584 
    20664 Axis point 60.66605513 0.00000000 223.51111811 
    20665 Rotation angle (degrees) 115.55645450 
    20666 Shift along axis -35.07718649 
    20667  
    20668 
    20669 > save "D:/OneDrive - Nanyang Technological
    20670 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
    20671 > includeMaps true
    20672 
    20673 > close #9
    20674 
    20675 > show #!2 models
    20676 
    20677 > hide #!11 models
    20678 
    20679 > ~select #11
    20680 
    20681 Nothing selected 
    20682 
    20683 > show #6 models
    20684 
    20685 > hide #!2 models
    20686 
    20687 > show #!2 models
    20688 
    20689 Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
    20690 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 434908 points 
    20691 correlation = 0.8681, correlation about mean = 0.7943, overlap = 2.493e+04 
    20692 steps = 100, shift = 2.6, angle = 5.47 degrees 
    20693  
    20694 Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
    20695 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20696 Matrix rotation and translation 
    20697 0.99999417 -0.00078818 -0.00332112 0.86833791 
    20698 0.00079720 0.99999599 0.00271726 -0.70720618 
    20699 0.00331897 -0.00271989 0.99999079 0.00769659 
    20700 Axis -0.62300052 -0.76083593 0.18165636 
    20701 Axis point -1.67706066 0.00000000 261.17922578 
    20702 Rotation angle (degrees) 0.25002110 
    20703 Shift along axis -0.00150896 
    20704  
    20705 
    20706 > hide #!1 models
    20707 
    20708 Fit molecule D2NS1-F562.pdb (#6) to map
    20709 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 12404 atoms 
    20710 average map value = 0.1247, steps = 124 
    20711 shifted from previous position = 2.69 
    20712 rotated from previous position = 12.5 degrees 
    20713 atoms outside contour = 7351, contour level = 0.14151 
    20714  
    20715 Position of D2NS1-F562.pdb (#6) relative to
    20716 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20717 Matrix rotation and translation 
    20718 0.25275147 -0.43670415 -0.86336907 353.51447381 
    20719 -0.44938591 -0.84323715 0.29496333 308.88812835 
    20720 -0.85683660 0.31343349 -0.40937812 323.84932290 
    20721 Axis 0.79143097 -0.27991074 -0.54340316 
    20722 Axis point 0.00000000 215.73050893 284.44415750 
    20723 Rotation angle (degrees) 179.33140963 
    20724 Shift along axis 17.34045325 
    20725  
    20726 Fit molecule D2NS1-F562.pdb (#6) to map
    20727 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 12404 atoms 
    20728 average map value = 0.1247, steps = 36 
    20729 shifted from previous position = 0.00249 
    20730 rotated from previous position = 0.00661 degrees 
    20731 atoms outside contour = 7351, contour level = 0.14151 
    20732  
    20733 Position of D2NS1-F562.pdb (#6) relative to
    20734 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20735 Matrix rotation and translation 
    20736 0.25279114 -0.43660663 -0.86340677 353.49888697 
    20737 -0.44933375 -0.84329450 0.29487884 308.90364784 
    20738 -0.85685225 0.31341505 -0.40935948 323.85331097 
    20739 Axis 0.79144345 -0.27985911 -0.54341158 
    20740 Axis point 0.00000000 215.71863017 284.44492018 
    20741 Rotation angle (degrees) 179.32902903 
    20742 Shift along axis 17.33923677 
    20743  
    20744 
    20745 > transparency #2.1#10.1 50
    20746 
    20747 > hide #!2 models
    20748 
    20749 > show #!8 models
    20750 
    20751 > select #8
    20752 
    20753 2 models selected 
    20754 
    20755 > view matrix models
    20756 > #8,0.33902,0.03981,-0.93994,229.8,-0.92382,-0.17477,-0.34061,394.45,-0.17784,0.9838,-0.022475,72.918
    20757 
    20758 > view matrix models
    20759 > #8,-0.19081,0.15972,-0.96855,298.63,-0.9771,-0.1256,0.17178,326.79,-0.094217,0.97914,0.18003,33.4
    20760 
    20761 > ui mousemode right "translate selected models"
    20762 
    20763 > view matrix models
    20764 > #8,-0.19081,0.15972,-0.96855,333.9,-0.9771,-0.1256,0.17178,339.76,-0.094217,0.97914,0.18003,31.589
    20765 
    20766 > view matrix models
    20767 > #8,-0.19081,0.15972,-0.96855,336.31,-0.9771,-0.1256,0.17178,330.87,-0.094217,0.97914,0.18003,34.463
    20768 
    20769 > view matrix models
    20770 > #8,-0.19081,0.15972,-0.96855,332.19,-0.9771,-0.1256,0.17178,338.81,-0.094217,0.97914,0.18003,28.17
    20771 
    20772 > view matrix models
    20773 > #8,-0.19081,0.15972,-0.96855,344.81,-0.9771,-0.1256,0.17178,333.8,-0.094217,0.97914,0.18003,27.752
    20774 
    20775 > ui mousemode right "rotate selected models"
    20776 
    20777 > view matrix models
    20778 > #8,0.39538,0.22669,-0.8901,233.97,0.79273,0.40527,0.45534,-53.893,0.46395,-0.88565,-0.019473,233.43
    20779 
    20780 > ui mousemode right "translate selected models"
    20781 
    20782 > view matrix models
    20783 > #8,0.39538,0.22669,-0.8901,225.01,0.79273,0.40527,0.45534,-60.792,0.46395,-0.88565,-0.019473,244.4
    20784 
    20785 > view matrix models
    20786 > #8,0.39538,0.22669,-0.8901,226.27,0.79273,0.40527,0.45534,-67.659,0.46395,-0.88565,-0.019473,244.84
    20787 
    20788 Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
    20789 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 47154 points 
    20790 correlation = 0.3601, correlation about mean = -0.01926, overlap = 2801 
    20791 steps = 244, shift = 6.57, angle = 20.9 degrees 
    20792  
    20793 Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
    20794 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20795 Matrix rotation and translation 
    20796 -0.50275518 0.77664634 0.37954926 71.44698114 
    20797 0.77480667 0.59955666 -0.20051529 -35.12156246 
    20798 -0.38329076 0.19326720 -0.90318100 318.59922133 
    20799 Axis 0.45869577 0.88859079 -0.00214294 
    20800 Axis point 85.22138435 0.00000000 150.24137730 
    20801 Rotation angle (degrees) 154.58056842 
    20802 Shift along axis 0.88099311 
    20803  
    20804 
    20805 > save "D:/OneDrive - Nanyang Technological
    20806 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
    20807 > includeMaps true
    20808 
    20809 ——— End of log from Tue Feb 22 21:05:12 2022 ———
    20810 
    20811 opened ChimeraX session 
    20812 
    20813 > hide #!10 models
    20814 
    20815 > show #!10 models
    20816 
    20817 > hide #!8 models
    20818 
    20819 > show #!1 models
    20820 
    20821 > show #!2 models
    20822 
    20823 > close #11
    20824 
    20825 > close #8
    20826 
    20827 > open "D:/OneDrive - Nanyang Technological
    20828 > University/Temporal/202109_zvNS1/3_Structures/2n5e.pdb"
    20829 
    20830 2n5e.pdb title: 
    20831 The 3D solution structure of discoidal high-density lipoprotein particles
    20832 [more info...] 
    20833  
    20834 Chain information for 2n5e.pdb 
    20835 --- 
    20836 Chain | Description 
    20837 7.1/A 7.2/A 7.3/A 7.4/A 7.5/A 7.6/A 7.7/A 7.8/A 7.9/A 7.10/A 7.1/B 7.2/B 7.3/B
    20838 7.4/B 7.5/B 7.6/B 7.7/B 7.8/B 7.9/B 7.10/B | apolipoprotein A-I 
    20839  
    20840 
    20841 > close #7.2-10
    20842 
    20843 > hide #7.1 models
    20844 
    20845 > show #7.1 models
    20846 
    20847 > hide #7.1 models
    20848 
    20849 > hide #!2 models
    20850 
    20851 > hide #!1 models
    20852 
    20853 > ui tool show "Fit in Map"
    20854 
    20855 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    20856 copy (#10) using 5602 atoms 
    20857 average map value = 0.1754, steps = 352 
    20858 shifted from previous position = 4.55 
    20859 rotated from previous position = 50.7 degrees 
    20860 atoms outside contour = 2605, contour level = 0.14151 
    20861  
    20862 Position of D2NS1.pdb (#3) relative to
    20863 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20864 Matrix rotation and translation 
    20865 -0.51892205 0.80965860 -0.27417668 164.22917225 
    20866 -0.84272074 -0.43077092 0.32289035 300.54198392 
    20867 0.14332362 0.39860929 0.90585262 -107.70830576 
    20868 Axis 0.04438420 -0.24472630 -0.96857580 
    20869 Axis point 169.29706156 116.85077370 0.00000000 
    20870 Rotation angle (degrees) 121.46114137 
    20871 Shift along axis 38.06231174 
    20872  
    20873 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    20874 copy (#10) using 5602 atoms 
    20875 average map value = 0.1754, steps = 40 
    20876 shifted from previous position = 0.00569 
    20877 rotated from previous position = 0.00161 degrees 
    20878 atoms outside contour = 2609, contour level = 0.14151 
    20879  
    20880 Position of D2NS1.pdb (#3) relative to
    20881 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20882 Matrix rotation and translation 
    20883 -0.51894067 0.80965192 -0.27416117 164.23500046 
    20884 -0.84270669 -0.43078495 0.32290828 300.54258112 
    20885 0.14333881 0.39860769 0.90585092 -107.71085737 
    20886 Axis 0.04437330 -0.24472913 -0.96857558 
    20887 Axis point 169.29862447 116.85084764 0.00000000 
    20888 Rotation angle (degrees) 121.46229524 
    20889 Shift along axis 38.06223078 
    20890  
    20891 
    20892 > show #4 models
    20893 
    20894 > hide #!7 models
    20895 
    20896 > hide #6 models
    20897 
    20898 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    20899 copy (#10) using 3401 atoms 
    20900 average map value = 0.2415, steps = 184 
    20901 shifted from previous position = 2.68 
    20902 rotated from previous position = 43.1 degrees 
    20903 atoms outside contour = 1055, contour level = 0.14151 
    20904  
    20905 Position of F562a.pdb (#4) relative to
    20906 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20907 Matrix rotation and translation 
    20908 0.23696585 -0.97040692 -0.04644960 286.31819473 
    20909 0.13996862 0.08141367 -0.98680321 234.14224375 
    20910 0.96138231 0.22733718 0.15511878 -33.92541253 
    20911 Axis 0.62926604 -0.52234025 0.57548668 
    20912 Axis point 0.00000000 269.88096267 6.34604794 
    20913 Rotation angle (degrees) 105.26304401 
    20914 Shift along axis 38.34477607 
    20915  
    20916 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    20917 copy (#10) using 3401 atoms 
    20918 average map value = 0.2415, steps = 40 
    20919 shifted from previous position = 0.0163 
    20920 rotated from previous position = 0.0184 degrees 
    20921 atoms outside contour = 1053, contour level = 0.14151 
    20922  
    20923 Position of F562a.pdb (#4) relative to
    20924 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20925 Matrix rotation and translation 
    20926 0.23699244 -0.97040417 -0.04637137 286.30251238 
    20927 0.14028426 0.08141314 -0.98675843 234.09383454 
    20928 0.96132975 0.22734912 0.15542673 -33.96007421 
    20929 Axis 0.62921931 -0.52224780 0.57562166 
    20930 Axis point 0.00000000 269.87054516 6.30278577 
    20931 Rotation angle (degrees) 105.25312557 
    20932 Shift along axis 38.34392482 
    20933  
    20934 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    20935 copy (#10) using 3401 atoms 
    20936 average map value = 0.2415, steps = 44 
    20937 shifted from previous position = 0.0177 
    20938 rotated from previous position = 0.024 degrees 
    20939 atoms outside contour = 1055, contour level = 0.14151 
    20940  
    20941 Position of F562a.pdb (#4) relative to
    20942 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20943 Matrix rotation and translation 
    20944 0.23699037 -0.97040260 -0.04641486 286.30808679 
    20945 0.13987427 0.08136006 -0.98682101 234.17141287 
    20946 0.96139000 0.22737483 0.15501591 -33.91830894 
    20947 Axis 0.62930653 -0.52233598 0.57544628 
    20948 Axis point 0.00000000 269.87165306 6.36745226 
    20949 Rotation angle (degrees) 105.26696289 
    20950 Shift along axis 38.34122922 
    20951  
    20952 
    20953 > show #3 models
    20954 
    20955 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    20956 copy (#10) using 3401 atoms 
    20957 average map value = 0.2415, steps = 44 
    20958 shifted from previous position = 0.0174 
    20959 rotated from previous position = 0.02 degrees 
    20960 atoms outside contour = 1053, contour level = 0.14151 
    20961  
    20962 Position of F562a.pdb (#4) relative to
    20963 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20964 Matrix rotation and translation 
    20965 0.23696878 -0.97040926 -0.04638578 286.31082660 
    20966 0.14021616 0.08140780 -0.98676855 234.10798884 
    20967 0.96134552 0.22732931 0.15535816 -33.95179699 
    20968 Axis 0.62922296 -0.52227064 0.57559694 
    20969 Axis point 0.00000000 269.87770153 6.30937551 
    20970 Rotation angle (degrees) 105.25602295 
    20971 Shift along axis 38.34306534 
    20972  
    20973 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    20974 copy (#10) using 3401 atoms 
    20975 average map value = 0.2415, steps = 28 
    20976 shifted from previous position = 0.0182 
    20977 rotated from previous position = 0.0232 degrees 
    20978 atoms outside contour = 1055, contour level = 0.14151 
    20979  
    20980 Position of F562a.pdb (#4) relative to
    20981 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    20982 Matrix rotation and translation 
    20983 0.23695180 -0.97040946 -0.04646826 286.32373425 
    20984 0.13981736 0.08139458 -0.98682623 234.17404048 
    20985 0.96140779 0.22733318 0.15496668 -33.91113966 
    20986 Axis 0.62929239 -0.52237681 0.57542468 
    20987 Axis point 0.00000000 269.88626156 6.36736238 
    20988 Rotation angle (degrees) 105.26854490 
    20989 Shift along axis 38.34095150 
    20990  
    20991 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    20992 copy (#10) using 3401 atoms 
    20993 average map value = 0.2415, steps = 40 
    20994 shifted from previous position = 0.00386 
    20995 rotated from previous position = 0.0076 degrees 
    20996 atoms outside contour = 1055, contour level = 0.14151 
    20997  
    20998 Position of F562a.pdb (#4) relative to
    20999 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21000 Matrix rotation and translation 
    21001 0.23701158 -0.97039892 -0.04638334 286.30019564 
    21002 0.13991374 0.08134082 -0.98681700 234.16833276 
    21003 0.96137903 0.22739739 0.15505086 -33.92599735 
    21004 Axis 0.62931286 -0.52231123 0.57546182 
    21005 Axis point 0.00000000 269.86512738 6.36383820 
    21006 Rotation angle (degrees) 105.26586629 
    21007 Shift along axis 38.34052770 
    21008  
    21009 
    21010 > show #!2 models
    21011 
    21012 > show #6 models
    21013 
    21014 > hide #!2 models
    21015 
    21016 > hide #!10 models
    21017 
    21018 > hide #6 models
    21019 
    21020 > show #6 models
    21021 
    21022 > mmaker #6 to #3
    21023 
    21024 Parameters 
    21025 --- 
    21026 Chain pairing | bb 
    21027 Alignment algorithm | Needleman-Wunsch 
    21028 Similarity matrix | BLOSUM-62 
    21029 SS fraction | 0.3 
    21030 Gap open (HH/SS/other) | 18/18/6 
    21031 Gap extend | 1 
    21032 SS matrix |  |  | H | S | O 
    21033 ---|---|---|--- 
    21034 H | 6 | -9 | -6 
    21035 S |  | 6 | -6 
    21036 O |  |  | 4 
    21037 Iteration cutoff | 2 
    21038  
    21039 Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
    21040 alignment score = 1871.9 
    21041 RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
    21042 0.023) 
    21043  
    21044 
    21045 > hide #6 models
    21046 
    21047 > show #6 models
    21048 
    21049 > hide #6 models
    21050 
    21051 > show #6 models
    21052 
    21053 > hide #6 models
    21054 
    21055 > show #!2 models
    21056 
    21057 > show #!1 models
    21058 
    21059 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    21060 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points 
    21061 correlation = 0.4911, correlation about mean = 0.2779, overlap = 6002 
    21062 steps = 1308, shift = 0.661, angle = 22 degrees 
    21063  
    21064 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    21065 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21066 Matrix rotation and translation 
    21067 -0.27793747 -0.14035072 -0.95029069 409.92559615 
    21068 0.39452131 0.88530641 -0.24614115 -49.02432671 
    21069 0.87584454 -0.44332178 -0.19068848 109.24693947 
    21070 Axis -0.10307165 -0.95457032 0.27959209 
    21071 Axis point 169.03926821 0.00000000 207.85299225 
    21072 Rotation angle (degrees) 106.95735055 
    21073 Shift along axis 35.09003774 
    21074  
    21075 
    21076 > show #!10 models
    21077 
    21078 > hide #!2 models
    21079 
    21080 > hide #!1 models
    21081 
    21082 > show #!2 models
    21083 
    21084 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    21085 copy (#10) using 5602 atoms 
    21086 average map value = 0.1754, steps = 44 
    21087 shifted from previous position = 0.00219 
    21088 rotated from previous position = 0.0172 degrees 
    21089 atoms outside contour = 2607, contour level = 0.14151 
    21090  
    21091 Position of D2NS1.pdb (#3) relative to
    21092 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21093 Matrix rotation and translation 
    21094 -0.51889139 0.80974271 -0.27398626 164.17754795 
    21095 -0.84268736 -0.43067692 0.32310277 300.48501792 
    21096 0.14363056 0.39854000 0.90583449 -107.74724207 
    21097 Axis 0.04421738 -0.24478525 -0.96856853 
    21098 Axis point 169.27126594 116.83993981 0.00000000 
    21099 Rotation angle (degrees) 121.45756347 
    21100 Shift along axis 38.06578928 
    21101  
    21102 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    21103 copy (#10) using 5602 atoms 
    21104 average map value = 0.1754, steps = 44 
    21105 shifted from previous position = 0.00282 
    21106 rotated from previous position = 0.00397 degrees 
    21107 atoms outside contour = 2606, contour level = 0.14151 
    21108  
    21109 Position of D2NS1.pdb (#3) relative to
    21110 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21111 Matrix rotation and translation 
    21112 -0.51894411 0.80971407 -0.27397106 164.19040191 
    21113 -0.84265984 -0.43073928 0.32309143 300.49449446 
    21114 0.14360158 0.39853079 0.90584314 -107.74009884 
    21115 Axis 0.04422032 -0.24476870 -0.96857258 
    21116 Axis point 169.27313448 116.84271119 0.00000000 
    21117 Rotation angle (degrees) 121.46113819 
    21118 Shift along axis 38.06301215 
    21119  
    21120 
    21121 > select #3
    21122 
    21123 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    21124 
    21125 > ui mousemode right "rotate selected models"
    21126 
    21127 > view matrix models
    21128 > #3,-0.14665,-0.10019,0.9841,42.803,-0.93066,-0.32317,-0.17158,431.35,0.33522,-0.94102,-0.045847,294.18
    21129 
    21130 > view matrix models
    21131 > #3,-0.24212,-0.16715,0.95574,75.904,-0.91312,-0.29375,-0.2827,443.12,0.328,-0.94116,-0.081503,301.82
    21132 
    21133 > view matrix models
    21134 > #3,-0.22781,0.0025001,0.9737,41.665,-0.95433,-0.19906,-0.22277,423.77,0.19327,-0.97998,0.047735,309.02
    21135 
    21136 > view matrix models
    21137 > #3,-0.31679,-0.24249,0.91698,108.61,-0.87534,-0.29756,-0.38109,454.64,0.36527,-0.92339,-0.118,298.78
    21138 
    21139 > view matrix models
    21140 > #3,-0.20831,0.16138,0.96466,13.134,-0.97765,-0.063166,-0.20055,401.06,0.028569,-0.98487,0.17093,316.86
    21141 
    21142 > view matrix models
    21143 > #3,-0.18189,0.029376,0.98288,27.434,-0.97841,0.094327,-0.18388,371.75,-0.098114,-0.99511,0.011585,369.25
    21144 
    21145 > ui mousemode right "translate selected models"
    21146 
    21147 > view matrix models
    21148 > #3,-0.18189,0.029376,0.98288,26.801,-0.97841,0.094327,-0.18388,370.7,-0.098114,-0.99511,0.011585,365.44
    21149 
    21150 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    21151 copy (#10) using 5602 atoms 
    21152 average map value = 0.1754, steps = 220 
    21153 shifted from previous position = 5.16 
    21154 rotated from previous position = 26.4 degrees 
    21155 atoms outside contour = 2605, contour level = 0.14151 
    21156  
    21157 Position of D2NS1.pdb (#3) relative to
    21158 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21159 Matrix rotation and translation 
    21160 -0.51865164 0.80982057 -0.27420999 164.16314366 
    21161 -0.84285174 -0.43044060 0.32298891 300.49787860 
    21162 0.14353196 0.39863709 0.90580740 -107.73453379 
    21163 Axis 0.04433389 -0.24481919 -0.96855463 
    21164 Axis point 169.29026360 116.83700867 0.00000000 
    21165 Rotation angle (degrees) 121.44248630 
    21166 Shift along axis 38.05712471 
    21167  
    21168 
    21169 > hide #!2 models
    21170 
    21171 > view matrix models
    21172 > #3,-0.095949,-0.048917,0.99418,23.903,-0.93262,-0.34465,-0.10697,422.69,0.34788,-0.93745,-0.012552,284.37
    21173 
    21174 > view matrix models
    21175 > #3,-0.095949,-0.048917,0.99418,24.499,-0.93262,-0.34465,-0.10697,420.51,0.34788,-0.93745,-0.012552,282.55
    21176 
    21177 > ui mousemode right "map eraser"
    21178 
    21179 > volume erase #10 center 197.01,182.51,231.59 radius 31.633
    21180 
    21181 > volume erase #10 center 213.27,171.82,231.83 radius 31.633
    21182 
    21183 > volume erase #10 center 199.27,226.74,192.59 radius 31.633
    21184 
    21185 > volume erase #10 center 201.83,210.63,213.73 radius 31.633
    21186 
    21187 > close #8
    21188 
    21189 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    21190 copy (#10) using 5602 atoms 
    21191 average map value = 0.1735, steps = 84 
    21192 shifted from previous position = 4.01 
    21193 rotated from previous position = 2.96 degrees 
    21194 atoms outside contour = 2586, contour level = 0.14151 
    21195  
    21196 Position of D2NS1.pdb (#3) relative to
    21197 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21198 Matrix rotation and translation 
    21199 -0.47450864 0.83236882 -0.28636287 154.63058051 
    21200 -0.86693279 -0.38553270 0.31589884 297.74905925 
    21201 0.15254210 0.39815408 0.90454642 -108.87748698 
    21202 Axis 0.04681588 -0.24980441 -0.96716391 
    21203 Axis point 169.11832797 115.96117517 0.00000000 
    21204 Rotation angle (degrees) 118.53838807 
    21205 Shift along axis 38.16251411 
    21206  
    21207 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    21208 copy (#10) using 5602 atoms 
    21209 average map value = 0.1735, steps = 48 
    21210 shifted from previous position = 0.00277 
    21211 rotated from previous position = 0.00477 degrees 
    21212 atoms outside contour = 2584, contour level = 0.14151 
    21213  
    21214 Position of D2NS1.pdb (#3) relative to
    21215 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21216 Matrix rotation and translation 
    21217 -0.47448892 0.83239630 -0.28631566 154.61369255 
    21218 -0.86692974 -0.38549828 0.31594921 297.73456104 
    21219 0.15262076 0.39812996 0.90454377 -108.88430164 
    21220 Axis 0.04677274 -0.24981834 -0.96716240 
    21221 Axis point 169.11102884 115.95863363 0.00000000 
    21222 Rotation angle (degrees) 118.53670909 
    21223 Shift along axis 38.16095498 
    21224  
    21225 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    21226 copy (#10) using 5602 atoms 
    21227 average map value = 0.1735, steps = 60 
    21228 shifted from previous position = 0.0162 
    21229 rotated from previous position = 0.0207 degrees 
    21230 atoms outside contour = 2591, contour level = 0.14151 
    21231  
    21232 Position of D2NS1.pdb (#3) relative to
    21233 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21234 Matrix rotation and translation 
    21235 -0.47456944 0.83227118 -0.28654585 154.70120447 
    21236 -0.86694397 -0.38562941 0.31575007 297.80757285 
    21237 0.15228918 0.39826452 0.90454042 -108.84769154 
    21238 Axis 0.04696579 -0.24977725 -0.96716366 
    21239 Axis point 169.15292707 115.96995015 0.00000000 
    21240 Rotation angle (degrees) 118.54372018 
    21241 Shift along axis 38.15363917 
    21242  
    21243 
    21244 > show #!2 models
    21245 
    21246 > show #!7 models
    21247 
    21248 > show #7.1 models
    21249 
    21250 > select #7.1
    21251 
    21252 5464 atoms, 5510 bonds, 334 residues, 1 model selected 
    21253 
    21254 > close #8
    21255 
    21256 > close #8
    21257 
    21258 > ui mousemode right "translate selected models"
    21259 
    21260 > view matrix models #7.1,1,0,0,169.78,0,1,0,228.66,0,0,1,242.62
    21261 
    21262 > view matrix models #7.1,1,0,0,141.19,0,1,0,179.49,0,0,1,253.16
    21263 
    21264 > view matrix models #7.1,1,0,0,139.34,0,1,0,181.33,0,0,1,279.32
    21265 
    21266 > view matrix models #7.1,1,0,0,140.66,0,1,0,199.74,0,0,1,261.78
    21267 
    21268 > view matrix models #7.1,1,0,0,152.52,0,1,0,194.28,0,0,1,257.24
    21269 
    21270 > ui mousemode right "rotate selected models"
    21271 
    21272 > view matrix models
    21273 > #7.1,0.96441,0.048869,0.25985,165.75,0.098602,0.8454,-0.52495,167.67,-0.24533,0.53189,0.8105,246.45
    21274 
    21275 > view matrix models
    21276 > #7.1,0.52404,0.070357,0.84878,205.22,0.25659,0.93724,-0.23611,177.31,-0.81212,0.34152,0.4731,245.12
    21277 
    21278 > ui mousemode right "translate selected models"
    21279 
    21280 > view matrix models
    21281 > #7.1,0.52404,0.070357,0.84878,218.96,0.25659,0.93724,-0.23611,166.4,-0.81212,0.34152,0.4731,253.15
    21282 
    21283 > view matrix models
    21284 > #7.1,0.52404,0.070357,0.84878,218.06,0.25659,0.93724,-0.23611,172.5,-0.81212,0.34152,0.4731,255.75
    21285 
    21286 > view matrix models
    21287 > #7.1,0.52404,0.070357,0.84878,220.15,0.25659,0.93724,-0.23611,172.23,-0.81212,0.34152,0.4731,250.53
    21288 
    21289 > view matrix models
    21290 > #7.1,0.52404,0.070357,0.84878,218.93,0.25659,0.93724,-0.23611,169.22,-0.81212,0.34152,0.4731,253.47
    21291 
    21292 > view matrix models
    21293 > #7.1,0.52404,0.070357,0.84878,218.24,0.25659,0.93724,-0.23611,170.23,-0.81212,0.34152,0.4731,253.64
    21294 
    21295 > view matrix models
    21296 > #7.1,0.52404,0.070357,0.84878,216.82,0.25659,0.93724,-0.23611,165.96,-0.81212,0.34152,0.4731,248.26
    21297 
    21298 > ui mousemode right "rotate selected models"
    21299 
    21300 > view matrix models
    21301 > #7.1,0.73952,-0.17388,0.65029,205.07,0.14405,0.98456,0.099452,184.79,-0.65754,0.020126,0.75315,262.95
    21302 
    21303 > view matrix models
    21304 > #7.1,0.73125,-0.084624,0.67684,205.42,0.062378,0.99641,0.057187,184.4,-0.67925,0.00040129,0.73391,262.74
    21305 
    21306 > view matrix models
    21307 > #7.1,0.69799,-0.10334,0.70861,208.03,0.074484,0.99464,0.071682,184.87,-0.71222,0.0027467,0.70195,261.87
    21308 
    21309 > view matrix models
    21310 > #7.1,0.63726,0.053079,0.76882,210.42,0.18684,0.95722,-0.22096,168.07,-0.74766,0.28445,0.60008,253.89
    21311 
    21312 > ui mousemode right "translate selected models"
    21313 
    21314 > view matrix models
    21315 > #7.1,0.63726,0.053079,0.76882,208.69,0.18684,0.95722,-0.22096,171.97,-0.74766,0.28445,0.60008,254.92
    21316 
    21317 > view matrix models
    21318 > #7.1,0.63726,0.053079,0.76882,209.09,0.18684,0.95722,-0.22096,174.45,-0.74766,0.28445,0.60008,259.11
    21319 
    21320 > ui mousemode right "rotate selected models"
    21321 
    21322 > view matrix models
    21323 > #7.1,0.62362,0.070465,0.77855,209.66,0.22628,0.93702,-0.26606,171.53,-0.74826,0.34209,0.5684,256.78
    21324 
    21325 > view matrix models
    21326 > #7.1,0.61203,0.086506,0.78609,210.1,0.26096,0.91623,-0.30401,169.1,-0.74654,0.3912,0.53819,254.58
    21327 
    21328 > ui mousemode right "rotate selected models"
    21329 
    21330 > ~select #7.1
    21331 
    21332 Nothing selected 
    21333 
    21334 > save "D:/OneDrive - Nanyang Technological
    21335 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
    21336 > includeMaps true
    21337 
    21338 ——— End of log from Tue Feb 22 21:54:19 2022 ———
    21339 
    21340 opened ChimeraX session 
    21341 
    21342 > open "D:/OneDrive - Nanyang Technological
    21343 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/2n5e.pdb"
    21344 
    21345 2n5e.pdb title: 
    21346 The 3D solution structure of discoidal high-density lipoprotein particles
    21347 [more info...] 
    21348  
    21349 Chain information for 2n5e.pdb 
    21350 --- 
    21351 Chain | Description 
    21352 8.1/A 8.2/A 8.3/A 8.4/A 8.5/A 8.6/A 8.7/A 8.8/A 8.9/A 8.10/A 8.1/B 8.2/B 8.3/B
    21353 8.4/B 8.5/B 8.6/B 8.7/B 8.8/B 8.9/B 8.10/B | apolipoprotein A-I 
    21354  
    21355 
    21356 > mmaker #8 to #7
    21357 
    21358 Parameters 
    21359 --- 
    21360 Chain pairing | bb 
    21361 Alignment algorithm | Needleman-Wunsch 
    21362 Similarity matrix | BLOSUM-62 
    21363 SS fraction | 0.3 
    21364 Gap open (HH/SS/other) | 18/18/6 
    21365 Gap extend | 1 
    21366 SS matrix |  |  | H | S | O 
    21367 ---|---|---|--- 
    21368 H | 6 | -9 | -6 
    21369 S |  | 6 | -6 
    21370 O |  |  | 4 
    21371 Iteration cutoff | 2 
    21372  
    21373 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.1), sequence
    21374 alignment score = 889.9 
    21375 RMSD between 167 pruned atom pairs is 0.000 angstroms; (across all 167 pairs:
    21376 0.000) 
    21377  
    21378 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.2), sequence
    21379 alignment score = 889.9 
    21380 RMSD between 99 pruned atom pairs is 0.967 angstroms; (across all 167 pairs:
    21381 2.405) 
    21382  
    21383 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.3), sequence
    21384 alignment score = 882.7 
    21385 RMSD between 146 pruned atom pairs is 0.614 angstroms; (across all 167 pairs:
    21386 6.590) 
    21387  
    21388 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.4), sequence
    21389 alignment score = 879.1 
    21390 RMSD between 90 pruned atom pairs is 0.877 angstroms; (across all 167 pairs:
    21391 6.733) 
    21392  
    21393 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.5), sequence
    21394 alignment score = 886.3 
    21395 RMSD between 83 pruned atom pairs is 0.781 angstroms; (across all 167 pairs:
    21396 7.288) 
    21397  
    21398 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.6), sequence
    21399 alignment score = 889.9 
    21400 RMSD between 150 pruned atom pairs is 0.625 angstroms; (across all 167 pairs:
    21401 4.094) 
    21402  
    21403 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.7), sequence
    21404 alignment score = 886.3 
    21405 RMSD between 150 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    21406 2.428) 
    21407  
    21408 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.8), sequence
    21409 alignment score = 882.7 
    21410 RMSD between 114 pruned atom pairs is 1.220 angstroms; (across all 167 pairs:
    21411 8.487) 
    21412  
    21413 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.9), sequence
    21414 alignment score = 886.3 
    21415 RMSD between 137 pruned atom pairs is 0.954 angstroms; (across all 167 pairs:
    21416 7.152) 
    21417  
    21418 Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.10), sequence
    21419 alignment score = 886.3 
    21420 RMSD between 149 pruned atom pairs is 0.855 angstroms; (across all 167 pairs:
    21421 1.629) 
    21422  
    21423 
    21424 > close #7
    21425 
    21426 > save "D:/OneDrive - Nanyang Technological
    21427 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
    21428 > includeMaps true
    21429 
    21430 ——— End of log from Tue Feb 22 22:03:06 2022 ———
    21431 
    21432 opened ChimeraX session 
    21433 
    21434 > open "D:/OneDrive - Nanyang Technological
    21435 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb"
    21436 
    21437 Chain information for ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb #7 
    21438 --- 
    21439 Chain | Description 
    21440 B C | No description available 
    21441  
    21442 
    21443 > select #7
    21444 
    21445 4272 atoms, 4342 bonds, 530 residues, 1 model selected 
    21446 
    21447 > view matrix models #7,1,0,0,155.3,0,1,0,-32.66,0,0,1,15.862
    21448 
    21449 > view matrix models #7,1,0,0,227.55,0,1,0,182.45,0,0,1,257.42
    21450 
    21451 > view matrix models #7,1,0,0,226.69,0,1,0,184.64,0,0,1,255.63
    21452 
    21453 > view matrix models #7,1,0,0,204.58,0,1,0,234.23,0,0,1,235.65
    21454 
    21455 > ui mousemode right "rotate selected models"
    21456 
    21457 > view matrix models
    21458 > #7,0.67294,0.6481,-0.35654,204.55,-0.4966,0.03861,-0.86712,237.02,-0.54821,0.76058,0.34783,236.07
    21459 
    21460 > ui mousemode right "translate selected models"
    21461 
    21462 > view matrix models
    21463 > #7,0.67294,0.6481,-0.35654,202.23,-0.4966,0.03861,-0.86712,223.37,-0.54821,0.76058,0.34783,214.9
    21464 
    21465 > view matrix models
    21466 > #7,0.67294,0.6481,-0.35654,204.71,-0.4966,0.03861,-0.86712,212.44,-0.54821,0.76058,0.34783,207.19
    21467 
    21468 > view matrix models
    21469 > #7,0.67294,0.6481,-0.35654,168.77,-0.4966,0.03861,-0.86712,212.73,-0.54821,0.76058,0.34783,213.42
    21470 
    21471 > view matrix models
    21472 > #7,0.67294,0.6481,-0.35654,168.7,-0.4966,0.03861,-0.86712,204.73,-0.54821,0.76058,0.34783,218.41
    21473 
    21474 > view matrix models
    21475 > #7,0.67294,0.6481,-0.35654,169.65,-0.4966,0.03861,-0.86712,208.53,-0.54821,0.76058,0.34783,221.42
    21476 
    21477 > ui mousemode right "rotate selected models"
    21478 
    21479 > view matrix models
    21480 > #7,0.74751,0.56918,-0.34243,169.65,-0.52825,0.19685,-0.82595,208.32,-0.40271,0.7983,0.44782,221.09
    21481 
    21482 > view matrix models
    21483 > #7,0.17157,-0.18647,-0.96736,171.99,0.92678,0.36358,0.094287,205.38,0.33413,-0.91271,0.23519,222.64
    21484 
    21485 > view matrix models
    21486 > #7,-0.43014,-0.90269,-0.011358,172.47,-0.7035,0.32728,0.63086,206.67,-0.56575,0.27935,-0.77582,223.35
    21487 
    21488 > view matrix models
    21489 > #7,-0.56096,-0.12743,-0.81798,172.58,-0.79405,0.36224,0.48812,206.9,0.2341,0.92333,-0.30439,221.07
    21490 
    21491 > view matrix models
    21492 > #7,-0.46527,-0.14524,-0.87317,172.56,-0.84174,0.37778,0.38568,207.05,0.27385,0.91443,-0.29802,221.03
    21493 
    21494 > ui mousemode right "translate selected models"
    21495 
    21496 > view matrix models
    21497 > #7,-0.46527,-0.14524,-0.87317,175.91,-0.84174,0.37778,0.38568,203.89,0.27385,0.91443,-0.29802,211.39
    21498 
    21499 > view matrix models
    21500 > #7,-0.46527,-0.14524,-0.87317,174.08,-0.84174,0.37778,0.38568,206.07,0.27385,0.91443,-0.29802,215.64
    21501 
    21502 > hide #!8 models
    21503 
    21504 > view matrix models
    21505 > #7,-0.46527,-0.14524,-0.87317,174.65,-0.84174,0.37778,0.38568,206.88,0.27385,0.91443,-0.29802,212.06
    21506 
    21507 > save "D:/OneDrive - Nanyang Technological
    21508 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220302_D2NS1ts-
    21509 > Ab56-apoa1.cxs" includeMaps true
    21510 
    21511 ——— End of log from Wed Mar 2 00:08:07 2022 ———
    21512 
    21513 opened ChimeraX session 
    21514 
    21515 > open "D:/OneDrive - Nanyang Technological
    21516 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb"
    21517 
    21518 Chain information for ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb
    21519 #9 
    21520 --- 
    21521 Chain | Description 
    21522 B C | No description available 
    21523  
    21524 
    21525 > mmaker #9 to #10
    21526 
    21527 No 'to' model specified 
    21528 
    21529 > mmaker #9 to #7
    21530 
    21531 Parameters 
    21532 --- 
    21533 Chain pairing | bb 
    21534 Alignment algorithm | Needleman-Wunsch 
    21535 Similarity matrix | BLOSUM-62 
    21536 SS fraction | 0.3 
    21537 Gap open (HH/SS/other) | 18/18/6 
    21538 Gap extend | 1 
    21539 SS matrix |  |  | H | S | O 
    21540 ---|---|---|--- 
    21541 H | 6 | -9 | -6 
    21542 S |  | 6 | -6 
    21543 O |  |  | 4 
    21544 Iteration cutoff | 2 
    21545  
    21546 Matchmaker ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb, chain B (#7) with
    21547 ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb, chain B (#9),
    21548 sequence alignment score = 1084.5 
    21549 RMSD between 74 pruned atom pairs is 0.985 angstroms; (across all 207 pairs:
    21550 10.547) 
    21551  
    21552 
    21553 > hide #7 models
    21554 
    21555 > select #9
    21556 
    21557 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    21558 
    21559 > ui mousemode right "rotate selected models"
    21560 
    21561 > view matrix models
    21562 > #9,0.52533,-0.58815,-0.61491,177.85,0.0047201,0.72466,-0.68909,201.87,0.85089,0.35909,0.38346,210.74
    21563 
    21564 > view matrix models
    21565 > #9,0.45946,-0.88174,0.10689,181.58,0.8882,0.45638,-0.053134,204.22,-0.0019327,0.11935,0.99285,214.69
    21566 
    21567 > ui mousemode right "translate selected models"
    21568 
    21569 > view matrix models
    21570 > #9,0.45946,-0.88174,0.10689,177.6,0.8882,0.45638,-0.053134,197.13,-0.0019327,0.11935,0.99285,218.41
    21571 
    21572 > view matrix models
    21573 > #9,0.45946,-0.88174,0.10689,175.75,0.8882,0.45638,-0.053134,203.48,-0.0019327,0.11935,0.99285,218.85
    21574 
    21575 > view matrix models
    21576 > #9,0.45946,-0.88174,0.10689,169.69,0.8882,0.45638,-0.053134,196.29,-0.0019327,0.11935,0.99285,214.81
    21577 
    21578 > view matrix models
    21579 > #9,0.45946,-0.88174,0.10689,169.27,0.8882,0.45638,-0.053134,199.29,-0.0019327,0.11935,0.99285,212.88
    21580 
    21581 > view matrix models
    21582 > #9,0.45946,-0.88174,0.10689,173.56,0.8882,0.45638,-0.053134,203.27,-0.0019327,0.11935,0.99285,212.35
    21583 
    21584 > view matrix models
    21585 > #9,0.45946,-0.88174,0.10689,176.72,0.8882,0.45638,-0.053134,202,-0.0019327,0.11935,0.99285,212.91
    21586 
    21587 > view matrix models
    21588 > #9,0.45946,-0.88174,0.10689,172.24,0.8882,0.45638,-0.053134,200.71,-0.0019327,0.11935,0.99285,209.78
    21589 
    21590 > view matrix models
    21591 > #9,0.45946,-0.88174,0.10689,171.54,0.8882,0.45638,-0.053134,200.71,-0.0019327,0.11935,0.99285,209.45
    21592 
    21593 > ui tool show "Fit in Map"
    21594 
    21595 Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
    21596 map cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 3334 atoms 
    21597 average map value = 0.1014, steps = 288 
    21598 shifted from previous position = 26.2 
    21599 rotated from previous position = 35.6 degrees 
    21600 atoms outside contour = 2236, contour level = 0.14151 
    21601  
    21602 Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
    21603 relative to cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21604 Matrix rotation and translation 
    21605 0.15030095 -0.25689088 -0.95468145 159.80559539 
    21606 0.91205850 0.40867945 0.03362089 142.63963221 
    21607 0.38152180 -0.87577859 0.29572442 147.85545078 
    21608 Axis -0.45590440 -0.66987165 0.58602316 
    21609 Axis point -104.50370211 0.00000000 221.35941513 
    21610 Rotation angle (degrees) 94.16607036 
    21611 Shift along axis -81.75960077 
    21612  
    21613 
    21614 > view matrix models
    21615 > #9,0.67727,-0.51922,0.52127,172.73,0.71543,0.63007,-0.30194,194.77,-0.17166,0.57742,0.7982,218.78
    21616 
    21617 > view matrix models
    21618 > #9,0.67727,-0.51922,0.52127,173.99,0.71543,0.63007,-0.30194,197.51,-0.17166,0.57742,0.7982,212.36
    21619 
    21620 > view matrix models
    21621 > #9,0.67727,-0.51922,0.52127,174.96,0.71543,0.63007,-0.30194,195,-0.17166,0.57742,0.7982,208.97
    21622 
    21623 > ui mousemode right "rotate selected models"
    21624 
    21625 > view matrix models
    21626 > #9,0.66193,-0.59819,0.45168,174.95,0.73725,0.62836,-0.24824,195.18,-0.13532,0.49732,0.85695,209.41
    21627 
    21628 > view matrix models
    21629 > #9,0.64956,-0.67275,0.35424,174.82,0.71372,0.70012,0.020895,196.02,-0.26207,0.23925,0.93492,210.62
    21630 
    21631 > save "D:/OneDrive - Nanyang Technological
    21632 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220302_D2NS1ts-
    21633 > Ab56-apoa1.cxs" includeMaps true
    21634 
    21635 ——— End of log from Wed Mar 2 00:18:18 2022 ———
    21636 
    21637 opened ChimeraX session 
    21638 
    21639 > show #!1 models
    21640 
    21641 > hide #!2 models
    21642 
    21643 > hide #9 models
    21644 
    21645 > hide #!10 models
    21646 
    21647 > show #6 models
    21648 
    21649 > hide #4 models
    21650 
    21651 > hide #3 models
    21652 
    21653 > ui tool show "Fit in Map"
    21654 
    21655 Fit molecule D2NS1-F562.pdb (#6) to map
    21656 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    21657 average map value = 0.07482, steps = 364 
    21658 shifted from previous position = 2.61 
    21659 rotated from previous position = 17.1 degrees 
    21660 atoms outside contour = 8195, contour level = 0.08 
    21661  
    21662 Position of D2NS1-F562.pdb (#6) relative to
    21663 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    21664 Matrix rotation and translation 
    21665 -0.99640848 0.07252019 0.04371456 331.26650068 
    21666 -0.01695668 -0.67668277 0.73607941 166.80204366 
    21667 0.08296151 0.73269451 0.67548215 -88.38561339 
    21668 Axis -0.03462299 -0.40144391 -0.91522895 
    21669 Axis point 169.54681270 98.35816249 0.00000000 
    21670 Rotation angle (degrees) 177.19813771 
    21671 Shift along axis 2.46197109 
    21672  
    21673 
    21674 > ui mousemode right "translate selected models"
    21675 
    21676 > view matrix models
    21677 > #9,0.64956,-0.67275,0.35424,175.54,0.71372,0.70012,0.020895,189.47,-0.26207,0.23925,0.93492,190.81
    21678 
    21679 > ~select #9
    21680 
    21681 Nothing selected 
    21682 
    21683 > select #6
    21684 
    21685 12404 atoms, 12730 bonds, 1588 residues, 1 model selected 
    21686 
    21687 > view matrix models
    21688 > #6,-0.99797,0.039575,0.049905,338.25,-0.014392,-0.90338,0.42859,266.52,0.062045,0.42701,0.90212,-62.663
    21689 
    21690 > ui mousemode right "rotate selected models"
    21691 
    21692 > view matrix models
    21693 > #6,-0.99623,0.082033,0.028348,334.24,-0.086585,-0.91673,-0.39002,429.14,-0.006007,-0.391,0.92037,92.117
    21694 
    21695 > view matrix models
    21696 > #6,-0.99623,0.082033,0.028348,335.42,-0.086585,-0.91673,-0.39002,430.38,-0.006007,-0.391,0.92037,88.929
    21697 
    21698 Fit molecule D2NS1-F562.pdb (#6) to map
    21699 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    21700 average map value = 0.09493, steps = 84 
    21701 shifted from previous position = 3.13 
    21702 rotated from previous position = 3.82 degrees 
    21703 atoms outside contour = 7003, contour level = 0.08 
    21704  
    21705 Position of D2NS1-F562.pdb (#6) relative to
    21706 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    21707 Matrix rotation and translation 
    21708 -0.99820989 0.05968746 0.00379835 345.43779112 
    21709 -0.05973880 -0.99809742 -0.01525811 372.27574829 
    21710 0.00288041 -0.01545771 0.99987637 1.80150722 
    21711 Axis -0.00167123 0.00768605 -0.99996907 
    21712 Axis point 178.28007958 180.98306790 0.00000000 
    21713 Rotation angle (degrees) 176.57654715 
    21714 Shift along axis 0.48257203 
    21715  
    21716 Fit molecule D2NS1-F562.pdb (#6) to map
    21717 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    21718 average map value = 0.09495, steps = 48 
    21719 shifted from previous position = 0.019 
    21720 rotated from previous position = 0.00432 degrees 
    21721 atoms outside contour = 7012, contour level = 0.08 
    21722  
    21723 Position of D2NS1-F562.pdb (#6) relative to
    21724 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    21725 Matrix rotation and translation 
    21726 -0.99820895 0.05970074 0.00383565 345.40975009 
    21727 -0.05975246 -0.99809759 -0.01519388 372.26991158 
    21728 0.00292127 -0.01539585 0.99987721 1.78218185 
    21729 Axis -0.00169079 0.00765450 -0.99996927 
    21730 Axis point 178.26722509 180.97930211 0.00000000 
    21731 Rotation angle (degrees) 176.57577490 
    21732 Shift along axis 0.48339683 
    21733  
    21734 
    21735 > set bgColor white
    21736 
    21737 > lighting full
    21738 
    21739 > ~select #6
    21740 
    21741 Nothing selected 
    21742 
    21743 > hide #6 models
    21744 
    21745 > show #6 models
    21746 
    21747 > color #6 bychain
    21748 
    21749 Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
    21750 models, 1 maps. 
    21751 
    21752 Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
    21753 models, 1 maps. 
    21754 
    21755 > select #1
    21756 
    21757 2 models selected 
    21758 
    21759 Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
    21760 models, 1 maps. 
    21761 
    21762 > ~select #1
    21763 
    21764 Nothing selected 
    21765 
    21766 > hide #!1 models
    21767 
    21768 > show #!2 models
    21769 
    21770 > hide #!2 models
    21771 
    21772 > show #!2 models
    21773 
    21774 > show #3 models
    21775 
    21776 > show #4 models
    21777 
    21778 > hide #6 models
    21779 
    21780 > volume #2 color #a7a49f80
    21781 
    21782 > volume #2 color #b8b5af80
    21783 
    21784 > color #3-4 bychain
    21785 
    21786 Color zone shortcut requires 1 displayed atomic model and 1 map, got 12 atomic
    21787 models, 1 maps. 
    21788 
    21789 > hide #4 models
    21790 
    21791 > show #4 models
    21792 
    21793 > hide #4 models
    21794 
    21795 > select #3
    21796 
    21797 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    21798 
    21799 > select #2
    21800 
    21801 2 models selected 
    21802 
    21803 > ~select #2
    21804 
    21805 Nothing selected 
    21806 
    21807 Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
    21808 models, 1 maps. 
    21809 
    21810 > show #4 models
    21811 
    21812 > ui tool show "Segment Map"
    21813 
    21814 > show #9 models
    21815 
    21816 > ui mousemode right "translate selected models"
    21817 
    21818 > select #9
    21819 
    21820 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    21821 
    21822 > view matrix models
    21823 > #9,0.64956,-0.67275,0.35424,173.28,0.71372,0.70012,0.020895,203.74,-0.26207,0.23925,0.93492,217.24
    21824 
    21825 > ui mousemode right "rotate selected models"
    21826 
    21827 > view matrix models
    21828 > #9,0.42545,-0.83111,0.35811,174.01,0.88507,0.46469,0.026952,204.31,-0.18881,0.30548,0.93329,216.96
    21829 
    21830 > view matrix models
    21831 > #9,0.36854,-0.89204,0.26163,173.89,0.89839,0.4141,0.14638,204.91,-0.23892,0.18109,0.954,217.47
    21832 
    21833 > view matrix models
    21834 > #9,0.39748,-0.85333,0.3374,174.03,0.89601,0.44024,0.057848,204.49,-0.1979,0.27932,0.93958,217.07
    21835 
    21836 > view matrix models
    21837 > #9,0.4249,-0.82293,0.37715,174.06,0.89397,0.44699,-0.03185,204.13,-0.14237,0.3507,0.9256,216.74
    21838 
    21839 > view matrix models
    21840 > #9,0.30959,-0.88763,0.34097,174.24,0.94929,0.30918,-0.057041,204.4,-0.05479,0.34134,0.93834,216.73
    21841 
    21842 > ~select #9
    21843 
    21844 Nothing selected 
    21845 
    21846 > ui mousemode right "translate selected models"
    21847 
    21848 > select #9
    21849 
    21850 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    21851 
    21852 > ~select #9
    21853 
    21854 Nothing selected 
    21855 
    21856 > select #9
    21857 
    21858 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    21859 
    21860 > view matrix models
    21861 > #9,0.30959,-0.88763,0.34097,171.78,0.94929,0.30918,-0.057041,200.45,-0.05479,0.34134,0.93834,215.77
    21862 
    21863 > ~select #9
    21864 
    21865 Nothing selected 
    21866 
    21867 > movie record
    21868 
    21869 > turn y 2 180
    21870 
    21871 > wait 180
    21872 
    21873 > movie encode "C:\Users\dahailuo\OneDrive - Nanyang Technological
    21874 > University\Temporal\202112_FlaviNS1\Data_EM_Alvin\movie2.mp4"
    21875 
    21876 Movie saved to \C:Users\\...\Data_EM_Alvin\movie2.mp4 
    21877  
    21878 
    21879 > show #6 models
    21880 
    21881 > mmaker #6 to #3
    21882 
    21883 Parameters 
    21884 --- 
    21885 Chain pairing | bb 
    21886 Alignment algorithm | Needleman-Wunsch 
    21887 Similarity matrix | BLOSUM-62 
    21888 SS fraction | 0.3 
    21889 Gap open (HH/SS/other) | 18/18/6 
    21890 Gap extend | 1 
    21891 SS matrix |  |  | H | S | O 
    21892 ---|---|---|--- 
    21893 H | 6 | -9 | -6 
    21894 S |  | 6 | -6 
    21895 O |  |  | 4 
    21896 Iteration cutoff | 2 
    21897  
    21898 Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
    21899 alignment score = 1871.9 
    21900 RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
    21901 0.023) 
    21902  
    21903 
    21904 > mmaker #6 to #4
    21905 
    21906 Parameters 
    21907 --- 
    21908 Chain pairing | bb 
    21909 Alignment algorithm | Needleman-Wunsch 
    21910 Similarity matrix | BLOSUM-62 
    21911 SS fraction | 0.3 
    21912 Gap open (HH/SS/other) | 18/18/6 
    21913 Gap extend | 1 
    21914 SS matrix |  |  | H | S | O 
    21915 ---|---|---|--- 
    21916 H | 6 | -9 | -6 
    21917 S |  | 6 | -6 
    21918 O |  |  | 4 
    21919 Iteration cutoff | 2 
    21920  
    21921 Matchmaker F562a.pdb, chain B (#4) with D2NS1-F562.pdb, chain C (#6), sequence
    21922 alignment score = 1200 
    21923 RMSD between 228 pruned atom pairs is 0.000 angstroms; (across all 228 pairs:
    21924 0.000) 
    21925  
    21926 
    21927 > hide #!2 models
    21928 
    21929 > hide #9 models
    21930 
    21931 > hide #3 models
    21932 
    21933 > hide #4 models
    21934 
    21935 > show #!2 models
    21936 
    21937 > hide #6 models
    21938 
    21939 > show #!1 models
    21940 
    21941 > show #!10 models
    21942 
    21943 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    21944 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points 
    21945 correlation = 0.493, correlation about mean = 0.2808, overlap = 5991 
    21946 steps = 48, shift = 0.0601, angle = 0.109 degrees 
    21947  
    21948 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    21949 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21950 Matrix rotation and translation 
    21951 -0.27792284 -0.14164293 -0.95010322 410.09306464 
    21952 0.39540197 0.88452622 -0.24752902 -48.83916554 
    21953 0.87545196 -0.44446666 -0.18982414 109.38604242 
    21954 Axis -0.10294301 -0.95425209 0.28072349 
    21955 Axis point 169.05771360 0.00000000 208.04394464 
    21956 Rotation angle (degrees) 106.95439226 
    21957 Shift along axis 35.09589160 
    21958  
    21959 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    21960 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points 
    21961 correlation = 0.493, correlation about mean = 0.2809, overlap = 5991 
    21962 steps = 48, shift = 0.0078, angle = 0.0885 degrees 
    21963  
    21964 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    21965 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    21966 Matrix rotation and translation 
    21967 -0.27794843 -0.14312388 -0.94987377 410.31424613 
    21968 0.39534589 0.88416435 -0.24890760 -48.51539453 
    21969 0.87546917 -0.44471217 -0.18916865 109.30275225 
    21970 Axis -0.10234637 -0.95410041 0.28145627 
    21971 Axis point 169.16249688 0.00000000 208.15543264 
    21972 Rotation angle (degrees) 106.94636481 
    21973 Shift along axis 35.05832906 
    21974  
    21975 
    21976 > hide #!2 models
    21977 
    21978 > select #1
    21979 
    21980 2 models selected 
    21981 
    21982 > ui mousemode right "rotate selected models"
    21983 
    21984 > view matrix models
    21985 > #1,0.74046,0.62541,0.24616,-107.44,-0.65719,0.75044,0.070241,152.95,-0.1408,-0.21378,0.96668,70.267
    21986 
    21987 > view matrix models
    21988 > #1,0.72193,-0.13867,0.67793,-42.597,0.2204,0.97477,-0.035306,-25.414,-0.65593,0.1749,0.73428,133.11
    21989 
    21990 > view matrix models
    21991 > #1,0.74615,0.64297,-0.17276,-38.999,0.62682,-0.76589,-0.14322,231.4,-0.22441,-0.0014231,-0.97449,383.68
    21992 
    21993 > view matrix models
    21994 > #1,0.80841,0.29993,0.50648,-106.59,0.51816,-0.77083,-0.37058,291.07,0.27926,0.56202,-0.77856,159.28
    21995 
    21996 > view matrix models
    21997 > #1,0.96135,-0.23483,0.14371,24.411,0.25186,0.96097,-0.11451,-14.839,-0.11121,0.14628,0.98297,-2.0945
    21998 
    21999 > view matrix models
    22000 > #1,0.99141,-0.075528,-0.10677,34.022,0.051461,0.97582,-0.21244,35.244,0.12024,0.20512,0.97132,-51.881
    22001 
    22002 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    22003 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points 
    22004 correlation = 0.493, correlation about mean = 0.2808, overlap = 5991 
    22005 steps = 716, shift = 1.66, angle = 12.6 degrees 
    22006  
    22007 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    22008 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    22009 Matrix rotation and translation 
    22010 -0.27785362 -0.14026525 -0.95032783 409.88132947 
    22011 0.39567157 0.88475643 -0.24627224 -49.16134094 
    22012 0.87535212 -0.44444535 -0.19033380 109.50506725 
    22013 Axis -0.10359229 -0.95434929 0.28015367 
    22014 Axis point 168.94433960 0.00000000 207.96495201 
    22015 Rotation angle (degrees) 106.96068830 
    22016 Shift along axis 35.13479072 
    22017  
    22018 
    22019 > show #!2 models
    22020 
    22021 > hide #!2 models
    22022 
    22023 > show #!2 models
    22024 
    22025 > ~select #1
    22026 
    22027 Nothing selected 
    22028 
    22029 > select #1
    22030 
    22031 2 models selected 
    22032 
    22033 > view matrix models
    22034 > #1,0.9987,0.030982,-0.040533,2.2432,0.0036821,0.74864,0.66296,-67.414,0.050884,-0.66225,0.74755,154.04
    22035 
    22036 > view matrix models
    22037 > #1,0.87306,0.20075,-0.44437,64.348,0.48063,-0.20061,0.85367,-16.172,0.082229,-0.95888,-0.27163,378
    22038 
    22039 > view matrix models
    22040 > #1,0.83244,0.37492,-0.40802,34.215,0.55119,-0.48475,0.67912,52.19,0.056831,-0.79023,-0.61017,411.1
    22041 
    22042 > view matrix models
    22043 > #1,0.68639,0.56283,-0.46053,35.845,0.69489,-0.69435,0.1871,149.22,-0.21447,-0.44844,-0.8677,443.15
    22044 
    22045 > hide #!10 models
    22046 
    22047 > show #!10 models
    22048 
    22049 > hide #!10 models
    22050 
    22051 > show #!10 models
    22052 
    22053 > hide #!1 models
    22054 
    22055 > hide #!2 models
    22056 
    22057 > show #!1 models
    22058 
    22059 > view matrix models
    22060 > #1,0.82844,0.50873,-0.23428,-19.057,0.47101,-0.40647,0.7829,34.547,0.30305,-0.75893,-0.57635,355.71
    22061 
    22062 > view matrix models
    22063 > #1,0.84453,-0.094928,-0.52703,136.53,-0.025459,-0.99017,0.13755,339.15,-0.5349,-0.10275,-0.83864,433.6
    22064 
    22065 > view matrix models
    22066 > #1,0.97799,-0.18464,-0.097184,54.238,-0.1969,-0.66248,-0.72274,460.34,0.069068,0.72597,-0.68425,151.17
    22067 
    22068 > view matrix models
    22069 > #1,0.97796,-0.19168,-0.082782,53.003,-0.16644,-0.47632,-0.86337,446.06,0.12606,0.85812,-0.49773,85.086
    22070 
    22071 > view matrix models
    22072 > #1,0.99726,0.035713,-0.06472,5.846,-0.039623,-0.48086,-0.8759,426.41,-0.062402,0.87607,-0.47813,112.12
    22073 
    22074 > view matrix models
    22075 > #1,-0.96752,0.24305,-0.069446,320.31,-0.20699,-0.60408,0.76957,193.12,0.14509,0.75896,0.63477,-96.862
    22076 
    22077 > view matrix models
    22078 > #1,-0.85416,0.24266,-0.45992,367.81,-0.51768,-0.48048,0.70792,237.19,-0.049202,0.84277,0.53603,-60.033
    22079 
    22080 > view matrix models
    22081 > #1,-0.98697,0.14048,-0.078425,343.64,-0.16057,-0.82904,0.53564,265.52,0.010232,0.54125,0.8408,-69.644
    22082 
    22083 > view matrix models
    22084 > #1,-0.99016,0.10292,-0.094853,353.76,-0.13794,-0.83244,0.53668,261.91,-0.023726,0.54448,0.83844,-63.751
    22085 
    22086 > ui mousemode right "translate selected models"
    22087 
    22088 > view matrix models
    22089 > #1,-0.99016,0.10292,-0.094853,357.93,-0.13794,-0.83244,0.53668,248.71,-0.023726,0.54448,0.83844,-68.308
    22090 
    22091 > view matrix models
    22092 > #1,-0.99016,0.10292,-0.094853,358.29,-0.13794,-0.83244,0.53668,250.68,-0.023726,0.54448,0.83844,-68.894
    22093 
    22094 > ui mousemode right "rotate selected models"
    22095 
    22096 > view matrix models
    22097 > #1,-0.9422,-0.030752,0.33364,299.34,0.13856,-0.9424,0.30443,261.21,0.30506,0.33307,0.89219,-99.156
    22098 
    22099 > view matrix models
    22100 > #1,-0.77548,-0.32284,0.54259,285.5,0.28029,-0.94609,-0.16233,317.46,0.56574,0.026196,0.82416,-79.125
    22101 
    22102 > ui mousemode right "translate selected models"
    22103 
    22104 > view matrix models
    22105 > #1,-0.77548,-0.32284,0.54259,268.3,0.28029,-0.94609,-0.16233,334.8,0.56574,0.026196,0.82416,-67.645
    22106 
    22107 > view matrix models
    22108 > #1,-0.77548,-0.32284,0.54259,265.58,0.28029,-0.94609,-0.16233,338.57,0.56574,0.026196,0.82416,-65.98
    22109 
    22110 > view matrix models
    22111 > #1,-0.77548,-0.32284,0.54259,285.03,0.28029,-0.94609,-0.16233,352.61,0.56574,0.026196,0.82416,-59.271
    22112 
    22113 > ui mousemode right "rotate selected models"
    22114 
    22115 > view matrix models
    22116 > #1,-0.91194,-0.17978,0.36883,313.96,0.10929,-0.97286,-0.20397,395.12,0.39549,-0.1457,0.90684,-12.537
    22117 
    22118 > view matrix models
    22119 > #1,-0.91113,-0.10679,0.39805,295.73,0.021642,-0.97691,-0.21254,412.97,0.41156,-0.18504,0.8924,-5.8812
    22120 
    22121 > view matrix models
    22122 > #1,-0.99135,-0.088862,0.096564,359.09,0.037913,-0.89841,-0.43753,435.05,0.12563,-0.43008,0.894,88.599
    22123 
    22124 > ui mousemode right "translate selected models"
    22125 
    22126 > view matrix models
    22127 > #1,-0.99135,-0.088862,0.096564,361.35,0.037913,-0.89841,-0.43753,415.99,0.12563,-0.43008,0.894,90.946
    22128 
    22129 > ui mousemode right "rotate selected models"
    22130 
    22131 > view matrix models
    22132 > #1,-0.99008,-0.020034,0.1391,341.47,-0.013738,-0.97125,-0.23766,403.58,0.13986,-0.23721,0.96134,42.319
    22133 
    22134 > ui mousemode right "translate selected models"
    22135 
    22136 > view matrix models
    22137 > #1,-0.99008,-0.020034,0.1391,341.46,-0.013738,-0.97125,-0.23766,399.55,0.13986,-0.23721,0.96134,42.616
    22138 
    22139 > view matrix models
    22140 > #1,-0.99008,-0.020034,0.1391,338.93,-0.013738,-0.97125,-0.23766,400.44,0.13986,-0.23721,0.96134,32.494
    22141 
    22142 > view matrix models
    22143 > #1,-0.99008,-0.020034,0.1391,335.49,-0.013738,-0.97125,-0.23766,400.28,0.13986,-0.23721,0.96134,33.65
    22144 
    22145 > view matrix models
    22146 > #1,-0.99008,-0.020034,0.1391,333.14,-0.013738,-0.97125,-0.23766,400.18,0.13986,-0.23721,0.96134,33.756
    22147 
    22148 > ui mousemode right "rotate selected models"
    22149 
    22150 > view matrix models
    22151 > #1,-0.99347,-0.11227,0.020092,370.83,0.11149,-0.99309,-0.036498,346.87,0.024051,-0.03402,0.99913,11.612
    22152 
    22153 > view matrix models
    22154 > #1,-0.99314,-0.11513,0.02023,371.26,0.11367,-0.99155,-0.06254,350.72,0.027259,-0.059812,0.99784,15.866
    22155 
    22156 > view matrix models
    22157 > #1,-0.99502,-0.048682,0.086949,348.18,0.043004,-0.99689,-0.06602,364.89,0.089893,-0.061952,0.99402,5.7314
    22158 
    22159 > view matrix models
    22160 > #1,-0.9999,-0.011841,0.0079016,356.17,0.012535,-0.99545,0.094484,342.25,0.0067469,0.094574,0.9955,-7.6193
    22161 
    22162 > view matrix models
    22163 > #1,-0.99955,0.029264,0.006465,349.02,-0.028596,-0.99584,0.086513,351.05,0.0089699,0.086289,0.99623,-6.6648
    22164 
    22165 > show #!2 models
    22166 
    22167 > hide #!2 models
    22168 
    22169 > view matrix models
    22170 > #1,-0.99431,-0.012476,0.10579,338.32,0.013343,-0.99988,0.0074894,357.98,0.10568,0.0088583,0.99436,-9.7821
    22171 
    22172 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    22173 cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points 
    22174 correlation = 0.493, correlation about mean = 0.2808, overlap = 5991 
    22175 steps = 948, shift = 10.3, angle = 23.5 degrees 
    22176  
    22177 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    22178 cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates: 
    22179 Matrix rotation and translation 
    22180 0.27780939 0.13998726 -0.95038174 260.70800172 
    22181 -0.39575740 -0.88479067 -0.24601119 407.82841194 
    22182 -0.87532735 0.44446484 -0.19040216 263.31428797 
    22183 Axis 0.78717074 -0.08556506 -0.61077070 
    22184 Axis point 0.00000000 178.59809032 292.75645151 
    22185 Rotation angle (degrees) 153.98663078 
    22186 Shift along axis 9.50119898 
    22187  
    22188 
    22189 > hide #!10 models
    22190 
    22191 > show #6 models
    22192 
    22193 > select #6
    22194 
    22195 12404 atoms, 12730 bonds, 1588 residues, 1 model selected 
    22196 
    22197 > ~select #6
    22198 
    22199 Nothing selected 
    22200 
    22201 > select #6
    22202 
    22203 12404 atoms, 12730 bonds, 1588 residues, 1 model selected 
    22204 
    22205 > view matrix models
    22206 > #6,0.80584,-0.033933,0.59116,-60.641,-0.18803,0.93202,0.30982,-22.728,-0.56149,-0.36082,0.74468,228.14
    22207 
    22208 > view matrix models
    22209 > #6,0.84169,0.23741,0.48497,-96.336,-0.031206,0.91804,-0.39525,78.603,-0.53906,0.31754,0.78012,96.759
    22210 
    22211 > view matrix models
    22212 > #6,0.95752,0.28708,0.027255,-43.538,-0.26323,0.90873,-0.32391,108.93,-0.11776,0.30298,0.94569,-5.8011
    22213 
    22214 > ui mousemode right "translate selected models"
    22215 
    22216 > view matrix models
    22217 > #6,0.95752,0.28708,0.027255,-47.959,-0.26323,0.90873,-0.32391,118,-0.11776,0.30298,0.94569,-22.337
    22218 
    22219 > ui mousemode right "rotate selected models"
    22220 
    22221 > view matrix models
    22222 > #6,0.99918,0.040001,0.0063686,-7.5857,-0.036305,0.95416,-0.29708,64.472,-0.01796,0.2966,0.95483,-40.695
    22223 
    22224 Fit molecule D2NS1-F562.pdb (#6) to map
    22225 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms 
    22226 average map value = 0.1026, steps = 96 
    22227 shifted from previous position = 4.3 
    22228 rotated from previous position = 4.93 degrees 
    22229 atoms outside contour = 6857, contour level = 0.08 
    22230  
    22231 Position of D2NS1-F562.pdb (#6) relative to
    22232 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    22233 Matrix rotation and translation 
    22234 -1.00000000 -0.00003889 0.00000390 356.92132489 
    22235 0.00003889 -0.99999983 -0.00059770 357.02795185 
    22236 0.00000392 -0.00059770 0.99999983 0.10572384 
    22237 Axis -0.00000446 -0.00030232 0.99999995 
    22238 Axis point 178.45719114 178.51746241 0.00000000 
    22239 Rotation angle (degrees) 179.99777155 
    22240 Shift along axis -0.00380630 
    22241  
    22242 
    22243 > ~select #6
    22244 
    22245 Nothing selected 
    22246 
    22247 > interfaces #6 & ~solvent
    22248 
    22249 7 buried areas: A B 2354, E F 2040, C D 2040, B C 1572, A F 1542, B D 1312, A
    22250 E 1190 
    22251 
    22252 > open "C:/Users/dahailuo/Downloads/cryosparc_P35_J100_005_volume_map_sharp
    22253 > (1).mrc"
    22254 
    22255 Opened cryosparc_P35_J100_005_volume_map_sharp (1).mrc as #11, grid size
    22256 416,416,416, pixel 0.858, shown at level 0.0415, step 2, values float32 
    22257 
    22258 QWindowsWindow::setGeometry: Unable to set geometry 1920x1102+1920+23 (frame:
    22259 1936x1141+1912-8) on QWidgetWindow/"MainWindowClassWindow" on
    22260 "\\\\.\DISPLAY1". Resulting geometry: 1920x1017+1920+23 (frame:
    22261 1936x1056+1912-8) margins: 8, 31, 8, 8 minimum size: 493x1102 MINMAXINFO
    22262 maxSize=0,0 maxpos=0,0 mintrack=509,1141 maxtrack=0,0) 
    22263 
    22264 > volume #11 step 1
    22265 
    22266 > surface dust #1 size 8.58
    22267 
    22268 > surface dust #11 size 8.58
    22269 
    22270 > volume #11 level 0.045
    22271 
    22272 > volume #11 level 0.05
    22273 
    22274 Fit molecule D2NS1-F562.pdb (#6) to map
    22275 cryosparc_P35_J100_005_volume_map_sharp (1).mrc (#11) using 12404 atoms 
    22276 average map value = 0.08442, steps = 152 
    22277 shifted from previous position = 1.4 
    22278 rotated from previous position = 4.71 degrees 
    22279 atoms outside contour = 5898, contour level = 0.05 
    22280  
    22281 Position of D2NS1-F562.pdb (#6) relative to
    22282 cryosparc_P35_J100_005_volume_map_sharp (1).mrc (#11) coordinates: 
    22283 Matrix rotation and translation 
    22284 0.99897026 0.04182548 -0.01757995 -4.15590074 
    22285 -0.04516063 0.95385198 -0.29686178 69.02604187 
    22286 0.00435228 0.29735001 0.95475862 -45.20466997 
    22287 Axis 0.98879513 -0.03649622 -0.14474879 
    22288 Axis point 0.00000000 183.11150795 204.04343868 
    22289 Rotation angle (degrees) 17.48599398 
    22290 Shift along axis -0.08520266 
    22291  
    22292 
    22293 > transparency #11.1 50
    22294 
    22295 > show #3 models
    22296 
    22297 > mmaker #3 to #6
    22298 
    22299 Parameters 
    22300 --- 
    22301 Chain pairing | bb 
    22302 Alignment algorithm | Needleman-Wunsch 
    22303 Similarity matrix | BLOSUM-62 
    22304 SS fraction | 0.3 
    22305 Gap open (HH/SS/other) | 18/18/6 
    22306 Gap extend | 1 
    22307 SS matrix |  |  | H | S | O 
    22308 ---|---|---|--- 
    22309 H | 6 | -9 | -6 
    22310 S |  | 6 | -6 
    22311 O |  |  | 4 
    22312 Iteration cutoff | 2 
    22313  
    22314 Matchmaker D2NS1-F562.pdb, chain A (#6) with D2NS1.pdb, chain B (#3), sequence
    22315 alignment score = 1871.9 
    22316 RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
    22317 0.023) 
    22318  
    22319 
    22320 > hide #6 models
    22321 
    22322 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
    22323 (1).mrc (#11) using 5602 atoms 
    22324 average map value = 0.07338, steps = 60 
    22325 shifted from previous position = 1.1 
    22326 rotated from previous position = 2.61 degrees 
    22327 atoms outside contour = 3025, contour level = 0.05 
    22328  
    22329 Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
    22330 (1).mrc (#11) coordinates: 
    22331 Matrix rotation and translation 
    22332 0.14875593 -0.08639183 -0.98509297 342.36735832 
    22333 0.98470147 -0.07847453 0.15557896 -15.12271804 
    22334 -0.09074546 -0.99316577 0.07339661 361.18209695 
    22335 Axis -0.63557683 -0.49482408 0.59261389 
    22336 Axis point 0.00000000 37.80172615 346.76474569 
    22337 Rotation angle (degrees) 115.35090835 
    22338 Shift along axis 3.92385104 
    22339  
    22340 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
    22341 (1).mrc (#11) using 5602 atoms 
    22342 average map value = 0.07339, steps = 44 
    22343 shifted from previous position = 0.0117 
    22344 rotated from previous position = 0.00688 degrees 
    22345 atoms outside contour = 3021, contour level = 0.05 
    22346  
    22347 Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
    22348 (1).mrc (#11) coordinates: 
    22349 Matrix rotation and translation 
    22350 0.14885535 -0.08637602 -0.98507934 342.35458834 
    22351 0.98468094 -0.07852972 0.15568097 -15.13336069 
    22352 -0.09080510 -0.99316278 0.07336326 361.19655370 
    22353 Axis -0.63562980 -0.49478213 0.59259210 
    22354 Axis point 0.00000000 37.81870419 346.75288311 
    22355 Rotation angle (degrees) 115.35056364 
    22356 Shift along axis 3.91916090 
    22357  
    22358 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
    22359 (1).mrc (#11) using 5602 atoms 
    22360 average map value = 0.07338, steps = 28 
    22361 shifted from previous position = 0.0166 
    22362 rotated from previous position = 0.0195 degrees 
    22363 atoms outside contour = 3027, contour level = 0.05 
    22364  
    22365 Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
    22366 (1).mrc (#11) coordinates: 
    22367 Matrix rotation and translation 
    22368 0.14869429 -0.08663603 -0.98508083 342.41395707 
    22369 0.98471526 -0.07839157 0.15553350 -15.12882419 
    22370 -0.09069683 -0.99315105 0.07365544 361.12491138 
    22371 Axis -0.63549687 -0.49480794 0.59271311 
    22372 Axis point 0.00000000 37.79183158 346.80910583 
    22373 Rotation angle (degrees) 115.34202749 
    22374 Shift along axis 3.92633355 
    22375  
    22376 
    22377 > select #3
    22378 
    22379 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    22380 
    22381 > view matrix models
    22382 > #3,0.052602,-0.042076,-0.99773,354.08,0.96197,-0.26603,0.061936,37.093,-0.26803,-0.96305,0.026482,395.65
    22383 
    22384 > view matrix models
    22385 > #3,0.0070452,-0.012575,-0.9999,357.51,0.93425,-0.35645,0.011066,66.236,-0.35656,-0.93423,0.0092369,409.45
    22386 
    22387 > view matrix models
    22388 > #3,-0.0058622,0.0073093,-0.99996,356.45,0.91272,-0.40851,-0.0083368,82.232,-0.40855,-0.91272,-0.0042765,417.39
    22389 
    22390 > view matrix models
    22391 > #3,-0.020074,-0.027951,-0.99941,364.78,0.92365,-0.38315,-0.0078364,75.954,-0.3827,-0.92326,0.033508,407.88
    22392 
    22393 > view matrix models
    22394 > #3,0.0017745,-0.041136,-0.99915,363.11,0.92163,-0.38766,0.017597,72.537,-0.38806,-0.92088,0.037224,407.76
    22395 
    22396 > view matrix models
    22397 > #3,-0.017771,-0.12129,-0.99246,378.83,0.9086,-0.41622,0.034596,76.603,-0.41728,-0.90114,0.1176,395.26
    22398 
    22399 > view matrix models
    22400 > #3,0.012861,-0.10916,-0.99394,371.67,0.88601,-0.45952,0.061933,82.986,-0.46349,-0.88144,0.09081,404.85
    22401 
    22402 > view matrix models
    22403 > #3,0.012034,-0.092833,-0.99561,369.37,0.88338,-0.46553,0.054084,85.858,-0.46851,-0.88015,0.076405,408.08
    22404 
    22405 > view matrix models
    22406 > #3,0.022255,-0.099641,-0.99477,368.56,0.88274,-0.46516,0.066341,83.724,-0.46934,-0.8796,0.077605,407.92
    22407 
    22408 > ui mousemode right "translate selected models"
    22409 
    22410 > view matrix models
    22411 > #3,0.022255,-0.099641,-0.99477,369.16,0.88274,-0.46516,0.066341,83.998,-0.46934,-0.8796,0.077605,407.23
    22412 
    22413 > view matrix models
    22414 > #3,0.022255,-0.099641,-0.99477,368.06,0.88274,-0.46516,0.066341,83.639,-0.46934,-0.8796,0.077605,407.78
    22415 
    22416 > view matrix models
    22417 > #3,0.022255,-0.099641,-0.99477,369.91,0.88274,-0.46516,0.066341,85.463,-0.46934,-0.8796,0.077605,407.43
    22418 
    22419 > ~select #3
    22420 
    22421 Nothing selected 
    22422 
    22423 > show #6 models
    22424 
    22425 > mmaker #6 to #3
    22426 
    22427 Parameters 
    22428 --- 
    22429 Chain pairing | bb 
    22430 Alignment algorithm | Needleman-Wunsch 
    22431 Similarity matrix | BLOSUM-62 
    22432 SS fraction | 0.3 
    22433 Gap open (HH/SS/other) | 18/18/6 
    22434 Gap extend | 1 
    22435 SS matrix |  |  | H | S | O 
    22436 ---|---|---|--- 
    22437 H | 6 | -9 | -6 
    22438 S |  | 6 | -6 
    22439 O |  |  | 4 
    22440 Iteration cutoff | 2 
    22441  
    22442 Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
    22443 alignment score = 1871.9 
    22444 RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
    22445 0.023) 
    22446  
    22447 
    22448 > show #4 models
    22449 
    22450 > hide #4 models
    22451 
    22452 > show #4 models
    22453 
    22454 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J100_005_volume_map_sharp
    22455 (1).mrc (#11) using 3401 atoms 
    22456 average map value = 0.1004, steps = 64 
    22457 shifted from previous position = 1.84 
    22458 rotated from previous position = 3.05 degrees 
    22459 atoms outside contour = 1419, contour level = 0.05 
    22460  
    22461 Position of F562a.pdb (#4) relative to cryosparc_P35_J100_005_volume_map_sharp
    22462 (1).mrc (#11) coordinates: 
    22463 Matrix rotation and translation 
    22464 0.82616267 0.51307542 -0.23282799 17.45941536 
    22465 -0.12390784 -0.23766697 -0.96341127 357.00880636 
    22466 -0.54963816 0.82478363 -0.13277751 149.37621508 
    22467 Axis 0.92916660 0.16461820 -0.33098381 
    22468 Axis point 0.00000000 112.71394709 221.40097809 
    22469 Rotation angle (degrees) 105.79170262 
    22470 Shift along axis 25.55174348 
    22471  
    22472 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J100_005_volume_map_sharp
    22473 (1).mrc (#11) using 3401 atoms 
    22474 average map value = 0.1004, steps = 48 
    22475 shifted from previous position = 0.011 
    22476 rotated from previous position = 0.0276 degrees 
    22477 atoms outside contour = 1418, contour level = 0.05 
    22478  
    22479 Position of F562a.pdb (#4) relative to cryosparc_P35_J100_005_volume_map_sharp
    22480 (1).mrc (#11) coordinates: 
    22481 Matrix rotation and translation 
    22482 0.82596970 0.51342982 -0.23273140 17.41926576 
    22483 -0.12364669 -0.23778983 -0.96341451 356.97717269 
    22484 -0.54998689 0.82452765 -0.13292329 149.51361297 
    22485 Axis 0.92909832 0.16486078 -0.33105473 
    22486 Axis point 0.00000000 112.65571575 221.42366392 
    22487 Rotation angle (degrees) 105.80544612 
    22488 Shift along axis 25.53855668 
    22489  
    22490 
    22491 > hide #6 models
    22492 
    22493 > show #5 models
    22494 
    22495 Fit molecule F562b.pdb (#5) to map cryosparc_P35_J100_005_volume_map_sharp
    22496 (1).mrc (#11) using 3401 atoms 
    22497 average map value = 0.1083, steps = 76 
    22498 shifted from previous position = 0.951 
    22499 rotated from previous position = 3.36 degrees 
    22500 atoms outside contour = 1258, contour level = 0.05 
    22501  
    22502 Position of F562b.pdb (#5) relative to cryosparc_P35_J100_005_volume_map_sharp
    22503 (1).mrc (#11) coordinates: 
    22504 Matrix rotation and translation 
    22505 0.91100184 -0.19027699 -0.36588295 82.97740999 
    22506 -0.38499639 -0.71041595 -0.58914087 517.50161240 
    22507 -0.14782913 0.67757202 -0.72044619 248.76959820 
    22508 Axis 0.97438742 -0.16773248 -0.14978305 
    22509 Axis point 0.00000000 219.97208546 227.46670853 
    22510 Rotation angle (degrees) 139.45804049 
    22511 Shift along axis -43.21115606 
    22512  
    22513 
    22514 > color #3-5 bychain
    22515 
    22516 > hide #!11 models
    22517 
    22518 > save "C:/Users/dahailuo/OneDrive - Nanyang Technological
    22519 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-Fab56
    22520 > .cxs"
    22521 
    22522 > save "C:/Users/dahailuo/OneDrive - Nanyang Technological
    22523 > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-
    22524 > Fab5-DL.cxs" includeMaps true
    22525 
    22526 ——— End of log from Thu Mar 3 12:01:46 2022 ———
    22527 
    22528 opened ChimeraX session 
    22529 
    22530 > show #!2 models
    22531 
    22532 > hide #!2 models
    22533 
    22534 > show #!1 models
    22535 
    22536 > hide #!1 models
    22537 
    22538 > show #!2 models
    22539 
    22540 > hide #!2 models
    22541 
    22542 > show #!1 models
    22543 
    22544 > hide #!1 models
    22545 
    22546 > select #5
    22547 
    22548 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    22549 
    22550 > ~select #5
    22551 
    22552 Nothing selected 
    22553 
    22554 > select #4
    22555 
    22556 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    22557 
    22558 > ~select #4
    22559 
    22560 Nothing selected 
    22561 
    22562 > select #4
    22563 
    22564 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    22565 
    22566 > ~select #4
    22567 
    22568 Nothing selected 
    22569 
    22570 > select #4
    22571 
    22572 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    22573 
    22574 > ~select #4
    22575 
    22576 Nothing selected 
    22577 
    22578 > select #3
    22579 
    22580 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    22581 
    22582 > ~select #3
    22583 
    22584 Nothing selected 
    22585 
    22586 > select #3
    22587 
    22588 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    22589 
    22590 > ~select #3
    22591 
    22592 Nothing selected 
    22593 
    22594 > select #3
    22595 
    22596 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    22597 
    22598 > ~select #3
    22599 
    22600 Nothing selected 
    22601 
    22602 > show #!2 models
    22603 
    22604 > show #!1 models
    22605 
    22606 > hide #!1 models
    22607 
    22608 > hide #!2 models
    22609 
    22610 > show #6 models
    22611 
    22612 > hide #6 models
    22613 
    22614 > show #6 models
    22615 
    22616 > hide #6 models
    22617 
    22618 > show #7 models
    22619 
    22620 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    22621 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    22622 
    22623 > show #!1 models
    22624 
    22625 > hide #!1 models
    22626 
    22627 > show #!2 models
    22628 
    22629 > hide #!2 models
    22630 
    22631 > show #!2 models
    22632 
    22633 > hide #!2 models
    22634 
    22635 > show #!2 models
    22636 
    22637 > hide #!2 models
    22638 
    22639 > hide #3 models
    22640 
    22641 > hide #4 models
    22642 
    22643 > hide #5 models
    22644 
    22645 > show #6 models
    22646 
    22647 > hide #6 models
    22648 
    22649 > show #6 models
    22650 
    22651 > hide #6 models
    22652 
    22653 > show #!8 models
    22654 
    22655 > hide #!8 models
    22656 
    22657 > show #!8 models
    22658 
    22659 > show #9 models
    22660 
    22661 > hide #9 models
    22662 
    22663 > show #9 models
    22664 
    22665 > hide #7 models
    22666 
    22667 > hide #!8 models
    22668 
    22669 > hide #9 models
    22670 
    22671 > close #8
    22672 
    22673 > show #9 models
    22674 
    22675 > hide #9 models
    22676 
    22677 > show #7 models
    22678 
    22679 > show #9 models
    22680 
    22681 > hide #7 models
    22682 
    22683 > ui tool show "Show Sequence Viewer"
    22684 
    22685 > sequence chain #9/B
    22686 
    22687 Alignment identifier is 9/B 
    22688 
    22689 > sequence chain #9/C
    22690 
    22691 Alignment identifier is 9/C 
    22692 
    22693 > select #9/B:2-149,151-206
    22694 
    22695 1648 atoms, 1670 bonds, 204 residues, 1 model selected 
    22696 
    22697 > select #9/B:9
    22698 
    22699 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22700 
    22701 > select #9/B:9-11
    22702 
    22703 25 atoms, 24 bonds, 3 residues, 1 model selected 
    22704 
    22705 > select #9/B:2-149,151-206
    22706 
    22707 1648 atoms, 1670 bonds, 204 residues, 1 model selected 
    22708 
    22709 > select #9/B:1
    22710 
    22711 6 atoms, 5 bonds, 1 residue, 1 model selected 
    22712 
    22713 > select #9/B:1-207
    22714 
    22715 1667 atoms, 1690 bonds, 207 residues, 1 model selected 
    22716 
    22717 > select #9/B:64
    22718 
    22719 7 atoms, 7 bonds, 1 residue, 1 model selected 
    22720 
    22721 > select #9/B:64-86
    22722 
    22723 208 atoms, 215 bonds, 23 residues, 1 model selected 
    22724 
    22725 > select #9/B:64
    22726 
    22727 7 atoms, 7 bonds, 1 residue, 1 model selected 
    22728 
    22729 > select #9/B:64-85
    22730 
    22731 201 atoms, 207 bonds, 22 residues, 1 model selected 
    22732 /Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    22733 packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an
    22734 ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-
    22735 tuples-or ndarrays with different lengths or shapes) is deprecated. If you
    22736 meant to do this, you must specify 'dtype=object' when creating the ndarray 
    22737 return array(a, dtype, copy=False, order=order) 
    22738 
    22739 > select #9/B:2-149,151-206
    22740 
    22741 1648 atoms, 1670 bonds, 204 residues, 1 model selected 
    22742 
    22743 > select #9/B:64
    22744 
    22745 7 atoms, 7 bonds, 1 residue, 1 model selected 
    22746 
    22747 > select #9/B:64-85
    22748 
    22749 201 atoms, 207 bonds, 22 residues, 1 model selected 
    22750 
    22751 > color sel blue
    22752 
    22753 > color sel cornflower blue
    22754 
    22755 > select #9/B:151-152
    22756 
    22757 10 atoms, 9 bonds, 2 residues, 1 model selected 
    22758 
    22759 > select #9/B:151-172
    22760 
    22761 163 atoms, 164 bonds, 22 residues, 1 model selected 
    22762 
    22763 > color sel cornflower blue
    22764 
    22765 > show #!10 models
    22766 
    22767 > hide #!10 models
    22768 
    22769 > show #!10 models
    22770 
    22771 > hide #!10 models
    22772 
    22773 > show #!11 models
    22774 
    22775 > hide #!11 models
    22776 
    22777 > close #10
    22778 
    22779 > close #11
    22780 
    22781 > show #7 models
    22782 
    22783 > hide #7 models
    22784 
    22785 > show #6 models
    22786 
    22787 > hide #6 models
    22788 
    22789 > show #5 models
    22790 
    22791 > hide #5 models
    22792 
    22793 > show #!2 models
    22794 
    22795 > show #!1 models
    22796 
    22797 > hide #!1 models
    22798 
    22799 > show #3 models
    22800 
    22801 > show #4 models
    22802 
    22803 > show #5 models
    22804 
    22805 > hide #5 models
    22806 
    22807 > select #3
    22808 
    22809 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    22810 
    22811 > ~select #3
    22812 
    22813 Nothing selected 
    22814 
    22815 > hide #4 models
    22816 
    22817 > show #4 models
    22818 
    22819 > hide #4 models
    22820 
    22821 > select #9/C:2-149,151-206
    22822 
    22823 1648 atoms, 1670 bonds, 204 residues, 1 model selected 
    22824 
    22825 > select #9/C:64
    22826 
    22827 7 atoms, 7 bonds, 1 residue, 1 model selected 
    22828 
    22829 > select #9/C:64-85
    22830 
    22831 201 atoms, 207 bonds, 22 residues, 1 model selected 
    22832 
    22833 > color sel medium blue
    22834 
    22835 > select #9/C:151
    22836 
    22837 4 atoms, 3 bonds, 1 residue, 1 model selected 
    22838 
    22839 > select #9/C:151-172
    22840 
    22841 163 atoms, 164 bonds, 22 residues, 1 model selected 
    22842 
    22843 > color sel medium blue
    22844 
    22845 > close #7
    22846 
    22847 > show #6 models
    22848 
    22849 > hide #6 models
    22850 
    22851 > show #6 models
    22852 
    22853 > hide #6 models
    22854 
    22855 > show #6 models
    22856 
    22857 > hide #6 models
    22858 
    22859 > show #6 models
    22860 
    22861 > hide #6 models
    22862 
    22863 > close #6
    22864 
    22865 > show #4 models
    22866 
    22867 > open "/Users/alvinchew/OneDrive - Nanyang Technological
    22868 > University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J142_005_volume_map_sharp.mrc"
    22869 
    22870 Opened cryosparc_P47_J142_005_volume_map_sharp.mrc as #6, grid size
    22871 360,360,360, pixel 0.85, shown at level 0.0449, step 2, values float32 
    22872 
    22873 > volume #6 step 1
    22874 
    22875 > volume #6 level 0.1656
    22876 
    22877 > volume #6 level 0.06061
    22878 
    22879 > close #6
    22880 
    22881 > open "/Users/alvinchew/OneDrive - Nanyang Technological
    22882 > University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J128_002_volume_map_sharp.mrc"
    22883 
    22884 Opened cryosparc_P47_J128_002_volume_map_sharp.mrc as #6, grid size
    22885 360,360,360, pixel 0.85, shown at level 0.0566, step 2, values float32 
    22886 
    22887 > hide #!2 models
    22888 
    22889 > hide #3 models
    22890 
    22891 > hide #4 models
    22892 
    22893 > hide #!6 models
    22894 
    22895 > hide #9 models
    22896 
    22897 > show #9 models
    22898 
    22899 > hide #9 models
    22900 
    22901 > show #9 models
    22902 
    22903 > hide #9 models
    22904 
    22905 > select #9
    22906 
    22907 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    22908 
    22909 > ~select #9
    22910 
    22911 Nothing selected 
    22912 
    22913 > show #!6 models
    22914 
    22915 > volume #6 step 1
    22916 
    22917 > volume #6 level 0.116
    22918 
    22919 > open "/Users/alvinchew/OneDrive - Nanyang Technological
    22920 > University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J132_002_volume_map_sharp.mrc"
    22921 
    22922 Opened cryosparc_P47_J132_002_volume_map_sharp.mrc as #7, grid size
    22923 360,360,360, pixel 0.85, shown at level 0.0558, step 2, values float32 
    22924 
    22925 > volume #7 step 1
    22926 
    22927 > volume #7 level 0.189
    22928 
    22929 > volume #6 level 0.148
    22930 
    22931 > volume #6 level 0.1384
    22932 
    22933 > volume #7 level 0.08193
    22934 
    22935 > volume #7 level 0.04862
    22936 
    22937 > volume #6 level 0.06462
    22938 
    22939 > close #7
    22940 
    22941 > volume #6 level 0.1336
    22942 
    22943 > volume #6 level 0.1256
    22944 
    22945 > show #!2 models
    22946 
    22947 > hide #!2 models
    22948 
    22949 > show #!1 models
    22950 
    22951 > hide #!1 models
    22952 
    22953 > show #!2 models
    22954 
    22955 > select #6
    22956 
    22957 2 models selected 
    22958 
    22959 > view matrix models
    22960 > #6,-0.83996,0.011508,0.54253,184.02,0.50426,0.3859,0.77253,-105.68,-0.20047,0.92247,-0.32995,103.36
    22961 
    22962 > view matrix models
    22963 > #6,0.1848,-0.18014,0.96613,-8.4193,0.46665,-0.84908,-0.24758,260.82,0.86492,0.4966,-0.072852,-31.125
    22964 
    22965 > view matrix models
    22966 > #6,0.25195,-0.19005,0.94889,-14.067,0.4832,-0.82485,-0.29351,262.08,0.83847,0.53245,-0.11599,-25.726
    22967 
    22968 > view matrix models
    22969 > #6,-0.035938,-0.13733,0.98987,13.939,0.38333,-0.91664,-0.11325,261.83,0.92291,0.37538,0.085583,-46.756
    22970 
    22971 > view matrix models
    22972 > #6,0.1558,-0.53982,0.82724,75.077,-0.30263,-0.82328,-0.48024,409.8,0.94029,-0.17552,-0.29163,98.871
    22973 
    22974 > ui mousemode right "translate selected models"
    22975 
    22976 > view matrix models
    22977 > #6,0.1558,-0.53982,0.82724,121.85,-0.30263,-0.82328,-0.48024,428.76,0.94029,-0.17552,-0.29163,116.7
    22978 
    22979 > view matrix models
    22980 > #6,0.1558,-0.53982,0.82724,122.7,-0.30263,-0.82328,-0.48024,438.5,0.94029,-0.17552,-0.29163,113.43
    22981 
    22982 > view matrix models
    22983 > #6,0.1558,-0.53982,0.82724,123.68,-0.30263,-0.82328,-0.48024,449.46,0.94029,-0.17552,-0.29163,118.59
    22984 
    22985 > ui mousemode right "rotate selected models"
    22986 
    22987 > view matrix models
    22988 > #6,0.15847,-0.55227,0.81847,126.67,-0.30396,-0.81597,-0.49173,450.39,0.93941,-0.17086,-0.29717,118.9
    22989 
    22990 > view matrix models
    22991 > #6,0.31733,-0.49565,0.80848,95.704,-0.41983,-0.83787,-0.34888,447.71,0.85032,-0.22872,-0.47397,170.26
    22992 
    22993 > ui mousemode right "translate selected models"
    22994 
    22995 > view matrix models
    22996 > #6,0.31733,-0.49565,0.80848,94.921,-0.41983,-0.83787,-0.34888,440.31,0.85032,-0.22872,-0.47397,180.5
    22997 
    22998 > view matrix models
    22999 > #6,0.31733,-0.49565,0.80848,96.096,-0.41983,-0.83787,-0.34888,439.7,0.85032,-0.22872,-0.47397,180.02
    23000 
    23001 > view matrix models
    23002 > #6,0.31733,-0.49565,0.80848,94.946,-0.41983,-0.83787,-0.34888,439.56,0.85032,-0.22872,-0.47397,179.06
    23003 
    23004 > view matrix models
    23005 > #6,0.31733,-0.49565,0.80848,94.851,-0.41983,-0.83787,-0.34888,439.42,0.85032,-0.22872,-0.47397,178.96
    23006 
    23007 > ui mousemode right "rotate selected models"
    23008 
    23009 > view matrix models
    23010 > #6,0.32806,-0.48111,0.81296,90.235,-0.37939,-0.85524,-0.35303,436.79,0.86512,-0.19262,-0.4631,169.31
    23011 
    23012 > view matrix models
    23013 > #6,0.36269,-0.41122,0.83627,70.284,-0.30986,-0.89953,-0.30795,425.95,0.87889,-0.14743,-0.45367,158.62
    23014 
    23015 > view matrix models
    23016 > #6,0.36637,-0.44198,0.8188,77.421,-0.35476,-0.87986,-0.31621,430.93,0.86019,-0.17462,-0.47915,169.85
    23017 
    23018 > view matrix models
    23019 > #6,0.36072,-0.39988,0.8426,67.762,-0.30034,-0.9051,-0.30097,424.26,0.88299,-0.1445,-0.44659,156.39
    23020 
    23021 > ui mousemode right "translate selected models"
    23022 
    23023 > view matrix models
    23024 > #6,0.36072,-0.39988,0.8426,67.7,-0.30034,-0.9051,-0.30097,421.64,0.88299,-0.1445,-0.44659,155.81
    23025 
    23026 > view matrix models
    23027 > #6,0.36072,-0.39988,0.8426,69.281,-0.30034,-0.9051,-0.30097,420.24,0.88299,-0.1445,-0.44659,157.09
    23028 
    23029 > view matrix models
    23030 > #6,0.36072,-0.39988,0.8426,69.528,-0.30034,-0.9051,-0.30097,421,0.88299,-0.1445,-0.44659,156.78
    23031 
    23032 > ui mousemode right "rotate selected models"
    23033 
    23034 > view matrix models
    23035 > #6,0.36427,-0.41429,0.83407,72.656,-0.28999,-0.90154,-0.32115,422.2,0.88499,-0.12489,-0.44854,153.73
    23036 
    23037 > view matrix models
    23038 > #6,0.35177,-0.40975,0.84164,72.569,-0.29057,-0.90249,-0.31793,421.91,0.88984,-0.13272,-0.43653,152.26
    23039 
    23040 > view matrix models
    23041 > #6,0.3599,-0.44231,0.82148,79.767,-0.28748,-0.89021,-0.35338,425.33,0.8876,-0.10898,-0.44754,150.68
    23042 
    23043 > view matrix models
    23044 > #6,0.37744,-0.43949,0.8151,77.749,-0.29539,-0.89136,-0.34382,425.13,0.87766,-0.11101,-0.46626,155.55
    23045 
    23046 > ui mousemode right "translate selected models"
    23047 
    23048 > view matrix models
    23049 > #6,0.37744,-0.43949,0.8151,76.75,-0.29539,-0.89136,-0.34382,424.99,0.87766,-0.11101,-0.46626,155.59
    23050 
    23051 > view matrix models
    23052 > #6,0.37744,-0.43949,0.8151,75.665,-0.29539,-0.89136,-0.34382,426.6,0.87766,-0.11101,-0.46626,156.42
    23053 
    23054 > view matrix models
    23055 > #6,0.37744,-0.43949,0.8151,77.299,-0.29539,-0.89136,-0.34382,425.99,0.87766,-0.11101,-0.46626,155.38
    23056 
    23057 > view matrix models
    23058 > #6,0.37744,-0.43949,0.8151,77.803,-0.29539,-0.89136,-0.34382,426.26,0.87766,-0.11101,-0.46626,155.31
    23059 
    23060 > ui mousemode right "rotate selected models"
    23061 
    23062 > view matrix models
    23063 > #6,0.3964,-0.4154,0.81873,70.6,-0.31009,-0.89996,-0.30647,423.68,0.86412,-0.13239,-0.48555,163.85
    23064 
    23065 > view matrix models
    23066 > #6,0.36188,-0.4339,0.82509,77.612,-0.3531,-0.88293,-0.30945,427.92,0.86276,-0.17936,-0.47273,169.32
    23067 
    23068 > view matrix models
    23069 > #6,0.34333,-0.43629,0.83173,79.67,-0.33947,-0.88333,-0.32323,428.21,0.87572,-0.17137,-0.45138,162.63
    23070 
    23071 > view matrix models
    23072 > #6,0.36882,-0.43654,0.82061,77.724,-0.34143,-0.88476,-0.31721,427.74,0.86452,-0.16319,-0.47537,166.95
    23073 
    23074 > view matrix models
    23075 > #6,0.37369,-0.42634,0.82377,74.88,-0.33111,-0.89091,-0.31088,426.13,0.86644,-0.15658,-0.47409,165.42
    23076 
    23077 > ui mousemode right "translate selected models"
    23078 
    23079 > view matrix models
    23080 > #6,0.37369,-0.42634,0.82377,75.079,-0.33111,-0.89091,-0.31088,425.43,0.86644,-0.15658,-0.47409,165.61
    23081 
    23082 > view matrix models
    23083 > #6,0.37369,-0.42634,0.82377,74.521,-0.33111,-0.89091,-0.31088,425.67,0.86644,-0.15658,-0.47409,165.89
    23084 
    23085 > view matrix models
    23086 > #6,0.37369,-0.42634,0.82377,74.154,-0.33111,-0.89091,-0.31088,425.74,0.86644,-0.15658,-0.47409,166.14
    23087 
    23088 > view matrix models
    23089 > #6,0.37369,-0.42634,0.82377,74.447,-0.33111,-0.89091,-0.31088,425.75,0.86644,-0.15658,-0.47409,166.59
    23090 
    23091 > ui mousemode right "rotate selected models"
    23092 
    23093 > view matrix models
    23094 > #6,0.5154,-0.37111,0.77242,53.045,-0.24207,-0.9277,-0.2842,413.84,0.82205,-0.040509,-0.56797,170.41
    23095 
    23096 > view matrix models
    23097 > #6,0.49373,-0.37696,0.78367,55.354,-0.26058,-0.92389,-0.28024,415.36,0.82966,-0.065846,-0.55437,171.02
    23098 
    23099 > ui mousemode right "rotate selected models"
    23100 
    23101 > ui mousemode right select
    23102 
    23103 > ~select #6
    23104 
    23105 Nothing selected 
    23106 
    23107 > vop resample #6 onGrid #2
    23108 
    23109 Opened cryosparc_P47_J128_002_volume_map_sharp.mrc resampled as #7, grid size
    23110 352,352,352, pixel 0.85, shown at step 1, values float32 
    23111 
    23112 > close #6
    23113 
    23114 > ui tool show "Fit to Segments"
    23115 
    23116 > ui tool show "Fit in Map"
    23117 
    23118 > volume #7 level 0.09689
    23119 
    23120 Fit map cryosparc_P47_J128_002_volume_map_sharp.mrc resampled in map
    23121 cryosparc_P47_J20_004_volume_map_sharp.mrc using 175454 points 
    23122 correlation = 0.8828, correlation about mean = 0.547, overlap = 7225 
    23123 steps = 168, shift = 7.84, angle = 17 degrees 
    23124  
    23125 Position of cryosparc_P47_J128_002_volume_map_sharp.mrc resampled (#7)
    23126 relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    23127 Matrix rotation and translation 
    23128 0.95949380 0.09544158 -0.26507085 39.26017660 
    23129 -0.07373087 0.99314477 0.09070403 -7.34539260 
    23130 0.27191066 -0.06748605 0.95995324 -23.66014125 
    23131 Axis -0.27050228 -0.91822900 -0.28928192 
    23132 Axis point 103.77985456 0.00000000 135.28320696 
    23133 Rotation angle (degrees) 17.00173416 
    23134 Shift along axis 2.96923623 
    23135  
    23136 
    23137 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    23138 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    23139 
    23140 Traceback (most recent call last): 
    23141 File
    23142 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23143 packages/chimerax/core/session.py", line 281, in process 
    23144 data = sm.take_snapshot(obj, session, self.state_flags) 
    23145 File
    23146 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23147 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    23148 'region browser': self.region_browser.state(), 
    23149 File
    23150 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23151 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    23152 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23153 File
    23154 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23155 packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp> 
    23156 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23157 File
    23158 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23159 packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp> 
    23160 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23161 ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
    23162 is not in list 
    23163  
    23164 The above exception was the direct cause of the following exception: 
    23165  
    23166 Traceback (most recent call last): 
    23167 File
    23168 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23169 packages/chimerax/core/session.py", line 260, in discovery 
    23170 self.processed[key] = self.process(obj, parents) 
    23171 File
    23172 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23173 packages/chimerax/core/session.py", line 284, in process 
    23174 raise RuntimeError(msg) from e 
    23175 RuntimeError: Error while saving session data for 'tools' ->
    23176 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23177 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23178  
    23179 During handling of the above exception, another exception occurred: 
    23180  
    23181 Traceback (most recent call last): 
    23182 File
    23183 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23184 packages/chimerax/core/session.py", line 877, in save 
    23185 session.save(output, version=version, include_maps=include_maps) 
    23186 File
    23187 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23188 packages/chimerax/core/session.py", line 607, in save 
    23189 mgr.discovery(self._state_containers) 
    23190 File
    23191 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23192 packages/chimerax/core/session.py", line 262, in discovery 
    23193 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23194 ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
    23195 0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
    23196 0x7fda721771c0>: Error while saving session data for 'tools' ->
    23197 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23198 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23199  
    23200 ValueError: error processing: 'tools' -> -> : Error while saving session data
    23201 for 'tools' -> -> 
    23202  
    23203 File
    23204 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23205 packages/chimerax/core/session.py", line 262, in discovery 
    23206 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23207  
    23208 See log for complete Python traceback. 
    23209  
    23210 Traceback (most recent call last): 
    23211 File
    23212 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23213 packages/chimerax/core/session.py", line 281, in process 
    23214 data = sm.take_snapshot(obj, session, self.state_flags) 
    23215 File
    23216 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23217 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    23218 'region browser': self.region_browser.state(), 
    23219 File
    23220 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23221 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    23222 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23223 File
    23224 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23225 packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp> 
    23226 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23227 File
    23228 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23229 packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp> 
    23230 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23231 ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
    23232 is not in list 
    23233  
    23234 The above exception was the direct cause of the following exception: 
    23235  
    23236 Traceback (most recent call last): 
    23237 File
    23238 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23239 packages/chimerax/core/session.py", line 260, in discovery 
    23240 self.processed[key] = self.process(obj, parents) 
    23241 File
    23242 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23243 packages/chimerax/core/session.py", line 284, in process 
    23244 raise RuntimeError(msg) from e 
    23245 RuntimeError: Error while saving session data for 'tools' ->
    23246 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23247 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23248  
    23249 During handling of the above exception, another exception occurred: 
    23250  
    23251 Traceback (most recent call last): 
    23252 File
    23253 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23254 packages/chimerax/save_command/dialog.py", line 116, in <lambda> 
    23255 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    23256 file", 
    23257 File
    23258 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23259 packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog 
    23260 _dlg.display(session, **kw) 
    23261 File
    23262 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23263 packages/chimerax/save_command/dialog.py", line 51, in display 
    23264 run(session, cmd) 
    23265 File
    23266 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23267 packages/chimerax/core/commands/run.py", line 36, in run 
    23268 results = command.run(text, log=log, return_json=return_json) 
    23269 File
    23270 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23271 packages/chimerax/core/commands/cli.py", line 2852, in run 
    23272 result = ci.function(session, **kw_args) 
    23273 File
    23274 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23275 packages/chimerax/save_command/cmd.py", line 75, in cmd_save 
    23276 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    23277 File
    23278 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23279 packages/chimerax/core/commands/cli.py", line 2852, in run 
    23280 result = ci.function(session, **kw_args) 
    23281 File
    23282 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23283 packages/chimerax/save_command/cmd.py", line 87, in provider_save 
    23284 provider_info.bundle_info.run_provider(session, provider_info.format_name, 
    23285 File
    23286 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23287 packages/chimerax/core_formats/__init__.py", line 79, in save 
    23288 return cxs_save(session, path, **kw) 
    23289 File
    23290 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23291 packages/chimerax/core/session.py", line 877, in save 
    23292 session.save(output, version=version, include_maps=include_maps) 
    23293 File
    23294 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23295 packages/chimerax/core/session.py", line 607, in save 
    23296 mgr.discovery(self._state_containers) 
    23297 File
    23298 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23299 packages/chimerax/core/session.py", line 262, in discovery 
    23300 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23301 ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
    23302 0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
    23303 0x7fda721771c0>: Error while saving session data for 'tools' ->
    23304 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23305 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23306  
    23307 ValueError: error processing: 'tools' -> -> : Error while saving session data
    23308 for 'tools' -> -> 
    23309  
    23310 File
    23311 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23312 packages/chimerax/core/session.py", line 262, in discovery 
    23313 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23314  
    23315 See log for complete Python traceback. 
    23316  
    23317 
    23318 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    23319 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_ac.cxs"
    23320 
    23321 Traceback (most recent call last): 
    23322 File
    23323 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23324 packages/chimerax/core/session.py", line 281, in process 
    23325 data = sm.take_snapshot(obj, session, self.state_flags) 
    23326 File
    23327 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23328 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    23329 'region browser': self.region_browser.state(), 
    23330 File
    23331 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23332 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    23333 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23334 File
    23335 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23336 packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp> 
    23337 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23338 File
    23339 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23340 packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp> 
    23341 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23342 ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
    23343 is not in list 
    23344  
    23345 The above exception was the direct cause of the following exception: 
    23346  
    23347 Traceback (most recent call last): 
    23348 File
    23349 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23350 packages/chimerax/core/session.py", line 260, in discovery 
    23351 self.processed[key] = self.process(obj, parents) 
    23352 File
    23353 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23354 packages/chimerax/core/session.py", line 284, in process 
    23355 raise RuntimeError(msg) from e 
    23356 RuntimeError: Error while saving session data for 'tools' ->
    23357 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23358 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23359  
    23360 During handling of the above exception, another exception occurred: 
    23361  
    23362 Traceback (most recent call last): 
    23363 File
    23364 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23365 packages/chimerax/core/session.py", line 877, in save 
    23366 session.save(output, version=version, include_maps=include_maps) 
    23367 File
    23368 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23369 packages/chimerax/core/session.py", line 607, in save 
    23370 mgr.discovery(self._state_containers) 
    23371 File
    23372 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23373 packages/chimerax/core/session.py", line 262, in discovery 
    23374 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23375 ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
    23376 0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
    23377 0x7fda721771c0>: Error while saving session data for 'tools' ->
    23378 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23379 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23380  
    23381 ValueError: error processing: 'tools' -> -> : Error while saving session data
    23382 for 'tools' -> -> 
    23383  
    23384 File
    23385 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23386 packages/chimerax/core/session.py", line 262, in discovery 
    23387 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23388  
    23389 See log for complete Python traceback. 
    23390  
    23391 Traceback (most recent call last): 
    23392 File
    23393 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23394 packages/chimerax/core/session.py", line 281, in process 
    23395 data = sm.take_snapshot(obj, session, self.state_flags) 
    23396 File
    23397 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23398 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    23399 'region browser': self.region_browser.state(), 
    23400 File
    23401 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23402 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    23403 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23404 File
    23405 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23406 packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp> 
    23407 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23408 File
    23409 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23410 packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp> 
    23411 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23412 ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
    23413 is not in list 
    23414  
    23415 The above exception was the direct cause of the following exception: 
    23416  
    23417 Traceback (most recent call last): 
    23418 File
    23419 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23420 packages/chimerax/core/session.py", line 260, in discovery 
    23421 self.processed[key] = self.process(obj, parents) 
    23422 File
    23423 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23424 packages/chimerax/core/session.py", line 284, in process 
    23425 raise RuntimeError(msg) from e 
    23426 RuntimeError: Error while saving session data for 'tools' ->
    23427 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23428 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23429  
    23430 During handling of the above exception, another exception occurred: 
    23431  
    23432 Traceback (most recent call last): 
    23433 File
    23434 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23435 packages/chimerax/save_command/dialog.py", line 116, in <lambda> 
    23436 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    23437 file", 
    23438 File
    23439 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23440 packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog 
    23441 _dlg.display(session, **kw) 
    23442 File
    23443 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23444 packages/chimerax/save_command/dialog.py", line 51, in display 
    23445 run(session, cmd) 
    23446 File
    23447 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23448 packages/chimerax/core/commands/run.py", line 36, in run 
    23449 results = command.run(text, log=log, return_json=return_json) 
    23450 File
    23451 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23452 packages/chimerax/core/commands/cli.py", line 2852, in run 
    23453 result = ci.function(session, **kw_args) 
    23454 File
    23455 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23456 packages/chimerax/save_command/cmd.py", line 75, in cmd_save 
    23457 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    23458 File
    23459 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23460 packages/chimerax/core/commands/cli.py", line 2852, in run 
    23461 result = ci.function(session, **kw_args) 
    23462 File
    23463 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23464 packages/chimerax/save_command/cmd.py", line 87, in provider_save 
    23465 provider_info.bundle_info.run_provider(session, provider_info.format_name, 
    23466 File
    23467 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23468 packages/chimerax/core_formats/__init__.py", line 79, in save 
    23469 return cxs_save(session, path, **kw) 
    23470 File
    23471 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23472 packages/chimerax/core/session.py", line 877, in save 
    23473 session.save(output, version=version, include_maps=include_maps) 
    23474 File
    23475 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23476 packages/chimerax/core/session.py", line 607, in save 
    23477 mgr.discovery(self._state_containers) 
    23478 File
    23479 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23480 packages/chimerax/core/session.py", line 262, in discovery 
    23481 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23482 ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
    23483 0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
    23484 0x7fda721771c0>: Error while saving session data for 'tools' ->
    23485 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23486 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23487  
    23488 ValueError: error processing: 'tools' -> -> : Error while saving session data
    23489 for 'tools' -> -> 
    23490  
    23491 File
    23492 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23493 packages/chimerax/core/session.py", line 262, in discovery 
    23494 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23495  
    23496 See log for complete Python traceback. 
    23497  
    23498 
    23499 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    23500 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    23501 > includeMaps true
    23502 
    23503 Traceback (most recent call last): 
    23504 File
    23505 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23506 packages/chimerax/core/session.py", line 281, in process 
    23507 data = sm.take_snapshot(obj, session, self.state_flags) 
    23508 File
    23509 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23510 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    23511 'region browser': self.region_browser.state(), 
    23512 File
    23513 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23514 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    23515 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23516 File
    23517 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23518 packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp> 
    23519 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23520 File
    23521 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23522 packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp> 
    23523 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23524 ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
    23525 is not in list 
    23526  
    23527 The above exception was the direct cause of the following exception: 
    23528  
    23529 Traceback (most recent call last): 
    23530 File
    23531 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23532 packages/chimerax/core/session.py", line 260, in discovery 
    23533 self.processed[key] = self.process(obj, parents) 
    23534 File
    23535 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23536 packages/chimerax/core/session.py", line 284, in process 
    23537 raise RuntimeError(msg) from e 
    23538 RuntimeError: Error while saving session data for 'tools' ->
    23539 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23540 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23541  
    23542 During handling of the above exception, another exception occurred: 
    23543  
    23544 Traceback (most recent call last): 
    23545 File
    23546 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23547 packages/chimerax/core/session.py", line 877, in save 
    23548 session.save(output, version=version, include_maps=include_maps) 
    23549 File
    23550 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23551 packages/chimerax/core/session.py", line 607, in save 
    23552 mgr.discovery(self._state_containers) 
    23553 File
    23554 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23555 packages/chimerax/core/session.py", line 262, in discovery 
    23556 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23557 ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
    23558 0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
    23559 0x7fda721771c0>: Error while saving session data for 'tools' ->
    23560 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23561 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23562  
    23563 ValueError: error processing: 'tools' -> -> : Error while saving session data
    23564 for 'tools' -> -> 
    23565  
    23566 File
    23567 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23568 packages/chimerax/core/session.py", line 262, in discovery 
    23569 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23570  
    23571 See log for complete Python traceback. 
    23572  
    23573 Traceback (most recent call last): 
    23574 File
    23575 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23576 packages/chimerax/core/session.py", line 281, in process 
    23577 data = sm.take_snapshot(obj, session, self.state_flags) 
    23578 File
    23579 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23580 packages/chimerax/seq-view/tool.py", line 698, in take_snapshot 
    23581 'region browser': self.region_browser.state(), 
    23582 File
    23583 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23584 packages/chimerax/seq-view/region_browser.py", line 1106, in state 
    23585 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23586 File
    23587 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23588 packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp> 
    23589 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23590 File
    23591 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23592 packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp> 
    23593 state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ] 
    23594 ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
    23595 is not in list 
    23596  
    23597 The above exception was the direct cause of the following exception: 
    23598  
    23599 Traceback (most recent call last): 
    23600 File
    23601 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23602 packages/chimerax/core/session.py", line 260, in discovery 
    23603 self.processed[key] = self.process(obj, parents) 
    23604 File
    23605 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23606 packages/chimerax/core/session.py", line 284, in process 
    23607 raise RuntimeError(msg) from e 
    23608 RuntimeError: Error while saving session data for 'tools' ->
    23609 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23610 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23611  
    23612 During handling of the above exception, another exception occurred: 
    23613  
    23614 Traceback (most recent call last): 
    23615 File
    23616 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23617 packages/chimerax/save_command/dialog.py", line 116, in <lambda> 
    23618 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    23619 file", 
    23620 File
    23621 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23622 packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog 
    23623 _dlg.display(session, **kw) 
    23624 File
    23625 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23626 packages/chimerax/save_command/dialog.py", line 51, in display 
    23627 run(session, cmd) 
    23628 File
    23629 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23630 packages/chimerax/core/commands/run.py", line 36, in run 
    23631 results = command.run(text, log=log, return_json=return_json) 
    23632 File
    23633 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23634 packages/chimerax/core/commands/cli.py", line 2852, in run 
    23635 result = ci.function(session, **kw_args) 
    23636 File
    23637 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23638 packages/chimerax/save_command/cmd.py", line 75, in cmd_save 
    23639 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    23640 File
    23641 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23642 packages/chimerax/core/commands/cli.py", line 2852, in run 
    23643 result = ci.function(session, **kw_args) 
    23644 File
    23645 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23646 packages/chimerax/save_command/cmd.py", line 87, in provider_save 
    23647 provider_info.bundle_info.run_provider(session, provider_info.format_name, 
    23648 File
    23649 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23650 packages/chimerax/core_formats/__init__.py", line 79, in save 
    23651 return cxs_save(session, path, **kw) 
    23652 File
    23653 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23654 packages/chimerax/core/session.py", line 877, in save 
    23655 session.save(output, version=version, include_maps=include_maps) 
    23656 File
    23657 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23658 packages/chimerax/core/session.py", line 607, in save 
    23659 mgr.discovery(self._state_containers) 
    23660 File
    23661 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23662 packages/chimerax/core/session.py", line 262, in discovery 
    23663 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23664 ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
    23665 0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
    23666 0x7fda721771c0>: Error while saving session data for 'tools' ->
    23667 <chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
    23668 view.tool.SequenceViewer object at 0x7fda721771c0> 
    23669  
    23670 ValueError: error processing: 'tools' -> -> : Error while saving session data
    23671 for 'tools' -> -> 
    23672  
    23673 File
    23674 "/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    23675 packages/chimerax/core/session.py", line 262, in discovery 
    23676 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    23677  
    23678 See log for complete Python traceback. 
    23679  
    23680 
    23681 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    23682 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    23683 > includeMaps true
    23684 
    23685 ——— End of log from Thu Mar 3 19:50:19 2022 ———
    23686 
    23687 opened ChimeraX session 
    23688 
    23689 > show #9 models
    23690 
    23691 > hide #!7 models
    23692 
    23693 > show #3 models
    23694 
    23695 > show #!7 models
    23696 
    23697 > volume #7 level 0.1304
    23698 
    23699 > hide #9 models
    23700 
    23701 > hide #!2 models
    23702 
    23703 > select #7
    23704 
    23705 2 models selected 
    23706 
    23707 > select #3
    23708 
    23709 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    23710 
    23711 > ui mousemode right "rotate selected models"
    23712 
    23713 > view matrix models
    23714 > #3,0.047588,-0.1037,-0.99347,365.91,0.86244,-0.4975,0.093243,89.677,-0.50392,-0.86124,0.065763,412.54
    23715 
    23716 > view matrix models
    23717 > #3,0.06743,-0.16738,-0.98358,371.36,0.85706,-0.49497,0.14299,81.335,-0.51078,-0.85264,0.11008,404.4
    23718 
    23719 > view matrix models
    23720 > #3,0.096228,-0.19565,-0.97594,369.69,0.85361,-0.48807,0.18201,73.83,-0.51194,-0.85059,0.12005,402.49
    23721 
    23722 > view matrix models
    23723 > #3,0.12326,-0.1737,-0.97705,361.44,0.80994,-0.55129,0.20019,88.903,-0.57341,-0.81603,0.072729,415.92
    23724 
    23725 > view matrix models
    23726 > #3,0.16662,-0.22348,-0.96036,359.21,0.80001,-0.5387,0.26416,77.136,-0.57639,-0.81231,0.089027,412.91
    23727 
    23728 > view matrix models
    23729 > #3,0.16293,-0.22083,-0.96161,359.64,0.8006,-0.54002,0.25966,78.055,-0.57663,-0.81217,0.088811,412.97
    23730 
    23731 > ui mousemode right "translate selected models"
    23732 
    23733 > view matrix models
    23734 > #3,0.16293,-0.22083,-0.96161,359.93,0.8006,-0.54002,0.25966,80.609,-0.57663,-0.81217,0.088811,411.39
    23735 
    23736 > view matrix models
    23737 > #3,0.16293,-0.22083,-0.96161,360.07,0.8006,-0.54002,0.25966,81.287,-0.57663,-0.81217,0.088811,412.29
    23738 
    23739 > ui mousemode right "rotate selected models"
    23740 
    23741 > view matrix models
    23742 > #3,0.17153,-0.1861,-0.96744,353.75,0.81713,-0.52169,0.24523,77.868,-0.55034,-0.83259,0.062584,415.78
    23743 
    23744 > view matrix models
    23745 > #3,0.18128,-0.16143,-0.97009,348.36,0.82389,-0.51369,0.23944,76.368,-0.53698,-0.84265,0.03988,419.16
    23746 
    23747 > view matrix models
    23748 > #3,0.15753,-0.14621,-0.97663,351.15,0.82063,-0.53075,0.21182,84.727,-0.54931,-0.83482,0.03638,420.64
    23749 
    23750 > view matrix models
    23751 > #3,0.14559,-0.14302,-0.97895,353.12,0.82526,-0.52818,0.1999,85.606,-0.54566,-0.837,0.04113,419.52
    23752 
    23753 > view matrix models
    23754 > #3,0.10891,-0.20392,-0.97291,368.74,0.80086,-0.56179,0.20739,94.212,-0.58886,-0.80175,0.10213,410.32
    23755 
    23756 > view matrix models
    23757 > #3,7.5917e-05,-0.38124,-0.92448,409.06,0.76186,-0.5988,0.247,100.24,-0.64774,-0.70434,0.29041,370.76
    23758 
    23759 > view matrix models
    23760 > #3,0.020851,-0.42125,-0.9067,408.97,0.8145,-0.51877,0.25975,75.255,-0.57979,-0.74392,0.33229,358
    23761 
    23762 > view matrix models
    23763 > #3,0.0058992,-0.41587,-0.90941,411.17,0.80554,-0.53687,0.25074,81.477,-0.59251,-0.73405,0.33183,358.66
    23764 
    23765 > view matrix models
    23766 > #3,0.010117,-0.39918,-0.91682,408.95,0.78121,-0.56916,0.25643,90.171,-0.62418,-0.71883,0.30608,366.25
    23767 
    23768 > show #!2 models
    23769 
    23770 > show #4 models
    23771 
    23772 > hide #!2 models
    23773 
    23774 > hide #4 models
    23775 
    23776 > hide #!7 models
    23777 
    23778 > show #!2 models
    23779 
    23780 > volume #2 level 0.1739
    23781 
    23782 > volume #2 level 0.2952
    23783 
    23784 > ui tool show "Show Sequence Viewer"
    23785 
    23786 > sequence chain #9/B #9/C
    23787 
    23788 Alignment identifier is 1 
    23789 
    23790 > select #3/B:2,7,40,94,101,112-114,116,120,122,233
    23791 
    23792 96 atoms, 87 bonds, 12 residues, 1 model selected 
    23793 
    23794 > color sel red
    23795 
    23796 > color sel red
    23797 
    23798 > volume #2 level 0.275
    23799 
    23800 > volume #2 level 0.2628
    23801 
    23802 > show #!7 models
    23803 
    23804 > show #9 models
    23805 
    23806 > hide #!7 models
    23807 
    23808 > hide #!2 models
    23809 
    23810 > select #9
    23811 
    23812 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    23813 
    23814 > view matrix models
    23815 > #9,0.38721,-0.79412,0.46845,171.91,0.90831,0.41577,-0.04598,200.21,-0.15825,0.4433,0.88229,215.35
    23816 
    23817 > view matrix models
    23818 > #9,-0.087483,-0.4123,0.90684,172.91,0.99343,0.031343,0.11009,201.89,-0.073812,0.91051,0.40685,212.01
    23819 
    23820 > view matrix models
    23821 > #9,-0.28915,-0.67075,0.68299,173.05,0.95728,-0.20238,0.20652,203.01,-0.00030104,0.71353,0.70062,213.67
    23822 
    23823 > view matrix models
    23824 > #9,-0.26136,-0.69506,0.66977,173.04,0.95462,-0.083484,0.28588,202.96,-0.14278,0.71409,0.68534,213.75
    23825 
    23826 > view matrix models
    23827 > #9,-0.24903,-0.6779,0.69169,173.06,0.94836,-0.025801,0.31615,202.9,-0.19647,0.7347,0.64932,213.61
    23828 
    23829 > view matrix models
    23830 > #9,-0.29521,-0.62627,0.72155,173.07,0.95342,-0.14413,0.26498,203.06,-0.061948,0.76617,0.63965,213.33
    23831 
    23832 > view matrix models
    23833 > #9,-0.20952,-0.51342,0.83217,173.06,0.97542,-0.05031,0.21455,202.56,-0.068285,0.85666,0.51134,212.57
    23834 
    23835 > view matrix models
    23836 > #9,0.10294,-0.34459,0.93309,172.61,0.93996,0.34057,0.022073,200.66,-0.32539,0.8748,0.35896,212.2
    23837 
    23838 > view matrix models
    23839 > #9,-0.16022,-0.18462,0.96966,172.53,0.98145,0.074958,0.17644,202.03,-0.10526,0.97995,0.16919,210.92
    23840 
    23841 > show #!2 models
    23842 
    23843 > view matrix models
    23844 > #9,-0.15367,-0.25507,0.95464,172.68,0.9497,-0.30492,0.0714,202.82,0.27288,0.91759,0.28909,211.18
    23845 
    23846 > view matrix models
    23847 > #9,-0.5038,0.50581,0.70024,169.74,0.53017,-0.45894,0.71295,206.18,0.68199,0.73043,-0.036959,210.08
    23848 
    23849 > view matrix models
    23850 > #9,-0.57338,0.5803,0.57834,169.11,0.40927,-0.40864,0.81579,206.54,0.70974,0.70446,-0.0031917,210.27
    23851 
    23852 > ui mousemode right "move picked models"
    23853 
    23854 > view matrix models
    23855 > #9,-0.57338,0.5803,0.57834,169.15,0.40927,-0.40864,0.81579,203.59,0.70974,0.70446,-0.0031917,212
    23856 
    23857 > view matrix models
    23858 > #3,0.010117,-0.39918,-0.91682,409.31,0.78121,-0.56916,0.25643,90.718,-0.62418,-0.71883,0.30608,366.04
    23859 
    23860 > view matrix models
    23861 > #3,0.010117,-0.39918,-0.91682,409.6,0.78121,-0.56916,0.25643,90.515,-0.62418,-0.71883,0.30608,366.16
    23862 
    23863 > view matrix models
    23864 > #2,-0.25925,0.42088,0.86928,32.265,0.23342,0.90067,-0.36647,74.017,-0.93718,0.1079,-0.33174,370.87
    23865 
    23866 > ui mousemode right "translate selected models"
    23867 
    23868 > ui mousemode right "rotate selected models"
    23869 
    23870 > view matrix models
    23871 > #9,-0.61844,0.56215,0.54911,169.14,0.3784,-0.39939,0.83505,203.67,0.68873,0.72421,0.034284,212.11
    23872 
    23873 > ui mousemode right "translate selected models"
    23874 
    23875 > view matrix models
    23876 > #9,-0.61844,0.56215,0.54911,177.9,0.3784,-0.39939,0.83505,199.13,0.68873,0.72421,0.034284,214.65
    23877 
    23878 > view matrix models
    23879 > #9,-0.61844,0.56215,0.54911,178.4,0.3784,-0.39939,0.83505,196.45,0.68873,0.72421,0.034284,215.17
    23880 
    23881 > view matrix models
    23882 > #9,-0.61844,0.56215,0.54911,178.59,0.3784,-0.39939,0.83505,195.92,0.68873,0.72421,0.034284,215.89
    23883 
    23884 > ui tool show "Fit in Map"
    23885 
    23886 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    23887 (#2) using 5602 atoms 
    23888 average map value = 0.1891, steps = 236 
    23889 shifted from previous position = 3.82 
    23890 rotated from previous position = 35.5 degrees 
    23891 atoms outside contour = 3840, contour level = 0.26284 
    23892  
    23893 Position of D2NS1.pdb (#3) relative to
    23894 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    23895 Matrix rotation and translation 
    23896 0.97831960 0.09903901 0.18188469 -62.54218727 
    23897 0.12885075 -0.97864261 -0.16017526 308.84298175 
    23898 0.16213651 0.18013858 -0.97018650 260.99607581 
    23899 Axis 0.99452465 0.05771160 0.08712110 
    23900 Axis point 0.00000000 144.84592078 146.67317576 
    23901 Rotation angle (degrees) 170.14858369 
    23902 Shift along axis -21.63765850 
    23903  
    23904 
    23905 > view matrix models
    23906 > #9,-0.61844,0.56215,0.54911,178.56,0.3784,-0.39939,0.83505,195.48,0.68873,0.72421,0.034284,215.15
    23907 
    23908 > ui mousemode right "rotate selected models"
    23909 
    23910 > view matrix models
    23911 > #9,-0.6283,0.53153,0.56808,178.73,0.62001,-0.098962,0.77833,194.1,0.46993,0.84124,-0.26738,213.86
    23912 
    23913 > view matrix models
    23914 > #9,-0.75088,0.39219,0.53138,179.14,0.55722,-0.055683,0.82849,194.22,0.35452,0.9182,-0.17673,214.09
    23915 
    23916 > view matrix models
    23917 > #9,-0.71529,0.36967,0.59305,179.41,0.62601,-0.03822,0.77888,193.91,0.31059,0.92838,-0.20408,214
    23918 
    23919 > ui mousemode right "translate selected models"
    23920 
    23921 > view matrix models
    23922 > #9,-0.71529,0.36967,0.59305,179.34,0.62601,-0.03822,0.77888,198.53,0.31059,0.92838,-0.20408,211.04
    23923 
    23924 > view matrix models
    23925 > #9,-0.71529,0.36967,0.59305,179.34,0.62601,-0.03822,0.77888,198.99,0.31059,0.92838,-0.20408,210.24
    23926 
    23927 > ui mousemode right "rotate selected models"
    23928 
    23929 > view matrix models
    23930 > #9,-0.63893,0.03031,0.76867,180.97,0.76527,0.12677,0.63111,197.77,-0.078317,0.99147,-0.10419,210.83
    23931 
    23932 > select #3/C:2,7,40,94,101,112-114,116,120,122,233
    23933 
    23934 96 atoms, 87 bonds, 12 residues, 1 model selected 
    23935 
    23936 > color sel red
    23937 
    23938 > show #4 models
    23939 
    23940 Average map value = 0.2376 for 3401 atoms, 1878 outside contour 
    23941 Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    23942 (#2) using 3401 atoms 
    23943 average map value = 0.2415, steps = 72 
    23944 shifted from previous position = 1.54 
    23945 rotated from previous position = 3.06 degrees 
    23946 atoms outside contour = 1864, contour level = 0.26284 
    23947  
    23948 Position of F562a.pdb (#4) relative to
    23949 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    23950 Matrix rotation and translation 
    23951 0.23699392 -0.97040420 -0.04636322 286.30117001 
    23952 0.14025454 0.08139807 -0.98676390 234.10565599 
    23953 0.96133372 0.22735440 0.15539445 -33.95669350 
    23954 Axis 0.62922896 -0.52224902 0.57561001 
    23955 Axis point 0.00000000 269.86990420 6.31008896 
    23956 Rotation angle (degrees) 105.25448782 
    23957 Shift along axis 38.34172327 
    23958  
    23959 Fit map cryosparc_P47_J128_002_volume_map_sharp.mrc resampled in map
    23960 cryosparc_P47_J20_004_volume_map_sharp.mrc using 81674 points 
    23961 correlation = 0.9169, correlation about mean = 0.5151, overlap = 5213 
    23962 steps = 48, shift = 1.14, angle = 0.0547 degrees 
    23963  
    23964 Position of cryosparc_P47_J128_002_volume_map_sharp.mrc resampled (#7)
    23965 relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    23966 Matrix rotation and translation 
    23967 0.95972235 0.09553744 -0.26420752 39.07093414 
    23968 -0.07396939 0.99315174 0.09043310 -7.28703314 
    23969 0.27103791 -0.06724740 0.96021677 -23.53165945 
    23970 Axis -0.27038667 -0.91782581 -0.29066618 
    23971 Axis point 103.47778140 0.00000000 135.13797870 
    23972 Rotation angle (degrees) 16.95277212 
    23973 Shift along axis 2.96382485 
    23974  
    23975 
    23976 > close #7
    23977 
    23978 > volume #1 level 0.127
    23979 
    23980 > hide #!1 models
    23981 
    23982 > volume #2 level 0.2119
    23983 
    23984 > select #3
    23985 
    23986 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    23987 
    23988 > view matrix models
    23989 > #3,-0.067254,-0.26525,-0.96183,404.94,0.33444,-0.91423,0.22874,235.99,-0.94001,-0.30629,0.1502,378.5
    23990 
    23991 > view matrix models
    23992 > #3,-0.062041,-0.27434,-0.95963,405.16,0.30586,-0.92045,0.24337,239.46,-0.95005,-0.27841,0.14102,377.22
    23993 
    23994 > view matrix models
    23995 > #3,-0.080997,-0.27474,-0.9581,408.29,0.28653,-0.9271,0.24163,244.29,-0.95464,-0.25496,0.15382,371.8
    23996 
    23997 > view matrix models
    23998 > #3,-0.097933,-0.27408,-0.95671,410.91,0.27959,-0.93019,0.23786,246.7,-0.95511,-0.24419,0.16773,367.59
    23999 
    24000 > undo
    24001 
    24002 > view matrix models
    24003 > #3,-0.093936,-0.28928,-0.95262,412.03,0.28743,-0.92399,0.25224,241.72,-0.95318,-0.25012,0.16994,367.86
    24004 
    24005 > view matrix models
    24006 > #3,-0.099224,-0.30095,-0.94846,414.19,0.28616,-0.92153,0.26247,239.7,-0.95303,-0.24537,0.17756,365.67
    24007 
    24008 > select #9
    24009 
    24010 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    24011 
    24012 > ui mousemode right "translate selected models"
    24013 
    24014 > view matrix models
    24015 > #9,-0.63893,0.03031,0.76867,180.02,0.76527,0.12677,0.63111,198.98,-0.078317,0.99147,-0.10419,210.72
    24016 
    24017 > view matrix models
    24018 > #9,-0.63893,0.03031,0.76867,179.9,0.76527,0.12677,0.63111,199.21,-0.078317,0.99147,-0.10419,210.64
    24019 
    24020 > view matrix models
    24021 > #9,-0.63893,0.03031,0.76867,179.76,0.76527,0.12677,0.63111,199.9,-0.078317,0.99147,-0.10419,210.02
    24022 
    24023 > view matrix models
    24024 > #9,-0.63893,0.03031,0.76867,180,0.76527,0.12677,0.63111,200.37,-0.078317,0.99147,-0.10419,210.39
    24025 
    24026 > view matrix models
    24027 > #9,-0.63893,0.03031,0.76867,180.28,0.76527,0.12677,0.63111,200.62,-0.078317,0.99147,-0.10419,210.66
    24028 
    24029 > ui mousemode right "rotate selected models"
    24030 
    24031 > view matrix models
    24032 > #9,-0.6138,0.057604,0.78735,180.24,0.78755,0.11393,0.60562,200.54,-0.054817,0.99182,-0.1153,210.59
    24033 
    24034 > hide #!2 models
    24035 
    24036 > view matrix models
    24037 > #9,-0.57468,0.068825,0.81548,180.27,0.81757,0.092677,0.56833,200.43,-0.036461,0.99331,-0.10953,210.59
    24038 
    24039 > view matrix models
    24040 > #9,-0.55308,0.076775,0.82958,180.28,0.83069,0.12691,0.54207,200.21,-0.063663,0.98894,-0.13397,210.54
    24041 
    24042 > view matrix models
    24043 > #9,-0.59939,0.13134,0.78961,180.01,0.79964,0.14277,0.58326,200.35,-0.036127,0.981,-0.1906,210.32
    24044 
    24045 > view matrix models
    24046 > #9,-0.6287,0.16179,0.76063,179.83,0.77763,0.13788,0.61342,200.5,-0.0056352,0.97715,-0.2125,210.21
    24047 
    24048 > view matrix models
    24049 > #9,-0.66075,0.22875,0.7149,179.49,0.74952,0.14988,0.64479,200.62,0.040346,0.96188,-0.27049,209.99
    24050 
    24051 > view matrix models
    24052 > #9,-0.67709,0.24845,0.69269,179.36,0.73306,0.14512,0.6645,200.72,0.064571,0.95771,-0.28039,209.94
    24053 
    24054 > show #!2 models
    24055 
    24056 > show #!1 models
    24057 
    24058 > hide #!1 models
    24059 
    24060 > ~select #9
    24061 
    24062 Nothing selected 
    24063 
    24064 > volume #2 level 0.1883
    24065 
    24066 > ui mousemode right "translate selected models"
    24067 
    24068 > select #9
    24069 
    24070 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    24071 
    24072 > view matrix models
    24073 > #9,-0.67709,0.24845,0.69269,178.01,0.73306,0.14512,0.6645,202.1,0.064571,0.95771,-0.28039,210.69
    24074 
    24075 > view matrix models
    24076 > #9,-0.67709,0.24845,0.69269,178.34,0.73306,0.14512,0.6645,203.46,0.064571,0.95771,-0.28039,208.74
    24077 
    24078 > ~select #9
    24079 
    24080 Nothing selected 
    24081 
    24082 > hide #!2 models
    24083 
    24084 > show #!2 models
    24085 
    24086 Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
    24087 map cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 3334 atoms 
    24088 average map value = 0.1762, steps = 284 
    24089 shifted from previous position = 2.13 
    24090 rotated from previous position = 46.6 degrees 
    24091 atoms outside contour = 1895, contour level = 0.18834 
    24092  
    24093 Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
    24094 relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    24095 Matrix rotation and translation 
    24096 0.67425254 -0.64675933 -0.35649092 139.61136773 
    24097 0.63282394 0.25716285 0.73034312 159.63361093 
    24098 -0.38068004 -0.71803171 0.58267751 133.55311546 
    24099 Axis -0.74936689 0.01251508 0.66203673 
    24100 Axis point 0.00000000 205.05562824 -10.25332907 
    24101 Rotation angle (degrees) 75.10511823 
    24102 Shift along axis -14.20524073 
    24103  
    24104 
    24105 > undo
    24106 
    24107 > undo
    24108 
    24109 > undo
    24110 
    24111 > ~select #9
    24112 
    24113 Nothing selected 
    24114 
    24115 > volume #2 level 0.2324
    24116 
    24117 Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
    24118 map cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 3334 atoms 
    24119 average map value = 0.1762, steps = 284 
    24120 shifted from previous position = 2.13 
    24121 rotated from previous position = 46.6 degrees 
    24122 atoms outside contour = 2433, contour level = 0.23244 
    24123  
    24124 Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
    24125 relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    24126 Matrix rotation and translation 
    24127 0.67425254 -0.64675933 -0.35649092 139.61136773 
    24128 0.63282394 0.25716285 0.73034312 159.63361093 
    24129 -0.38068004 -0.71803171 0.58267751 133.55311546 
    24130 Axis -0.74936689 0.01251508 0.66203673 
    24131 Axis point 0.00000000 205.05562824 -10.25332907 
    24132 Rotation angle (degrees) 75.10511823 
    24133 Shift along axis -14.20524073 
    24134  
    24135 
    24136 > ui mousemode right "rotate selected models"
    24137 
    24138 > select #9
    24139 
    24140 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    24141 
    24142 > view matrix models
    24143 > #9,-0.51095,-0.017684,0.85943,178.44,0.84026,0.20068,0.50368,202.45,-0.18138,0.9795,-0.087678,211.18
    24144 
    24145 > view matrix models
    24146 > #9,-0.56127,0.054587,0.82583,178.14,0.82479,0.1196,0.55265,202.9,-0.068599,0.99132,-0.11215,210.93
    24147 
    24148 > hide #!2 models
    24149 
    24150 > show #!2 models
    24151 
    24152 > volume #2 level 0.1785
    24153 
    24154 > hide #!2 models
    24155 
    24156 > view matrix models
    24157 > #9,-0.55438,-0.0074968,0.83223,178.35,0.81959,0.16891,0.54748,202.74,-0.14467,0.9856,-0.087495,211.12
    24158 
    24159 > show #!2 models
    24160 
    24161 > hide #!2 models
    24162 
    24163 > view matrix models
    24164 > #9,-0.6081,0.00065434,0.79386,178.23,0.7807,0.18184,0.59786,202.93,-0.14397,0.98333,-0.11109,211.04
    24165 
    24166 > view matrix models
    24167 > #9,-0.60898,-0.00026107,0.79319,178.23,0.7797,0.18341,0.59869,202.93,-0.14563,0.98304,-0.11149,211.04
    24168 
    24169 > view matrix models
    24170 > #9,-0.56366,0.059523,0.82386,178.12,0.81918,0.1683,0.54829,202.74,-0.10602,0.98394,-0.14362,210.87
    24171 
    24172 > view matrix models
    24173 > #9,-0.61089,0.11381,0.78349,177.85,0.79055,0.14142,0.59585,203.04,-0.042985,0.98339,-0.17637,210.68
    24174 
    24175 > show #!2 models
    24176 
    24177 > volume #2 level 0.1908
    24178 
    24179 > view matrix models
    24180 > #9,-0.59527,0.088593,0.79863,177.97,0.80315,0.095932,0.588,203.13,-0.024521,0.99144,-0.12826,210.82
    24181 
    24182 > ui mousemode right "rotate selected models"
    24183 
    24184 > ui mousemode right "translate selected models"
    24185 
    24186 > view matrix models
    24187 > #9,-0.59527,0.088593,0.79863,180.49,0.80315,0.095932,0.588,202.55,-0.024521,0.99144,-0.12826,210.1
    24188 
    24189 > ui mousemode right "rotate selected models"
    24190 
    24191 > view matrix models
    24192 > #9,-0.54746,0.12014,0.82816,180.46,0.83671,0.062088,0.54411,202.45,0.013951,0.99081,-0.13451,210.04
    24193 
    24194 > view matrix models
    24195 > #9,-0.61653,0.1277,0.77691,180.31,0.78731,0.092096,0.60964,202.66,0.0063037,0.98753,-0.15732,209.97
    24196 
    24197 > view matrix models
    24198 > #9,-0.62782,0.073433,0.77489,180.48,0.77517,-0.030986,0.63099,203.13,0.070346,0.99682,-0.03747,210.34
    24199 
    24200 > view matrix models
    24201 > #9,-0.62087,0.053369,0.7821,180.56,0.78091,-0.045216,0.62301,203.14,0.068612,0.99755,-0.013603,210.43
    24202 
    24203 > view matrix models
    24204 > #9,-0.5736,-0.023782,0.81879,180.89,0.81885,0.0096521,0.57392,202.74,-0.021552,0.99967,0.013938,210.62
    24205 
    24206 > ui mousemode right "translate selected models"
    24207 
    24208 > view matrix models
    24209 > #9,-0.5736,-0.023782,0.81879,180.02,0.81885,0.0096521,0.57392,202.98,-0.021552,0.99967,0.013938,210.7
    24210 
    24211 > ui mousemode right "rotate selected models"
    24212 
    24213 > view matrix models
    24214 > #9,-0.57847,0.031132,0.81511,179.85,0.81555,0.041881,0.57717,202.9,-0.01617,0.99864,-0.049616,210.46
    24215 
    24216 > view matrix models
    24217 > #9,-0.56603,-0.015391,0.82424,180.01,0.82431,0.0025727,0.56613,202.97,-0.010834,0.99988,0.011231,210.68
    24218 
    24219 > view matrix models
    24220 > #9,-0.71029,0.24008,0.6617,178.75,0.68817,0.039154,0.72449,203.6,0.14803,0.96996,-0.19303,209.83
    24221 
    24222 > view matrix models
    24223 > #9,-0.68393,0.22919,0.69261,178.88,0.71976,0.056987,0.69188,203.39,0.1191,0.97171,-0.20393,209.81
    24224 
    24225 > ui mousemode right "translate selected models"
    24226 
    24227 > view matrix models
    24228 > #9,-0.68393,0.22919,0.69261,177.76,0.71976,0.056987,0.69188,203.72,0.1191,0.97171,-0.20393,209.9
    24229 
    24230 > view matrix models
    24231 > #9,-0.68393,0.22919,0.69261,177.24,0.71976,0.056987,0.69188,203.81,0.1191,0.97171,-0.20393,210.17
    24232 
    24233 > view matrix models
    24234 > #9,-0.68393,0.22919,0.69261,176.83,0.71976,0.056987,0.69188,203.91,0.1191,0.97171,-0.20393,210.29
    24235 
    24236 > view matrix models
    24237 > #9,-0.68393,0.22919,0.69261,176.71,0.71976,0.056987,0.69188,203.93,0.1191,0.97171,-0.20393,210.32
    24238 
    24239 > view matrix models
    24240 > #9,-0.68393,0.22919,0.69261,177.17,0.71976,0.056987,0.69188,203.92,0.1191,0.97171,-0.20393,210.31
    24241 
    24242 > view matrix models
    24243 > #9,-0.68393,0.22919,0.69261,177.48,0.71976,0.056987,0.69188,203.79,0.1191,0.97171,-0.20393,210.28
    24244 
    24245 > view matrix models
    24246 > #9,-0.68393,0.22919,0.69261,177.92,0.71976,0.056987,0.69188,203.73,0.1191,0.97171,-0.20393,210.27
    24247 
    24248 > view matrix models
    24249 > #9,-0.68393,0.22919,0.69261,177.96,0.71976,0.056987,0.69188,203.75,0.1191,0.97171,-0.20393,210.29
    24250 
    24251 > view matrix models
    24252 > #9,-0.68393,0.22919,0.69261,177.7,0.71976,0.056987,0.69188,203.84,0.1191,0.97171,-0.20393,210.22
    24253 
    24254 > ui mousemode right "rotate selected models"
    24255 
    24256 > view matrix models
    24257 > #9,-0.64555,0.14914,0.74902,178.12,0.76365,0.11273,0.63571,203.41,0.010372,0.98237,-0.18667,210.37
    24258 
    24259 > ~select #9
    24260 
    24261 Nothing selected 
    24262 
    24263 > hide #!2 models
    24264 
    24265 > show #!2 models
    24266 
    24267 > select #9
    24268 
    24269 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    24270 
    24271 > view matrix models
    24272 > #9,-0.39517,0.13421,0.90875,178.52,0.91486,0.1468,0.37614,202.16,-0.082923,0.98002,-0.18079,210.49
    24273 
    24274 > ui mousemode right "translate selected models"
    24275 
    24276 > view matrix models
    24277 > #9,-0.39517,0.13421,0.90875,178.76,0.91486,0.1468,0.37614,202.52,-0.082923,0.98002,-0.18079,210.02
    24278 
    24279 > view matrix models
    24280 > #9,-0.39517,0.13421,0.90875,178.91,0.91486,0.1468,0.37614,202.6,-0.082923,0.98002,-0.18079,209.94
    24281 
    24282 > view matrix models
    24283 > #9,-0.39517,0.13421,0.90875,178.84,0.91486,0.1468,0.37614,202.6,-0.082923,0.98002,-0.18079,209.69
    24284 
    24285 > view matrix models
    24286 > #9,-0.39517,0.13421,0.90875,178.58,0.91486,0.1468,0.37614,202.13,-0.082923,0.98002,-0.18079,210.55
    24287 
    24288 > view matrix models
    24289 > #9,-0.39517,0.13421,0.90875,178.72,0.91486,0.1468,0.37614,203.01,-0.082923,0.98002,-0.18079,210.68
    24290 
    24291 > ui mousemode right "rotate selected models"
    24292 
    24293 > view matrix models
    24294 > #9,-0.44867,0.076406,0.89043,178.88,0.88471,0.17889,0.43044,203.15,-0.1264,0.9809,-0.14786,210.85
    24295 
    24296 > ~select #9
    24297 
    24298 Nothing selected 
    24299 
    24300 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    24301 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    24302 
    24303 ——— End of log from Thu Mar 3 21:24:07 2022 ———
    24304 
    24305 opened ChimeraX session 
    24306 
    24307 > ui tool show ViewDockX
    24308 
    24309 No suitable models found for ViewDockX 
    24310 
    24311 > ui tool show "Show Sequence Viewer"
    24312 
    24313 > sequence chain #3/B #3/C
    24314 
    24315 Alignment identifier is 1 
    24316 
    24317 > select #3/B-C:1
    24318 
    24319 16 atoms, 14 bonds, 2 residues, 1 model selected 
    24320 
    24321 > select #3/B-C:1-36
    24322 
    24323 582 atoms, 598 bonds, 72 residues, 1 model selected 
    24324 
    24325 > hide #!2 models
    24326 
    24327 > hide #9 models
    24328 
    24329 > select #3/B-C:1
    24330 
    24331 16 atoms, 14 bonds, 2 residues, 1 model selected 
    24332 
    24333 > select #3/B-C:1-31
    24334 
    24335 486 atoms, 496 bonds, 62 residues, 1 model selected 
    24336 
    24337 > select #3/B-C:1-2
    24338 
    24339 28 atoms, 26 bonds, 4 residues, 1 model selected 
    24340 
    24341 > select #3/B-C:1-28
    24342 
    24343 436 atoms, 446 bonds, 56 residues, 1 model selected 
    24344 
    24345 > select #3/B-C:25
    24346 
    24347 14 atoms, 12 bonds, 2 residues, 1 model selected 
    24348 
    24349 > select #3/B-C:1-25
    24350 
    24351 374 atoms, 378 bonds, 50 residues, 1 model selected 
    24352 
    24353 > color sel orange
    24354 
    24355 > select #3/B-C:32-33
    24356 
    24357 42 atoms, 42 bonds, 4 residues, 1 model selected 
    24358 
    24359 > select #3/B-C:32-139
    24360 
    24361 1726 atoms, 1764 bonds, 216 residues, 1 model selected 
    24362 
    24363 > select #3/B-C:32
    24364 
    24365 24 atoms, 24 bonds, 2 residues, 1 model selected 
    24366 
    24367 > select #3/B-C:32-144
    24368 
    24369 1794 atoms, 1834 bonds, 226 residues, 1 model selected 
    24370 
    24371 > select #3/B-C:32
    24372 
    24373 24 atoms, 24 bonds, 2 residues, 1 model selected 
    24374 
    24375 > select #3/B-C:32-150
    24376 
    24377 1900 atoms, 1944 bonds, 238 residues, 1 model selected 
    24378 
    24379 > select #3/B-C:32
    24380 
    24381 24 atoms, 24 bonds, 2 residues, 1 model selected 
    24382 
    24383 > select #3/B-C:32-159
    24384 
    24385 2042 atoms, 2088 bonds, 256 residues, 1 model selected 
    24386 
    24387 > select #3/B-C:32
    24388 
    24389 24 atoms, 24 bonds, 2 residues, 1 model selected 
    24390 
    24391 > select #3/B-C:32-171
    24392 
    24393 2246 atoms, 2300 bonds, 280 residues, 1 model selected 
    24394 
    24395 > select #3/B-C:23
    24396 
    24397 16 atoms, 14 bonds, 2 residues, 1 model selected 
    24398 
    24399 > select #3/B-C:23-171
    24400 
    24401 2404 atoms, 2464 bonds, 298 residues, 1 model selected 
    24402 
    24403 > select #3/B-C:26
    24404 
    24405 20 atoms, 20 bonds, 2 residues, 1 model selected 
    24406 
    24407 > select #3/B-C:26-171
    24408 
    24409 2358 atoms, 2418 bonds, 292 residues, 1 model selected 
    24410 
    24411 > select #3/B-C:172
    24412 
    24413 18 atoms, 16 bonds, 2 residues, 1 model selected 
    24414 
    24415 > select #3/B-C:26-172
    24416 
    24417 2376 atoms, 2436 bonds, 294 residues, 1 model selected 
    24418 
    24419 > select #3/B-C:174
    24420 
    24421 22 atoms, 20 bonds, 2 residues, 1 model selected 
    24422 
    24423 > select #3/B-C:26-174
    24424 
    24425 2416 atoms, 2476 bonds, 298 residues, 1 model selected 
    24426 
    24427 > color sel medium blue
    24428 
    24429 > color sel blue
    24430 
    24431 > select #3
    24432 
    24433 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    24434 
    24435 > ~select #3
    24436 
    24437 Nothing selected 
    24438 
    24439 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    24440 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    24441 > includeMaps true
    24442 
    24443 > show #!1 models
    24444 
    24445 > show #!2 models
    24446 
    24447 > hide #!1 models
    24448 
    24449 > volume #2 level 0.2959
    24450 
    24451 > volume #2 level 0.3364
    24452 
    24453 > volume #2 level 0.1382
    24454 
    24455 > ui mousemode right "map eraser"
    24456 
    24457 > volume erase #2 center 237.19,212.38,256.03 radius 33.098
    24458 
    24459 > volume #2 level 0.1382
    24460 
    24461 > volume erase #2 center 169.45,251.87,161.34 radius 16.218
    24462 
    24463 > volume erase #2 center 169.29,250.35,162.17 radius 16.218
    24464 
    24465 > volume erase #2 center 178.55,248.01,162.61 radius 16.218
    24466 
    24467 > volume erase #2 center 193.98,241.53,160.53 radius 16.218
    24468 
    24469 > volume erase #2 center 199.47,236.96,159.26 radius 16.218
    24470 
    24471 > volume erase #2 center 162.44,240.05,168.47 radius 10.426
    24472 
    24473 > volume erase #2 center 192.43,185.48,150.8 radius 10.426
    24474 
    24475 > volume erase #2 center 222.56,163.1,224.04 radius 10.426
    24476 
    24477 > volume erase #2 center 210.8,157.36,204.71 radius 4.3027
    24478 
    24479 > volume erase #2 center 213.21,164.78,209.75 radius 4.3027
    24480 
    24481 > volume erase #2 center 213.74,163.67,210.79 radius 4.3027
    24482 
    24483 > volume erase #2 center 140.42,146.88,222.98 radius 7.2815
    24484 
    24485 > volume erase #2 center 143.97,147.47,221.25 radius 7.2815
    24486 
    24487 > volume erase #2 center 148.25,145.4,219.55 radius 7.2815
    24488 
    24489 > volume erase #2 center 152.8,142.67,217.68 radius 7.2815
    24490 
    24491 > volume erase #2 center 152.46,140.9,223.5 radius 7.2815
    24492 
    24493 > volume erase #2 center 139.51,151.13,215.18 radius 7.2815
    24494 
    24495 > volume erase #2 center 146.44,146.78,211.4 radius 7.2815
    24496 
    24497 > volume erase #2 center 152.32,144.56,208.69 radius 7.2815
    24498 
    24499 > volume erase #2 center 146.84,150.8,208.72 radius 7.2815
    24500 
    24501 > volume erase #2 center 152.17,153.98,201.44 radius 7.2815
    24502 
    24503 > hide #!2 models
    24504 
    24505 > show #!2 models
    24506 
    24507 > volume #2 level 0.3838
    24508 
    24509 > volume #2 level 0.2253
    24510 
    24511 > volume #2 level 0.0986
    24512 
    24513 > volume #2 level 0.01
    24514 
    24515 > volume #2 level 0.001
    24516 
    24517 > volume #2 level 0.1
    24518 
    24519 > volume #2 level 0.1475
    24520 
    24521 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    24522 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    24523 
    24524 > color #3-4 bypolymer
    24525 
    24526 > undo
    24527 
    24528 > lighting flat
    24529 
    24530 > lighting shadows true intensity 0.5
    24531 
    24532 > graphics silhouettes false
    24533 
    24534 > graphics silhouettes true
    24535 
    24536 > lighting shadows false
    24537 
    24538 > lighting shadows true
    24539 
    24540 > lighting shadows false
    24541 
    24542 > ui tool show "Fit in Map"
    24543 
    24544 > hide #3 models
    24545 
    24546 > show #3 models
    24547 
    24548 > show #5 models
    24549 
    24550 > hide #5 models
    24551 
    24552 > select #3
    24553 
    24554 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    24555 
    24556 > ui mousemode right "translate selected models"
    24557 
    24558 > view matrix models
    24559 > #3,-0.099224,-0.30095,-0.94846,413.97,0.28616,-0.92153,0.26247,239.58,-0.95303,-0.24537,0.17756,365.68
    24560 
    24561 > view matrix models
    24562 > #3,-0.099224,-0.30095,-0.94846,414.09,0.28616,-0.92153,0.26247,239.88,-0.95303,-0.24537,0.17756,365.5
    24563 
    24564 > view matrix models
    24565 > #3,-0.099224,-0.30095,-0.94846,414.1,0.28616,-0.92153,0.26247,239.98,-0.95303,-0.24537,0.17756,365.39
    24566 
    24567 > ui mousemode right "rotate selected models"
    24568 
    24569 > view matrix models
    24570 > #3,-0.098121,-0.30274,-0.94801,414.12,0.28638,-0.9209,0.26444,239.49,-0.95308,-0.24554,0.17706,365.52
    24571 
    24572 > view matrix models
    24573 > #3,-0.10399,-0.29321,-0.95038,413.98,0.28519,-0.92422,0.25393,242.13,-0.95281,-0.24463,0.17973,364.84
    24574 
    24575 > view matrix models
    24576 > #3,-0.10804,-0.25387,-0.96119,410,0.28731,-0.93356,0.21428,250.39,-0.95173,-0.25301,0.1738,367.12
    24577 
    24578 > view matrix models
    24579 > #3,-0.089326,-0.26965,-0.95881,408.94,0.27746,-0.93128,0.23606,247.86,-0.95658,-0.24494,0.15801,369.43
    24580 
    24581 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    24582 (#1) using 5602 atoms 
    24583 average map value = 0.07054, steps = 76 
    24584 shifted from previous position = 1.56 
    24585 rotated from previous position = 7.95 degrees 
    24586 atoms outside contour = 4416, contour level = 0.12697 
    24587  
    24588 Position of D2NS1.pdb (#3) relative to
    24589 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    24590 Matrix rotation and translation 
    24591 0.01853403 0.20523285 0.97853769 -30.97334856 
    24592 0.00646830 0.97866071 -0.20538117 45.38206352 
    24593 -0.99980733 0.01013602 0.01681102 356.85899567 
    24594 Axis 0.10776124 0.98919674 -0.09938471 
    24595 Axis point 163.99516504 0.00000000 196.80902229 
    24596 Rotation angle (degrees) 89.59876110 
    24597 Shift along axis 6.08773536 
    24598  
    24599 
    24600 > select #4
    24601 
    24602 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    24603 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    24604 (#1) using 3401 atoms 
    24605 average map value = 0.1044, steps = 92 
    24606 shifted from previous position = 1.81 
    24607 rotated from previous position = 8.09 degrees 
    24608 atoms outside contour = 2312, contour level = 0.12697 
    24609  
    24610 Position of F562a.pdb (#4) relative to
    24611 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    24612 Matrix rotation and translation 
    24613 -0.87188277 -0.47824853 0.10535086 355.37302112 
    24614 0.20869056 -0.16823549 0.96340288 57.21596158 
    24615 -0.44302225 0.86196009 0.24648757 74.93473678 
    24616 Axis -0.11464921 0.61976358 0.77636889 
    24617 Axis point 179.54922209 52.98960138 0.00000000 
    24618 Rotation angle (degrees) 153.74256446 
    24619 Shift along axis 52.89413028 
    24620  
    24621 
    24622 > view matrix models
    24623 > #4,0.86605,0.44369,-0.23043,24.081,-0.15116,-0.20695,-0.9666,357.32,-0.47656,0.87196,-0.11216,122.76
    24624 
    24625 > view matrix models
    24626 > #4,0.24178,-0.10097,-0.96506,327.04,0.9586,-0.12931,0.25369,-9.1181,-0.15041,-0.98645,0.065523,378.67
    24627 
    24628 > view matrix models
    24629 > #4,0.29714,-0.29814,-0.9071,345.67,0.95329,0.14663,0.26408,-59.546,0.054273,-0.94319,0.32778,301.43
    24630 
    24631 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    24632 (#1) using 3401 atoms 
    24633 average map value = 0.1127, steps = 320 
    24634 shifted from previous position = 4.37 
    24635 rotated from previous position = 11.4 degrees 
    24636 atoms outside contour = 2213, contour level = 0.12697 
    24637  
    24638 Position of F562a.pdb (#4) relative to
    24639 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    24640 Matrix rotation and translation 
    24641 -0.22359030 0.19234587 0.95551582 13.46864170 
    24642 -0.96386692 0.10200874 -0.24607887 369.19247060 
    24643 -0.14480322 -0.97601092 0.16258766 360.07001914 
    24644 Axis -0.41589505 0.62693129 -0.65877801 
    24645 Axis point 62.48187352 351.98959539 0.00000000 
    24646 Rotation angle (degrees) 118.65255170 
    24647 Shift along axis -11.34943811 
    24648  
    24649 
    24650 > hide #!2 models
    24651 
    24652 > show #!2 models
    24653 
    24654 > hide #!2 models
    24655 
    24656 > show #5 models
    24657 
    24658 > hide #5 models
    24659 
    24660 > show #!2 models
    24661 
    24662 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    24663 (#1) using 3401 atoms 
    24664 average map value = 0.1127, steps = 44 
    24665 shifted from previous position = 0.0117 
    24666 rotated from previous position = 0.0621 degrees 
    24667 atoms outside contour = 2215, contour level = 0.12697 
    24668  
    24669 Position of F562a.pdb (#4) relative to
    24670 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    24671 Matrix rotation and translation 
    24672 -0.22386136 0.19222999 0.95547567 13.54489824 
    24673 -0.96395914 0.10094242 -0.24615736 369.41500556 
    24674 -0.14376685 -0.97614461 0.16270474 359.89902128 
    24675 Axis -0.41608471 0.62655616 -0.65901510 
    24676 Axis point 62.46779097 351.82779571 0.00000000 
    24677 Rotation angle (degrees) 118.69239674 
    24678 Shift along axis -11.35546781 
    24679  
    24680 
    24681 > ui mousemode right "translate selected models"
    24682 
    24683 > view matrix models
    24684 > #4,0.25124,-0.17542,-0.9519,335.64,0.9404,0.27709,0.19714,-70.324,0.22917,-0.9447,0.23458,277.59
    24685 
    24686 > view matrix models
    24687 > #4,0.25124,-0.17542,-0.9519,335.72,0.9404,0.27709,0.19714,-70.489,0.22917,-0.9447,0.23458,277.37
    24688 
    24689 > view matrix models
    24690 > #4,0.25124,-0.17542,-0.9519,336.84,0.9404,0.27709,0.19714,-70.794,0.22917,-0.9447,0.23458,276.49
    24691 
    24692 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
    24693 (#1) using 3401 atoms 
    24694 average map value = 0.1127, steps = 60 
    24695 shifted from previous position = 2.03 
    24696 rotated from previous position = 0.0879 degrees 
    24697 atoms outside contour = 2217, contour level = 0.12697 
    24698  
    24699 Position of F562a.pdb (#4) relative to
    24700 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    24701 Matrix rotation and translation 
    24702 -0.22340595 0.19254318 0.95551920 13.40638758 
    24703 -0.96384599 0.10241826 -0.24599073 369.10197141 
    24704 -0.14522645 -0.97592912 0.16270112 360.10914844 
    24705 Axis -0.41580714 0.62703635 -0.65873351 
    24706 Axis point 62.50395161 352.02889088 0.00000000 
    24707 Rotation angle (degrees) 118.62946316 
    24708 Shift along axis -11.35008346 
    24709  
    24710 
    24711 > ui tool show "Show Sequence Viewer"
    24712 
    24713 > sequence chain #4/C
    24714 
    24715 Alignment identifier is 4/C 
    24716 
    24717 > ui tool show "Show Sequence Viewer"
    24718 
    24719 > sequence chain #4/B
    24720 
    24721 Alignment identifier is 4/B 
    24722 
    24723 > select #4/B:1
    24724 
    24725 5 atoms, 4 bonds, 1 residue, 1 model selected 
    24726 
    24727 > select #4/B:1-228
    24728 
    24729 1769 atoms, 1825 bonds, 228 residues, 1 model selected 
    24730 
    24731 > color sel forest green
    24732 
    24733 > hide #!2 models
    24734 
    24735 > ui tool show "Color Actions"
    24736 
    24737 > color sel forest green
    24738 
    24739 > color sel #e0fff2ff
    24740 
    24741 > color sel #defff1ff
    24742 
    24743 > color sel #c2ffcdff
    24744 
    24745 > color sel #79ff7dff
    24746 
    24747 > color sel #00ff05ff
    24748 
    24749 > color sel #00ff07ff
    24750 
    24751 > color sel #00ff09ff
    24752 
    24753 > color sel #00ff07ff
    24754 
    24755 [Repeated 1 time(s)]
    24756 
    24757 > color sel #00f707ff
    24758 
    24759 > color sel #00f507ff
    24760 
    24761 > color sel #00f407ff
    24762 
    24763 > color sel #00f307ff
    24764 
    24765 > color sel #00f107ff
    24766 
    24767 > color sel #00eb07ff
    24768 
    24769 > color sel #00e907ff
    24770 
    24771 > color sel #00e707ff
    24772 
    24773 > color sel #00e106ff
    24774 
    24775 > color sel #00dd06ff
    24776 
    24777 > color sel #00db06ff
    24778 
    24779 > color sel #00d906ff
    24780 
    24781 > color sel #00d806ff
    24782 
    24783 [Repeated 1 time(s)]
    24784 
    24785 > color sel #00d606ff
    24786 
    24787 > color sel #00d006ff
    24788 
    24789 > color sel #00c706ff
    24790 
    24791 > color sel #00c205ff
    24792 
    24793 > color sel #00b905ff
    24794 
    24795 > color sel #00b305ff
    24796 
    24797 > color sel #00ab05ff
    24798 
    24799 > color sel #00a605ff
    24800 
    24801 > color sel #009d04ff
    24802 
    24803 > color sel #009a04ff
    24804 
    24805 > color sel #009604ff
    24806 
    24807 > color sel #009404ff
    24808 
    24809 > color sel #009204ff
    24810 
    24811 > color sel #009104ff
    24812 
    24813 > color sel #008f04ff
    24814 
    24815 > color sel #008e04ff
    24816 
    24817 [Repeated 1 time(s)]
    24818 
    24819 > color sel #008d04ff
    24820 
    24821 > color sel #008a04ff
    24822 
    24823 [Repeated 1 time(s)]
    24824 
    24825 > color sel #008804ff
    24826 
    24827 > color sel #008704ff
    24828 
    24829 > color sel #008604ff
    24830 
    24831 > color sel #008504ff
    24832 
    24833 [Repeated 1 time(s)]
    24834 
    24835 > color sel #008304ff
    24836 
    24837 > color sel #008204ff
    24838 
    24839 > color sel #007f04ff
    24840 
    24841 > color sel #007903ff
    24842 
    24843 > color sel #007303ff
    24844 
    24845 > color sel #006f03ff
    24846 
    24847 > color sel #006e03ff
    24848 
    24849 > color sel #006d03ff
    24850 
    24851 > color sel #006c03ff
    24852 
    24853 > color sel #006803ff
    24854 
    24855 > color sel #005f03ff
    24856 
    24857 > color sel #005c03ff
    24858 
    24859 [Repeated 1 time(s)]
    24860 
    24861 > color sel #005d03ff
    24862 
    24863 > color sel #005e03ff
    24864 
    24865 [Repeated 1 time(s)]
    24866 
    24867 > color sel #005f03ff
    24868 
    24869 > color sel #006003ff
    24870 
    24871 [Repeated 2 time(s)]
    24872 
    24873 > color sel #006103ff
    24874 
    24875 [Repeated 2 time(s)]
    24876 
    24877 > color sel #006203ff
    24878 
    24879 [Repeated 3 time(s)]
    24880 
    24881 > color sel #006103ff
    24882 
    24883 [Repeated 2 time(s)]
    24884 
    24885 > color sel #006003ff
    24886 
    24887 [Repeated 1 time(s)]
    24888 
    24889 > color sel #005f03ff
    24890 
    24891 [Repeated 1 time(s)]
    24892 
    24893 > color sel #005e03ff
    24894 
    24895 [Repeated 1 time(s)]
    24896 
    24897 > color sel #005d03ff
    24898 
    24899 [Repeated 1 time(s)]
    24900 
    24901 > color sel #005b03ff
    24902 
    24903 [Repeated 1 time(s)]
    24904 
    24905 > color sel #005a03ff
    24906 
    24907 [Repeated 1 time(s)]
    24908 
    24909 > color sel #005c03ff
    24910 
    24911 > select #4
    24912 
    24913 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    24914 
    24915 > ~select #4
    24916 
    24917 Nothing selected 
    24918 
    24919 > show #!2 models
    24920 
    24921 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    24922 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    24923 > includeMaps true
    24924 
    24925 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    24926 > (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C1.png"
    24927 > width 854 height 684 supersample 3 transparentBackground true
    24928 
    24929 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    24930 > (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C2.png"
    24931 > width 1167 height 801 supersample 3
    24932 
    24933 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    24934 > (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C2.png"
    24935 > width 1167 height 801 supersample 3 transparentBackground true
    24936 
    24937 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    24938 > (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C3.png"
    24939 > width 1167 height 801 supersample 3 transparentBackground true
    24940 
    24941 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    24942 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    24943 > includeMaps true
    24944 
    24945 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    24946 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    24947 > sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J90_005_volume_map_sharp.mrc
    24948 
    24949 Opened cryosparc_P35_J90_005_volume_map_sharp.mrc as #6, grid size
    24950 416,416,416, pixel 0.858, shown at level 0.0366, step 2, values float32 
    24951 
    24952 > hide #4 models
    24953 
    24954 > hide #3 models
    24955 
    24956 > volume #6 step 1
    24957 
    24958 > volume #6 level 0.05781
    24959 
    24960 > lighting flat
    24961 
    24962 > lighting shadows true intensity 0.5
    24963 
    24964 > lighting shadows false
    24965 
    24966 > graphics silhouettes false
    24967 
    24968 > lighting simple
    24969 
    24970 > volume #6 level 0.08608
    24971 
    24972 > volume #6 level 0.1744
    24973 
    24974 > volume #6 level 0.07548
    24975 
    24976 > volume #6 level 0.06841
    24977 
    24978 > volume #6 level 0.08255
    24979 
    24980 > color #6 #bfb700 models transparency 0
    24981 
    24982 > color #6 #bfb70039 models
    24983 
    24984 > color #6 #bfb70028 models
    24985 
    24986 > color #6 #fff40028 models
    24987 
    24988 > color #6 #33300028 models
    24989 
    24990 > color #6 #b4ac0028 models
    24991 
    24992 > color #6 #b4ac00 models transparency 0
    24993 
    24994 > color #6 #fff400 models transparency 0
    24995 
    24996 > color #6 #f0e500 models transparency 0
    24997 
    24998 > color #6 #f0e65a models transparency 0
    24999 
    25000 > color #6 #c3bb49 models transparency 0
    25001 
    25002 > color #6 #c3bb499a models
    25003 
    25004 > color #6 #c3bb4941 models
    25005 
    25006 > color #6 #c3bb4942 models
    25007 
    25008 > color #6 #fffb00 models transparency 0
    25009 
    25010 > color #6 #fffb0044 models
    25011 
    25012 > color #6 #fffb0016 models
    25013 
    25014 > color #6 #fffb0033 models
    25015 
    25016 > color #6 #fffc79 models transparency 0
    25017 
    25018 > color #6 #fffc7932 models
    25019 
    25020 > color #6 #fffc7943 models
    25021 
    25022 > color #6 #fffc794c models
    25023 
    25024 > color #6 #fffc794d models
    25025 
    25026 > select #6
    25027 
    25028 2 models selected 
    25029 
    25030 > ui mousemode right "rotate selected models"
    25031 
    25032 > view matrix models
    25033 > #6,0.022009,-0.94973,0.31229,283.41,-0.71721,-0.23262,-0.65689,470,0.69651,-0.20952,-0.68628,231.36
    25034 
    25035 > view matrix models
    25036 > #6,0.48413,-0.86475,0.13353,218.33,-0.43491,-0.37024,-0.82084,473.48,0.75926,0.33932,-0.55533,99.971
    25037 
    25038 > view matrix models
    25039 > #6,-0.32751,-0.77901,0.53468,275.33,-0.92972,0.16487,-0.32929,377.53,0.16837,-0.60495,-0.77826,413.98
    25040 
    25041 > view matrix models
    25042 > #6,-0.2755,-0.92018,0.27814,339.29,-0.85315,0.10072,-0.51185,409.53,0.44298,-0.37831,-0.8128,331.15
    25043 
    25044 > view matrix models
    25045 > #6,0.69873,-0.70402,0.127,152.52,0.37445,0.20866,-0.90346,241.09,0.60956,0.67883,0.40942,-115.9
    25046 
    25047 > view matrix models
    25048 > #6,0.45295,-0.31947,0.83233,-3.9083,0.64601,-0.52579,-0.55337,251.33,0.61441,0.78834,-0.031778,-51.296
    25049 
    25050 > ui mousemode right "translate selected models"
    25051 
    25052 > view matrix models
    25053 > #6,0.45295,-0.31947,0.83233,16.369,0.64601,-0.52579,-0.55337,269.43,0.61441,0.78834,-0.031778,-42.833
    25054 
    25055 > view matrix models
    25056 > #6,0.45295,-0.31947,0.83233,16.57,0.64601,-0.52579,-0.55337,267.55,0.61441,0.78834,-0.031778,-43.336
    25057 
    25058 > view matrix models
    25059 > #6,0.45295,-0.31947,0.83233,17.018,0.64601,-0.52579,-0.55337,268.42,0.61441,0.78834,-0.031778,-43.438
    25060 
    25061 > view matrix models
    25062 > #6,0.45295,-0.31947,0.83233,13.457,0.64601,-0.52579,-0.55337,265.98,0.61441,0.78834,-0.031778,-43.237
    25063 
    25064 > view matrix models
    25065 > #6,0.45295,-0.31947,0.83233,13.708,0.64601,-0.52579,-0.55337,267.25,0.61441,0.78834,-0.031778,-43.377
    25066 
    25067 > view matrix models
    25068 > #6,0.45295,-0.31947,0.83233,13.833,0.64601,-0.52579,-0.55337,266.18,0.61441,0.78834,-0.031778,-42.937
    25069 
    25070 > view matrix models
    25071 > #6,0.45295,-0.31947,0.83233,14.199,0.64601,-0.52579,-0.55337,266.61,0.61441,0.78834,-0.031778,-44.947
    25072 
    25073 > volume #2 color #b8b5af4b
    25074 
    25075 > volume #2 color #b8b5af4d
    25076 
    25077 > show #3 models
    25078 
    25079 > hide #!2 models
    25080 
    25081 > volume #6 level 0.2239
    25082 
    25083 > ui mousemode right "rotate selected models"
    25084 
    25085 > view matrix models
    25086 > #6,-0.29246,-0.71165,0.63876,258.29,-0.85627,-0.10251,-0.50625,462.3,0.42576,-0.69501,-0.57939,354.66
    25087 
    25088 > view matrix models
    25089 > #6,-0.47549,-0.59046,0.65212,268.57,-0.79255,-0.034193,-0.60885,458.81,0.3818,-0.80634,-0.45171,357.01
    25090 
    25091 > view matrix models
    25092 > #6,-0.34414,-0.36794,0.86382,164.08,-0.77861,-0.40232,-0.48157,495.02,0.52473,-0.8383,-0.14803,276.41
    25093 
    25094 > ui mousemode right "translate selected models"
    25095 
    25096 > view matrix models
    25097 > #6,-0.34414,-0.36794,0.86382,151.79,-0.77861,-0.40232,-0.48157,494.89,0.52473,-0.8383,-0.14803,279.06
    25098 
    25099 > view matrix models
    25100 > #6,-0.34414,-0.36794,0.86382,151.48,-0.77861,-0.40232,-0.48157,494.87,0.52473,-0.8383,-0.14803,277.43
    25101 
    25102 > volume #6 level 0.1673
    25103 
    25104 > view matrix models
    25105 > #6,-0.34414,-0.36794,0.86382,149.97,-0.77861,-0.40232,-0.48157,494.85,0.52473,-0.8383,-0.14803,278.57
    25106 
    25107 > view matrix models
    25108 > #6,-0.34414,-0.36794,0.86382,150.29,-0.77861,-0.40232,-0.48157,492.94,0.52473,-0.8383,-0.14803,277.18
    25109 
    25110 > ui mousemode right "rotate selected models"
    25111 
    25112 > view matrix models
    25113 > #6,-0.34656,-0.40224,0.84741,159.86,-0.77344,-0.38862,-0.50077,493.34,0.53075,-0.82896,-0.17642,279.97
    25114 
    25115 > view matrix models
    25116 > #6,-0.31668,-0.43946,0.84059,162.15,-0.77551,-0.39032,-0.49622,493.13,0.54617,-0.80903,-0.2172,281.6
    25117 
    25118 > view matrix models
    25119 > #6,-0.32094,-0.45467,0.83083,167.46,-0.7722,-0.38228,-0.5075,493.32,0.54836,-0.80445,-0.22841,282.58
    25120 
    25121 > view matrix models
    25122 > #6,-0.20123,-0.51264,0.83469,154.78,0.96454,0.044877,0.2601,-48.467,-0.1708,0.85743,0.48543,-11.902
    25123 
    25124 > view matrix models
    25125 > #6,-0.19126,-0.46003,0.86706,137.55,0.78245,0.46189,0.41766,-117.87,-0.59262,0.75831,0.27161,124.2
    25126 
    25127 > view matrix models
    25128 > #6,-0.16309,-0.47088,0.86699,134.27,0.77568,0.48185,0.40761,-118.14,-0.6097,0.73898,0.28667,127.76
    25129 
    25130 > ui mousemode right "move picked models"
    25131 
    25132 > view matrix models
    25133 > #6,-0.16309,-0.47088,0.86699,134.42,0.77568,0.48185,0.40761,-149.14,-0.6097,0.73898,0.28667,101.11
    25134 
    25135 > view matrix models
    25136 > #3,0.001066,-0.23035,-0.97311,385.86,0.36811,-0.90469,0.21456,228.51,-0.92978,-0.35844,0.08383,403.03
    25137 
    25138 > ui mousemode right "rotate selected models"
    25139 
    25140 > view matrix models
    25141 > #6,-0.043523,-0.55853,0.82834,135.17,0.777,0.50225,0.37948,-147.46,-0.62799,0.66014,0.41212,93.77
    25142 
    25143 > view matrix models
    25144 > #6,-0.13478,-0.49296,0.85955,134.49,0.77638,0.48647,0.40073,-148.74,-0.61569,0.72134,0.31716,99.344
    25145 
    25146 > view matrix models
    25147 > #6,0.96181,-0.16288,-0.21999,85.595,0.2594,0.79899,0.54252,-135.51,0.087404,-0.57887,0.81072,99.737
    25148 
    25149 > show #4 models
    25150 
    25151 > view matrix models
    25152 > #6,0.67607,-0.69317,-0.24988,235.71,0.28695,0.56004,-0.77719,157.01,0.67866,0.45373,0.57753,-142.42
    25153 
    25154 > view matrix models
    25155 > #6,0.24716,-0.80723,0.536,181.65,0.88374,0.41465,0.21697,-120.33,-0.39739,0.42006,0.81586,14.664
    25156 
    25157 > view matrix models
    25158 > #6,-0.091274,-0.52365,0.84703,134.26,0.8991,0.32235,0.29617,-122.53,-0.42813,0.7886,0.44139,29.149
    25159 
    25160 > view matrix models
    25161 > #6,-0.11554,-0.4685,0.87587,123.56,0.69127,0.59529,0.40961,-153.69,-0.7133,0.65279,0.25508,141.19
    25162 
    25163 > view matrix models
    25164 > #6,-0.046411,-0.35281,0.93454,79.438,0.59316,0.74302,0.30997,-141.93,-0.80374,0.56872,0.17479,187.94
    25165 
    25166 > view matrix models
    25167 > #6,-0.069072,-0.35388,0.93274,84.134,0.6004,0.73194,0.32216,-143.71,-0.79671,0.58226,0.16191,186.8
    25168 
    25169 > view matrix models
    25170 > #6,-0.057044,-0.36632,0.92874,84.856,0.64945,0.69291,0.31319,-144.21,-0.75826,0.62103,0.19838,165.95
    25171 
    25172 > view matrix models
    25173 > #6,-0.079957,-0.35928,0.9298,87.636,0.65299,0.68589,0.32118,-145.19,-0.75313,0.63283,0.17976,166.58
    25174 
    25175 > view matrix models
    25176 > #6,-0.1341,-0.37541,0.91711,102.83,0.65851,0.65782,0.36557,-149.96,-0.74053,0.65295,0.159,164.81
    25177 
    25178 > view matrix models
    25179 > #6,-0.12427,-0.37199,0.91988,99.899,0.65174,0.66844,0.35836,-149.16,-0.74819,0.64406,0.15938,167.68
    25180 
    25181 > view matrix models
    25182 > #6,-0.11498,-0.39854,0.90992,104.73,0.64766,0.66446,0.37287,-150.54,-0.7532,0.63219,0.18172,166.32
    25183 
    25184 > view matrix models
    25185 > #6,0.0002274,-0.40749,0.91321,84.492,0.63579,0.70493,0.3144,-144.02,-0.77186,0.58054,0.25924,163.65
    25186 
    25187 > volume #6 level 0.1497
    25188 
    25189 > view matrix models
    25190 > #6,0.0046913,-0.41214,0.91111,84.898,0.66603,0.68091,0.30458,-143.4,-0.74591,0.60539,0.27769,151.16
    25191 
    25192 > view matrix models
    25193 > #6,-0.048323,-0.43445,0.8994,100.5,0.7189,0.61,0.33328,-146.09,-0.69343,0.66268,0.28285,130.85
    25194 
    25195 > view matrix models
    25196 > #6,-0.10978,-0.42931,0.89646,111.19,0.68648,0.6195,0.38074,-151.02,-0.71881,0.6572,0.22671,147.1
    25197 
    25198 > view matrix models
    25199 > #6,-0.12181,-0.41902,0.89977,110.93,0.69056,0.61537,0.38006,-150.91,-0.71294,0.66764,0.2144,146.6
    25200 
    25201 > ui mousemode right "translate selected models"
    25202 
    25203 > view matrix models
    25204 > #6,-0.12181,-0.41902,0.89977,108.89,0.69056,0.61537,0.38006,-148.49,-0.71294,0.66764,0.2144,143.63
    25205 
    25206 > view matrix models
    25207 > #6,-0.12181,-0.41902,0.89977,110.07,0.69056,0.61537,0.38006,-147.38,-0.71294,0.66764,0.2144,145.3
    25208 
    25209 > ui mousemode right "rotate selected models"
    25210 
    25211 > view matrix models
    25212 > #6,-0.59223,-0.7712,-0.2335,472.46,-0.072251,0.33944,-0.93785,289.57,0.80252,-0.53855,-0.25675,172.86
    25213 
    25214 > ui mousemode right "move picked models"
    25215 
    25216 > ui mousemode right "translate selected models"
    25217 
    25218 > view matrix models
    25219 > #6,-0.59223,-0.7712,-0.2335,487.54,-0.072251,0.33944,-0.93785,305.54,0.80252,-0.53855,-0.25675,191.57
    25220 
    25221 > view matrix models
    25222 > #6,-0.59223,-0.7712,-0.2335,493,-0.072251,0.33944,-0.93785,306.92,0.80252,-0.53855,-0.25675,188.04
    25223 
    25224 > view matrix models
    25225 > #6,-0.59223,-0.7712,-0.2335,502.5,-0.072251,0.33944,-0.93785,311.18,0.80252,-0.53855,-0.25675,188.67
    25226 
    25227 > view matrix models
    25228 > #6,-0.59223,-0.7712,-0.2335,499.52,-0.072251,0.33944,-0.93785,313.18,0.80252,-0.53855,-0.25675,187.29
    25229 
    25230 > ui mousemode right "rotate selected models"
    25231 
    25232 > view matrix models
    25233 > #6,-0.82421,-0.553,0.12194,435.21,-0.037209,-0.16199,-0.98609,402.96,0.56506,-0.81729,0.11294,207.26
    25234 
    25235 > view matrix models
    25236 > #6,-0.44543,-0.86122,0.24473,397.17,-0.26729,-0.13296,-0.9544,433.08,0.85449,-0.49053,-0.17097,153.23
    25237 
    25238 > view matrix models
    25239 > #6,-0.36539,-0.89648,0.25061,387.81,-0.30567,-0.13874,-0.94198,438.58,0.87924,-0.4208,-0.22333,146.76
    25240 
    25241 > volume #6 level 0.2451
    25242 
    25243 > view matrix models
    25244 > #6,-0.26247,-0.55243,0.79116,201.13,-0.8293,-0.29003,-0.47764,470,0.49332,-0.78148,-0.382,313.01
    25245 
    25246 > view matrix models
    25247 > #6,-0.28569,-0.52355,0.80267,198.17,-0.82429,-0.29297,-0.48448,470.94,0.48881,-0.80004,-0.34786,310.26
    25248 
    25249 > ui mousemode right "move picked models"
    25250 
    25251 > ui mousemode right "translate selected models"
    25252 
    25253 > view matrix models
    25254 > #6,-0.28569,-0.52355,0.80267,180.48,-0.82429,-0.29297,-0.48448,474.67,0.48881,-0.80004,-0.34786,307.45
    25255 
    25256 > volume #6 level 0.1673
    25257 
    25258 > view matrix models
    25259 > #6,-0.28569,-0.52355,0.80267,178.35,-0.82429,-0.29297,-0.48448,476.02,0.48881,-0.80004,-0.34786,306.81
    25260 
    25261 > ui mousemode right "rotate selected models"
    25262 
    25263 > view matrix models
    25264 > #6,-0.14718,-0.54954,0.8224,153.6,-0.85753,-0.34346,-0.38298,471.17,0.49292,-0.7616,-0.4207,313.54
    25265 
    25266 > view matrix models
    25267 > #6,-0.14519,-0.57785,0.80312,161.88,-0.8523,-0.33921,-0.39815,472.41,0.5025,-0.74231,-0.44325,312.81
    25268 
    25269 > view matrix models
    25270 > #6,-0.14171,-0.61705,0.77406,173.68,-0.84479,-0.3322,-0.41948,473.96,0.51599,-0.71336,-0.47421,311.33
    25271 
    25272 > view matrix models
    25273 > #6,-0.123,-0.64321,0.75574,178.33,-0.8848,-0.2738,-0.37704,462.95,0.44944,-0.71506,-0.53544,335.73
    25274 
    25275 > view matrix models
    25276 > #6,0.10222,-0.64957,0.7534,138.55,-0.86358,-0.43386,-0.2569,463.46,0.49374,-0.62436,-0.6053,325.44
    25277 
    25278 > view matrix models
    25279 > #6,0.10839,-0.64998,0.75218,137.72,-0.86646,-0.4327,-0.24905,462.27,0.48734,-0.62473,-0.61008,327.61
    25280 
    25281 > view matrix models
    25282 > #6,-0.17656,-0.48355,0.85733,140.78,-0.84554,-0.37137,-0.38359,473.92,0.50387,-0.79263,-0.34329,301.87
    25283 
    25284 > view matrix models
    25285 > #6,-0.23478,-0.43523,0.86917,140.8,-0.85004,-0.34178,-0.40076,472.95,0.47149,-0.83292,-0.28972,304.4
    25286 
    25287 > view matrix models
    25288 > #6,-0.22867,-0.43704,0.86989,139.85,-0.85367,-0.33948,-0.39497,472.09,0.46792,-0.83292,-0.29546,306.17
    25289 
    25290 > ui mousemode right "translate selected models"
    25291 
    25292 > view matrix models
    25293 > #6,-0.22867,-0.43704,0.86989,137.64,-0.85367,-0.33948,-0.39497,471.42,0.46792,-0.83292,-0.29546,310.38
    25294 
    25295 > view matrix models
    25296 > #6,-0.22867,-0.43704,0.86989,137.55,-0.85367,-0.33948,-0.39497,472.47,0.46792,-0.83292,-0.29546,308.95
    25297 
    25298 > ui mousemode right "rotate selected models"
    25299 
    25300 > view matrix models
    25301 > #6,-0.25766,-0.4215,0.86945,140.27,-0.85126,-0.32669,-0.41064,472.85,0.45712,-0.84594,-0.27463,309.15
    25302 
    25303 > view matrix models
    25304 > #6,-0.24131,-0.47116,0.8484,149.96,-0.84523,-0.32751,-0.42229,474.15,0.47682,-0.81899,-0.3192,309.52
    25305 
    25306 > view matrix models
    25307 > #6,-0.22049,-0.52796,0.82015,161.46,-0.83815,-0.32752,-0.43617,475.54,0.4989,-0.78357,-0.37029,309.25
    25308 
    25309 > view matrix models
    25310 > #6,-0.16435,-0.57156,0.80393,161.86,-0.87529,-0.29128,-0.38603,466.35,0.45481,-0.76712,-0.45241,330.43
    25311 
    25312 > view matrix models
    25313 > #6,-0.18555,-0.55494,0.81094,161.51,-0.86165,-0.30484,-0.40575,470.03,0.47237,-0.77403,-0.4216,322.42
    25314 
    25315 > view matrix models
    25316 > #6,-0.2448,-0.5224,0.8168,165.61,-0.85708,-0.27726,-0.4342,469.93,0.4533,-0.80636,-0.37987,323.42
    25317 
    25318 > view matrix models
    25319 > #6,-0.1668,-0.4734,0.86491,133.46,-0.84447,-0.38422,-0.37316,474.3,0.50897,-0.79263,-0.33568,302.25
    25320 
    25321 > ui mousemode right "translate selected models"
    25322 
    25323 > view matrix models
    25324 > #6,-0.1668,-0.4734,0.86491,132.36,-0.84447,-0.38422,-0.37316,474.18,0.50897,-0.79263,-0.33568,304.38
    25325 
    25326 > view matrix models
    25327 > #6,-0.1668,-0.4734,0.86491,132.99,-0.84447,-0.38422,-0.37316,474.25,0.50897,-0.79263,-0.33568,304.17
    25328 
    25329 > view matrix models
    25330 > #6,-0.1668,-0.4734,0.86491,133.6,-0.84447,-0.38422,-0.37316,474.33,0.50897,-0.79263,-0.33568,303.95
    25331 
    25332 > ui mousemode right "rotate selected models"
    25333 
    25334 > view matrix models
    25335 > #6,-0.32695,-0.44627,0.83303,164.48,-0.82463,-0.29585,-0.48214,476.54,0.46162,-0.84458,-0.27128,309.14
    25336 
    25337 > ui mousemode right "translate selected models"
    25338 
    25339 > view matrix models
    25340 > #6,-0.32695,-0.44627,0.83303,165.99,-0.82463,-0.29585,-0.48214,476.36,0.46162,-0.84458,-0.27128,308.97
    25341 
    25342 > view matrix models
    25343 > #6,-0.32695,-0.44627,0.83303,166.94,-0.82463,-0.29585,-0.48214,479.3,0.46162,-0.84458,-0.27128,310.62
    25344 
    25345 > view matrix models
    25346 > #6,-0.32695,-0.44627,0.83303,166.99,-0.82463,-0.29585,-0.48214,477.92,0.46162,-0.84458,-0.27128,311.73
    25347 
    25348 > view matrix models
    25349 > #6,-0.32695,-0.44627,0.83303,166.29,-0.82463,-0.29585,-0.48214,478.59,0.46162,-0.84458,-0.27128,310.92
    25350 
    25351 > volume #6 level 0.1249
    25352 
    25353 > view matrix models
    25354 > #6,-0.32695,-0.44627,0.83303,165.96,-0.82463,-0.29585,-0.48214,479.04,0.46162,-0.84458,-0.27128,311.24
    25355 
    25356 > show #!1 models
    25357 
    25358 > hide #3 models
    25359 
    25360 > hide #4 models
    25361 
    25362 > select #1
    25363 
    25364 2 models selected 
    25365 
    25366 > view matrix models
    25367 > #1,-0.99948,-0.025572,-0.01976,364.95,0.031105,-0.92707,-0.3736,414.45,-0.0087649,-0.37402,0.92738,76.793
    25368 
    25369 > ui mousemode right "rotate selected models"
    25370 
    25371 > view matrix models
    25372 > #1,-0.93251,0.32395,-0.15963,316.09,0.35214,0.71758,-0.6009,105.04,-0.080113,-0.61656,-0.78322,444.34
    25373 
    25374 > view matrix models
    25375 > #1,-0.92079,0.38867,0.032827,267.4,0.38993,0.91934,0.052624,-56.723,-0.009726,0.061257,-0.99807,349.94
    25376 
    25377 > view matrix models
    25378 > #1,-0.87777,0.3565,0.32005,213.16,0.3764,0.92646,0.00035867,-46.06,-0.29638,0.12078,-0.9474,381.24
    25379 
    25380 > view matrix models
    25381 > #1,-0.89237,0.44968,0.038176,250.47,0.16187,0.3979,-0.90304,251.08,-0.42127,-0.79967,-0.42786,473.18
    25382 
    25383 > ui mousemode right "translate selected models"
    25384 
    25385 > view matrix models
    25386 > #1,-0.89237,0.44968,0.038176,252.64,0.16187,0.3979,-0.90304,250.64,-0.42127,-0.79967,-0.42786,471.5
    25387 
    25388 > ui mousemode right "rotate selected models"
    25389 
    25390 > view matrix models
    25391 > #1,-0.91313,0.40742,0.014419,268.22,0.16668,0.40537,-0.89883,247.68,-0.37205,-0.81834,-0.43806,467.9
    25392 
    25393 > view matrix models
    25394 > #1,-0.86639,0.4978,-0.039456,253.56,0.25363,0.37062,-0.89348,237.39,-0.43015,-0.78411,-0.44736,473.86
    25395 
    25396 > ui mousemode right "translate selected models"
    25397 
    25398 > view matrix models
    25399 > #1,-0.86639,0.4978,-0.039456,247.82,0.25363,0.37062,-0.89348,237.47,-0.43015,-0.78411,-0.44736,473.22
    25400 
    25401 > ui mousemode right "rotate selected models"
    25402 
    25403 > view matrix models
    25404 > #1,-0.87597,0.47955,-0.052144,255.09,0.30604,0.46893,-0.82852,198.74,-0.37286,-0.74171,-0.55753,475.49
    25405 
    25406 > view matrix models
    25407 > #1,-0.88553,0.45898,0.071919,237.88,0.23094,0.5692,-0.7891,187.07,-0.40311,-0.68216,-0.61004,479.83
    25408 
    25409 > ui mousemode right "translate selected models"
    25410 
    25411 > view matrix models
    25412 > #1,-0.88553,0.45898,0.071919,232.83,0.23094,0.5692,-0.7891,186.52,-0.40311,-0.68216,-0.61004,479.89
    25413 
    25414 > ui mousemode right "rotate selected models"
    25415 
    25416 > view matrix models
    25417 > #1,-0.93268,0.36026,0.017859,268.7,0.20808,0.57784,-0.78918,189.07,-0.29463,-0.73234,-0.6139,470.19
    25418 
    25419 > view matrix models
    25420 > #1,-0.9521,0.2987,0.065475,274.48,0.12858,0.58532,-0.80054,204,-0.27744,-0.75378,-0.59569,467.63
    25421 
    25422 Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
    25423 cryosparc_P35_J90_005_volume_map_sharp.mrc using 125084 points 
    25424 correlation = 0.7737, correlation about mean = 0.5148, overlap = 4611 
    25425 steps = 324, shift = 10.7, angle = 12.5 degrees 
    25426  
    25427 Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
    25428 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    25429 Matrix rotation and translation 
    25430 -0.00018548 -0.96024693 0.27915190 304.64819825 
    25431 0.47329448 0.24582180 0.84591014 -90.95034872 
    25432 -0.88090425 0.13227795 0.45443398 232.87270604 
    25433 Axis -0.36089737 0.58666245 0.72496915 
    25434 Axis point 266.13823335 42.12806522 0.00000000 
    25435 Rotation angle (degrees) 98.62488972 
    25436 Shift along axis 5.52163959 
    25437  
    25438 
    25439 > show #!2 models
    25440 
    25441 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    25442 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
    25443 > NS1ts.cxs"
    25444 
    25445 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    25446 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
    25447 > NS1ts.cxs" includeMaps true
    25448 
    25449 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    25450 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    25451 > sNS1-Fab56-2/NS1ts-HDL/cryosparc_P35_J88_003_volume_map_sharp.mrc
    25452 
    25453 Opened cryosparc_P35_J88_003_volume_map_sharp.mrc as #7, grid size
    25454 416,416,416, pixel 0.858, shown at level 0.0322, step 2, values float32 
    25455 
    25456 > hide #!6 models
    25457 
    25458 > hide #!1 models
    25459 
    25460 > hide #!2 models
    25461 
    25462 > volume #7 level 0.08768
    25463 
    25464 > volume #7 level 0.03374
    25465 
    25466 > volume #7 level 0.01342
    25467 
    25468 > volume #7 level 0.05407
    25469 
    25470 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    25471 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    25472 > sNS1-Fab56-2/NS1ts-HDL/cryosparc_P35_J87_003_volume_map_sharp.mrc
    25473 
    25474 Opened cryosparc_P35_J87_003_volume_map_sharp.mrc as #8, grid size
    25475 416,416,416, pixel 0.858, shown at level 0.0329, step 2, values float32 
    25476 
    25477 > close #7
    25478 
    25479 > volume #8 level 0.07979
    25480 
    25481 > volume #8 level 0.05868
    25482 
    25483 > volume #8 level 0.0493
    25484 
    25485 > volume #8 color #b2ffff76
    25486 
    25487 > volume #8 color #b2ffff75
    25488 
    25489 > show #3 models
    25490 
    25491 > select #8
    25492 
    25493 2 models selected 
    25494 
    25495 > ui mousemode right "translate selected models"
    25496 
    25497 > view matrix models #8,1,0,0,-5.0701,0,1,0,25.403,0,0,1,13.725
    25498 
    25499 > view matrix models #8,1,0,0,-2.4128,0,1,0,22.261,0,0,1,17.693
    25500 
    25501 > view matrix models #8,1,0,0,13.637,0,1,0,15.538,0,0,1,17.629
    25502 
    25503 > view matrix models #8,1,0,0,17.759,0,1,0,21.107,0,0,1,15.457
    25504 
    25505 > ui mousemode right "rotate selected models"
    25506 
    25507 > view matrix models
    25508 > #8,0.9437,0.30533,-0.12727,-1.7134,-0.30648,0.95181,0.01092,77.369,0.12448,0.028702,0.99181,-8.2592
    25509 
    25510 > view matrix models
    25511 > #8,0.93379,0.13868,-0.32987,64.541,0.05145,0.86023,0.5073,-55.026,0.35412,-0.49068,0.79614,77.197
    25512 
    25513 > view matrix models
    25514 > #8,0.93056,0.16968,-0.32446,58.857,0.023869,0.85614,0.5162,-51.428,0.36537,-0.48809,0.79263,75.552
    25515 
    25516 > view matrix models
    25517 > #8,0.92836,0.172,-0.32949,59.73,0.0092364,0.87553,0.48308,-46.35,0.37157,-0.45151,0.81122,65.012
    25518 
    25519 > view matrix models
    25520 > #8,0.90406,0.053265,-0.42407,100.79,0.15019,0.88934,0.43188,-62.499,0.40015,-0.45413,0.79602,63.521
    25521 
    25522 > view matrix models
    25523 > #8,0.90236,0.062663,-0.42639,99.9,0.13798,0.8953,0.42357,-60.014,0.40829,-0.44104,0.79924,59.399
    25524 
    25525 > view matrix models
    25526 > #8,0.95884,0.13052,-0.25215,47.832,0.14193,0.54884,0.82379,-74.184,0.24591,-0.82568,0.50772,203.41
    25527 
    25528 > view matrix models
    25529 > #8,0.8439,0.43609,-0.31252,25.859,0.15414,0.36088,0.91979,-61.706,0.51389,-0.82438,0.23733,208.08
    25530 
    25531 > view matrix models
    25532 > #8,0.72071,0.42588,-0.547,89.933,0.3615,0.44239,0.82074,-91.531,0.59152,-0.78925,0.16489,202.5
    25533 
    25534 > view matrix models
    25535 > #8,0.88841,0.1882,-0.4187,79.584,0.16981,0.71266,0.68065,-80.646,0.42648,-0.6758,0.60117,131.75
    25536 
    25537 > view matrix models
    25538 > #8,0.81278,0.18222,-0.55333,117.19,0.28518,0.70377,0.65067,-92.602,0.50799,-0.68666,0.52005,134.87
    25539 
    25540 > ui mousemode right "translate selected models"
    25541 
    25542 > view matrix models
    25543 > #8,0.81278,0.18222,-0.55333,111.12,0.28518,0.70377,0.65067,-89.214,0.50799,-0.68666,0.52005,131.56
    25544 
    25545 > ui mousemode right "rotate selected models"
    25546 
    25547 > view matrix models
    25548 > #8,0.66641,0.31634,-0.67515,134.32,0.37078,0.645,0.6682,-96.429,0.64685,-0.69563,0.31254,147.74
    25549 
    25550 > view matrix models
    25551 > #8,0.64719,0.35366,-0.67533,131.19,0.38471,0.61328,0.68984,-97.242,0.65814,-0.70627,0.26085,157
    25552 
    25553 > view matrix models
    25554 > #8,0.58239,0.30728,-0.75259,163.52,0.46192,0.63672,0.61743,-100.78,0.66892,-0.70723,0.22888,161.16
    25555 
    25556 > view matrix models
    25557 > #8,0.7541,0.27199,-0.59778,113.55,0.30905,0.65618,0.68842,-91.868,0.5795,-0.70388,0.41077,142.46
    25558 
    25559 > view matrix models
    25560 > #8,0.61599,0.12295,-0.7781,193.77,0.49388,0.70924,0.50306,-97.665,0.61371,-0.69417,0.37616,141.46
    25561 
    25562 > view matrix models
    25563 > #8,0.73698,0.11525,-0.66601,155.12,0.40454,0.71417,0.57123,-96.173,0.54148,-0.69041,0.47971,133.98
    25564 
    25565 > ui mousemode right "translate selected models"
    25566 
    25567 > view matrix models
    25568 > #8,0.73698,0.11525,-0.66601,155.56,0.40454,0.71417,0.57123,-90.04,0.54148,-0.69041,0.47971,141.01
    25569 
    25570 > view matrix models
    25571 > #8,0.73698,0.11525,-0.66601,154.44,0.40454,0.71417,0.57123,-89.633,0.54148,-0.69041,0.47971,140.1
    25572 
    25573 > view matrix models
    25574 > #8,0.73698,0.11525,-0.66601,153.2,0.40454,0.71417,0.57123,-89.182,0.54148,-0.69041,0.47971,139.08
    25575 
    25576 > ui mousemode right "rotate selected models"
    25577 
    25578 > view matrix models
    25579 > #8,0.73974,0.19261,-0.64473,135.84,0.34001,0.71983,0.60517,-85.705,0.58066,-0.66689,0.467,130.99
    25580 
    25581 > close #8
    25582 
    25583 > volume #1 color #b2b2b280
    25584 
    25585 [Repeated 1 time(s)]
    25586 
    25587 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    25588 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/011762271936024191787_FoilHole_12249383_Data_12248537_12248539_20211012_184153-341492_patch_aligned.mrc
    25589 
    25590 Opened
    25591 011762271936024191787_FoilHole_12249383_Data_12248537_12248539_20211012_184153-341492_patch_aligned.mrc
    25592 as #7, grid size 3838,3710,1, pixel 0.85,0.85,0.85, shown at step 1, values
    25593 float32 
    25594 
    25595 > close #7
    25596 
    25597 > show #!2 models
    25598 
    25599 > hide #3 models
    25600 
    25601 > show #3 models
    25602 
    25603 > hide #3 models
    25604 
    25605 > show #3 models
    25606 
    25607 > show #4 models
    25608 
    25609 > show #9 models
    25610 
    25611 > hide #!2 models
    25612 
    25613 > hide #4 models
    25614 
    25615 > show #4 models
    25616 
    25617 > hide #4 models
    25618 
    25619 > ui tool show "Show Sequence Viewer"
    25620 
    25621 > sequence chain #9/B
    25622 
    25623 Alignment identifier is 9/B 
    25624 
    25625 > sequence chain #9/C
    25626 
    25627 Alignment identifier is 9/C 
    25628 
    25629 > select #9/B:2-3
    25630 
    25631 13 atoms, 12 bonds, 2 residues, 1 model selected 
    25632 
    25633 > select #9/B:2-19
    25634 
    25635 142 atoms, 143 bonds, 18 residues, 1 model selected 
    25636 
    25637 > select #9/B:1
    25638 
    25639 6 atoms, 5 bonds, 1 residue, 1 model selected 
    25640 
    25641 > select #9/B:1-27
    25642 
    25643 211 atoms, 212 bonds, 27 residues, 1 model selected 
    25644 
    25645 > select #9/B:1-27
    25646 
    25647 211 atoms, 212 bonds, 27 residues, 1 model selected 
    25648 
    25649 > select #9/B:30
    25650 
    25651 4 atoms, 3 bonds, 1 residue, 1 model selected 
    25652 
    25653 > select #9/B:1-30
    25654 
    25655 232 atoms, 233 bonds, 30 residues, 1 model selected 
    25656 
    25657 > ui mousemode right "color key"
    25658 
    25659 > key delete
    25660 
    25661 > ui mousemode right "rotate selected models"
    25662 
    25663 > color sel cornflower blue
    25664 
    25665 > color sel #7a81ffff
    25666 
    25667 > ui tool show "Show Sequence Viewer"
    25668 
    25669 > sequence chain #9/B #9/C
    25670 
    25671 Alignment identifier is 1 
    25672 
    25673 > select #9/B-C:1
    25674 
    25675 12 atoms, 10 bonds, 2 residues, 1 model selected 
    25676 
    25677 > select #9/B-C:1-30
    25678 
    25679 464 atoms, 466 bonds, 60 residues, 1 model selected 
    25680 
    25681 > color sel #0433ffff
    25682 
    25683 > color sel #7a81ffff
    25684 
    25685 > select #9/B-C:31-33
    25686 
    25687 42 atoms, 42 bonds, 6 residues, 1 model selected 
    25688 
    25689 > select #9/B-C:31-63
    25690 
    25691 562 atoms, 570 bonds, 66 residues, 1 model selected 
    25692 
    25693 > color sel dim gray
    25694 
    25695 > select #9/B-C:64-65
    25696 
    25697 38 atoms, 40 bonds, 4 residues, 1 model selected 
    25698 
    25699 > select #9/B-C:64-85
    25700 
    25701 402 atoms, 414 bonds, 44 residues, 1 model selected 
    25702 
    25703 > color sel #d783ffff
    25704 
    25705 > color sel #7a81ffff
    25706 
    25707 > select #9/B-C:86
    25708 
    25709 14 atoms, 14 bonds, 2 residues, 1 model selected 
    25710 
    25711 > select #9/B-C:86-107
    25712 
    25713 358 atoms, 360 bonds, 44 residues, 1 model selected 
    25714 
    25715 > color sel dim gray
    25716 
    25717 > select #9/B-C:108-109
    25718 
    25719 30 atoms, 30 bonds, 4 residues, 1 model selected 
    25720 
    25721 > select #9/B-C:108-129
    25722 
    25723 360 atoms, 362 bonds, 44 residues, 1 model selected 
    25724 
    25725 > color sel #d783ffff
    25726 
    25727 > color sel #7a81ffff
    25728 
    25729 > select #9/B-C:130
    25730 
    25731 14 atoms, 14 bonds, 2 residues, 1 model selected 
    25732 
    25733 > select #9/B-C:130-140
    25734 
    25735 190 atoms, 192 bonds, 22 residues, 1 model selected 
    25736 
    25737 > select #9/B-C:130-201
    25738 
    25739 1092 atoms, 1102 bonds, 144 residues, 1 model selected 
    25740 
    25741 > select #9/B-C:130-150
    25742 
    25743 334 atoms, 336 bonds, 42 residues, 1 model selected 
    25744 
    25745 > select #9/B-C:88-151
    25746 
    25747 1030 atoms, 1038 bonds, 128 residues, 1 model selected 
    25748 
    25749 > select #9/B-C:130-151
    25750 
    25751 342 atoms, 344 bonds, 44 residues, 1 model selected 
    25752 
    25753 > color sel dim gray
    25754 
    25755 > select #9/B-C:2-149,151-206
    25756 
    25757 3296 atoms, 3340 bonds, 408 residues, 1 model selected 
    25758 
    25759 > select #9/B-C:151
    25760 
    25761 8 atoms, 6 bonds, 2 residues, 1 model selected 
    25762 
    25763 > select #9/B-C:151-157
    25764 
    25765 108 atoms, 110 bonds, 14 residues, 1 model selected 
    25766 
    25767 > select #9/B-C:152-153
    25768 
    25769 28 atoms, 26 bonds, 4 residues, 1 model selected 
    25770 
    25771 > select #9/B-C:152-172
    25772 
    25773 318 atoms, 320 bonds, 42 residues, 1 model selected 
    25774 
    25775 > select #9/B-C:31-34
    25776 
    25777 60 atoms, 60 bonds, 8 residues, 1 model selected 
    25778 
    25779 > select #9/B-C:31-63
    25780 
    25781 562 atoms, 570 bonds, 66 residues, 1 model selected 
    25782 
    25783 > select #9/B-C:2-149,151-206
    25784 
    25785 3296 atoms, 3340 bonds, 408 residues, 1 model selected 
    25786 
    25787 > select #9/B-C:53
    25788 
    25789 18 atoms, 16 bonds, 2 residues, 1 model selected 
    25790 
    25791 > select #9/B-C:53-63
    25792 
    25793 186 atoms, 184 bonds, 22 residues, 1 model selected 
    25794 
    25795 > color sel #d783ffff
    25796 
    25797 > color sel #7a81ffff
    25798 
    25799 > select #9/B-C:64
    25800 
    25801 14 atoms, 14 bonds, 2 residues, 1 model selected 
    25802 
    25803 > select #9/B-C:64-85
    25804 
    25805 402 atoms, 414 bonds, 44 residues, 1 model selected 
    25806 
    25807 > color sel dim gray
    25808 
    25809 > select #9/B-C:86-87
    25810 
    25811 30 atoms, 30 bonds, 4 residues, 1 model selected 
    25812 
    25813 > select #9/B-C:86-107
    25814 
    25815 358 atoms, 360 bonds, 44 residues, 1 model selected 
    25816 
    25817 > color sel #d783ffff
    25818 
    25819 > color sel #7a81ffff
    25820 
    25821 > color sel dim gray
    25822 
    25823 > select #9/B-C:108
    25824 
    25825 14 atoms, 14 bonds, 2 residues, 1 model selected 
    25826 
    25827 > select #9/B-C:108-129
    25828 
    25829 360 atoms, 362 bonds, 44 residues, 1 model selected 
    25830 
    25831 > select #9/B-C:107
    25832 
    25833 12 atoms, 10 bonds, 2 residues, 1 model selected 
    25834 
    25835 > select #9/B-C:86-107
    25836 
    25837 358 atoms, 360 bonds, 44 residues, 1 model selected 
    25838 
    25839 > color sel #d783ffff
    25840 
    25841 > color sel #7a81ffff
    25842 
    25843 > select #9/B-C:108-109
    25844 
    25845 30 atoms, 30 bonds, 4 residues, 1 model selected 
    25846 
    25847 > select #9/B-C:108-129
    25848 
    25849 360 atoms, 362 bonds, 44 residues, 1 model selected 
    25850 
    25851 > color sel dim gray
    25852 
    25853 > select #9/B-C:130
    25854 
    25855 14 atoms, 14 bonds, 2 residues, 1 model selected 
    25856 
    25857 > select #9/B-C:130-149
    25858 
    25859 326 atoms, 328 bonds, 40 residues, 1 model selected 
    25860 
    25861 > select #9/B-C:130-131
    25862 
    25863 38 atoms, 40 bonds, 4 residues, 1 model selected 
    25864 
    25865 > select #9/B-C:130-150
    25866 
    25867 334 atoms, 336 bonds, 42 residues, 1 model selected 
    25868 
    25869 > select #9/B-C:130
    25870 
    25871 14 atoms, 14 bonds, 2 residues, 1 model selected 
    25872 
    25873 > select #9/B-C:130-151
    25874 
    25875 342 atoms, 344 bonds, 44 residues, 1 model selected 
    25876 
    25877 > color sel #d783ffff
    25878 
    25879 > color sel #7a81ffff
    25880 
    25881 > select #9/B-C:152-153
    25882 
    25883 28 atoms, 26 bonds, 4 residues, 1 model selected 
    25884 
    25885 > select #9/B-C:152-172
    25886 
    25887 318 atoms, 320 bonds, 42 residues, 1 model selected 
    25888 
    25889 > color sel dim gray
    25890 
    25891 > select #9/B-C:174
    25892 
    25893 14 atoms, 12 bonds, 2 residues, 1 model selected 
    25894 
    25895 > select #9/B-C:174-176
    25896 
    25897 48 atoms, 46 bonds, 6 residues, 1 model selected 
    25898 
    25899 > select #9/B-C:173
    25900 
    25901 14 atoms, 14 bonds, 2 residues, 1 model selected 
    25902 
    25903 > select #9/B-C:173-183
    25904 
    25905 174 atoms, 174 bonds, 22 residues, 1 model selected 
    25906 
    25907 > color sel #d783ffff
    25908 
    25909 > color sel #7a81ffff
    25910 
    25911 > select #9/B-C:184
    25912 
    25913 14 atoms, 14 bonds, 2 residues, 1 model selected 
    25914 
    25915 > select #9/B-C:184-207
    25916 
    25917 354 atoms, 354 bonds, 48 residues, 1 model selected 
    25918 
    25919 > color sel dim gray
    25920 
    25921 > select #9
    25922 
    25923 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    25924 
    25925 > ~select #9
    25926 
    25927 Nothing selected 
    25928 
    25929 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    25930 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    25931 > includeMaps true
    25932 
    25933 > show #!2 models
    25934 
    25935 > show #4 models
    25936 
    25937 > hide #4 models
    25938 
    25939 > volume #2 level 0.1179
    25940 
    25941 > show #4 models
    25942 
    25943 > volume #2 level 0.13
    25944 
    25945 > volume #2 level 0.14
    25946 
    25947 > volume #2 level 0.15
    25948 
    25949 > lighting flat
    25950 
    25951 > graphics silhouettes false
    25952 
    25953 > graphics silhouettes true
    25954 
    25955 > lighting shadows true intensity 0.5
    25956 
    25957 > lighting shadows false
    25958 
    25959 > lighting shadows true
    25960 
    25961 > lighting shadows false
    25962 
    25963 > lighting shadows true
    25964 
    25965 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    25966 > (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig4_D.png"
    25967 > width 1009 height 824 supersample 3 transparentBackground true
    25968 
    25969 > show #!6 models
    25970 
    25971 > hide #!2 models
    25972 
    25973 > show #!2 models
    25974 
    25975 Fit map cryosparc_P35_J90_005_volume_map_sharp.mrc in map
    25976 cryosparc_P47_J20_004_volume_map_sharp.mrc using 114729 points 
    25977 correlation = 0.672, correlation about mean = 0.08483, overlap = 3988 
    25978 steps = 212, shift = 5.69, angle = 24.1 degrees 
    25979  
    25980 Position of cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) relative to
    25981 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    25982 Matrix rotation and translation 
    25983 -0.48667344 0.82476587 0.28794127 36.88441365 
    25984 -0.86459172 -0.40757626 -0.29387534 426.86136408 
    25985 -0.12502033 -0.39197297 0.91144230 73.88929120 
    25986 Axis -0.05631763 0.23708030 -0.96985631 
    25987 Axis point 142.84730785 210.89177337 0.00000000 
    25988 Rotation angle (degrees) 119.43288522 
    25989 Shift along axis 27.46118471 
    25990  
    25991 
    25992 > hide #!2 models
    25993 
    25994 > show #!2 models
    25995 
    25996 > hide #!2 models
    25997 
    25998 > volume #6 level 0.12
    25999 
    26000 > select #3
    26001 
    26002 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    26003 
    26004 > ~select #3
    26005 
    26006 Nothing selected 
    26007 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
    26008 (#6) using 5602 atoms 
    26009 average map value = 0.08293, steps = 148 
    26010 shifted from previous position = 4.12 
    26011 rotated from previous position = 15.3 degrees 
    26012 atoms outside contour = 4112, contour level = 0.12 
    26013  
    26014 Position of D2NS1.pdb (#3) relative to
    26015 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    26016 Matrix rotation and translation 
    26017 -0.47334151 0.84962673 0.23255592 79.20387762 
    26018 0.74805308 0.24829808 0.61543861 -93.30922995 
    26019 0.46514990 0.46527681 -0.75309567 157.40236379 
    26020 Axis -0.50919647 -0.78872280 -0.34443477 
    26021 Axis point 62.66416490 -0.00000000 102.29599347 
    26022 Rotation angle (degrees) 171.52083443 
    26023 Shift along axis -20.95006494 
    26024  
    26025 
    26026 > undo
    26027 
    26028 [Repeated 2 time(s)]
    26029 
    26030 > hide #!2 models
    26031 
    26032 > log metadata #3
    26033 
    26034 The model has no metadata
    26035 
    26036 > log chains #3
    26037 
    26038 Chain information for D2NS1.pdb #3 
    26039 --- 
    26040 Chain | Description 
    26041 B C | No description available 
    26042  
    26043 
    26044 > ui mousemode right "rotate selected models"
    26045 
    26046 > select #3
    26047 
    26048 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    26049 
    26050 > view matrix models
    26051 > #3,-0.0085676,-0.30727,-0.95158,398.88,0.38479,-0.87936,0.28049,211.07,-0.92297,-0.36375,0.12577,388.55
    26052 
    26053 > view matrix models
    26054 > #3,-0.13489,-0.29223,-0.94679,417.71,0.36981,-0.90133,0.22551,227.19,-0.91926,-0.31971,0.22965,361.99
    26055 
    26056 > view matrix models
    26057 > #3,-0.071496,-0.30058,-0.95107,408.73,0.37829,-0.89045,0.25298,218.98,-0.92292,-0.34169,0.17737,375.64
    26058 
    26059 > view matrix models
    26060 > #3,-0.18267,-0.34044,-0.92235,429.87,0.39852,-0.88325,0.24708,215.26,-0.89878,-0.32244,0.29702,346.84
    26061 
    26062 > view matrix models
    26063 > #3,-0.40995,0.57223,-0.71028,278.61,-0.10972,-0.804,-0.58442,439.45,-0.90548,-0.16165,0.39238,304
    26064 
    26065 > view matrix models
    26066 > #3,-0.46987,0.63995,-0.60802,259.54,-0.55045,-0.75089,-0.36493,468.93,-0.69009,0.16321,0.70508,155.79
    26067 
    26068 > view matrix models
    26069 > #3,-0.65716,0.081263,-0.74936,411.59,-0.053676,-0.99669,-0.061013,368.75,-0.75184,0.0001281,0.65934,202.22
    26070 
    26071 > view matrix models
    26072 > #3,-0.62292,-0.22233,0.75003,189.5,-0.068144,-0.9397,-0.33515,410.55,0.77931,-0.25988,0.5702,-7.4739
    26073 
    26074 > view matrix models
    26075 > #3,0.31022,-0.41267,0.85643,38.43,-0.2398,-0.90571,-0.34955,437.59,0.91992,-0.096935,-0.37993,109.67
    26076 
    26077 > view matrix models
    26078 > #3,0.14284,-0.48882,0.86061,79.927,-0.73689,-0.63302,-0.23725,459.16,0.66075,-0.60029,-0.45063,252.47
    26079 
    26080 > view matrix models
    26081 > #3,0.069717,-0.45875,0.88582,83.239,-0.93425,-0.34135,-0.10325,420.96,0.34974,-0.82038,-0.45239,344.49
    26082 
    26083 > view matrix models
    26084 > #3,-0.24695,0.22628,0.94224,13.705,-0.87659,-0.46663,-0.11768,434.45,0.41304,-0.85502,0.31359,202.72
    26085 
    26086 > view matrix models
    26087 > #3,-0.099087,-0.011917,0.99501,18.348,-0.8839,-0.45823,-0.09351,430.02,0.45706,-0.88875,0.034872,250.31
    26088 
    26089 > view matrix models
    26090 > #3,0.0096812,0.032947,0.99941,-9.1088,-0.93353,-0.3579,0.020842,401.51,0.35838,-0.93318,0.027292,276.48
    26091 
    26092 > view matrix models
    26093 > #3,-0.060408,-0.021128,0.99795,12.57,-0.98054,-0.18582,-0.063289,395.83,0.18678,-0.98236,-0.0094914,321.48
    26094 
    26095 > view matrix models
    26096 > #3,-0.14852,-0.072188,0.98627,38.731,-0.98683,-0.053816,-0.15254,390.64,0.064089,-0.99594,-0.063245,354.92
    26097 
    26098 > view matrix models
    26099 > #3,-0.35842,-0.23162,0.90437,117.04,-0.92969,0.00036447,-0.36835,409.93,0.084987,-0.97281,-0.21546,374.47
    26100 
    26101 > view matrix models
    26102 > #3,-0.16442,-0.085208,0.9827,44.354,-0.94873,-0.25901,-0.1812,423.54,0.26997,-0.96211,-0.038251,308.57
    26103 
    26104 > view matrix models
    26105 > #3,-0.29929,0.026962,0.95378,54.365,-0.9175,-0.28257,-0.27991,439.6,0.26196,-0.95887,0.10931,283.15
    26106 
    26107 > view matrix models
    26108 > #3,0.21447,0.471,0.85566,-93.169,0.97669,-0.095031,-0.1925,59.362,-0.0093522,0.877,-0.4804,127.25
    26109 
    26110 > view matrix models
    26111 > #3,0.56515,0.56728,0.59899,-125.3,0.82406,-0.42253,-0.37735,174.2,0.03903,0.70687,-0.70627,187.59
    26112 
    26113 > view matrix models
    26114 > #3,0.2047,0.3956,0.89532,-85.837,0.92678,0.21596,-0.30731,36.306,-0.31492,0.89267,-0.32243,150.21
    26115 
    26116 > view matrix models
    26117 > #3,0.26975,0.34464,0.89914,-89.39,0.91144,0.20987,-0.35388,48.323,-0.31067,0.91497,-0.25751,134.15
    26118 
    26119 > view matrix models
    26120 > #3,0.15293,0.16968,0.97356,-52.687,0.98145,0.089212,-0.16972,23.489,-0.11565,0.98145,-0.15289,70.037
    26121 
    26122 > view matrix models
    26123 > #3,0.042216,0.087727,0.99525,-23.3,0.97412,0.21777,-0.060515,-16.293,-0.22204,0.97205,-0.076263,76.678
    26124 
    26125 > view matrix models
    26126 > #3,0.035376,0.093709,0.99497,-23.053,0.9291,0.36366,-0.067284,-31.697,-0.36814,0.92681,-0.0742,109.61
    26127 
    26128 > view matrix models
    26129 > #3,-0.74086,0.45839,0.49092,141.95,-0.6574,-0.34504,-0.66991,473.84,-0.13769,-0.81904,0.55697,250.17
    26130 
    26131 > view matrix models
    26132 > #3,-0.12274,0.85219,0.50863,-36.128,-0.96225,-0.22764,0.1492,361.79,0.24294,-0.47111,0.84796,72.892
    26133 
    26134 > view matrix models
    26135 > #3,-0.67677,0.0678,0.73307,153.21,-0.71984,-0.26966,-0.63962,466.75,0.15432,-0.96057,0.2313,280.63
    26136 
    26137 > view matrix models
    26138 > #3,-0.31096,-0.28409,0.90697,117.06,-0.89867,-0.2227,-0.37788,443.68,0.30934,-0.93258,-0.18605,323.01
    26139 
    26140 > view matrix models
    26141 > #3,-0.31328,-0.20485,0.9273,100.52,-0.94642,-0.013217,-0.32266,407.02,0.078354,-0.9787,-0.18974,372.05
    26142 
    26143 > view matrix models
    26144 > #3,0.084796,0.15045,0.98497,-39.503,-0.99107,-0.089391,0.098974,352.56,0.10294,-0.98457,0.14152,309.7
    26145 
    26146 > view matrix models
    26147 > #3,-0.17084,-0.018385,0.98513,33.815,-0.98351,0.06341,-0.16938,373.35,-0.059353,-0.99782,-0.028915,370.83
    26148 
    26149 > view matrix models
    26150 > #3,-0.3307,0.24426,0.91158,30.874,-0.94057,-0.0062546,-0.33954,407.82,-0.077235,-0.96969,0.23181,322.8
    26151 
    26152 > view matrix models
    26153 > #3,-0.4809,0.025548,0.8764,100.33,-0.81554,-0.38005,-0.43642,465.94,0.32193,-0.92461,0.2036,250.04
    26154 
    26155 > view matrix models
    26156 > #3,-0.53944,-0.043921,0.84088,128.63,-0.79768,-0.29313,-0.52705,464.33,0.26964,-0.95506,0.12309,278.7
    26157 
    26158 > view matrix models
    26159 > #3,-0.45493,0.037354,0.88974,91.401,-0.78489,-0.48882,-0.3808,468.93,0.4207,-0.87159,0.2517,215.19
    26160 
    26161 > view matrix models
    26162 > #3,-0.42074,0.12675,0.89828,68.835,-0.79214,-0.53394,-0.29568,462.63,0.44215,-0.83597,0.32506,192.35
    26163 
    26164 > view matrix models
    26165 > #3,-0.55645,0.18988,0.80889,98.012,-0.74741,-0.53968,-0.38746,472.08,0.36297,-0.82018,0.44222,182.75
    26166 
    26167 > view matrix models
    26168 > #3,-0.56077,0.17343,0.8096,101.41,-0.75525,-0.50786,-0.41434,472.89,0.3393,-0.8438,0.41578,195.6
    26169 
    26170 > ui mousemode right "rotate selected models"
    26171 
    26172 > ui mousemode right "translate selected models"
    26173 
    26174 > view matrix models
    26175 > #3,-0.56077,0.17343,0.8096,97.107,-0.75525,-0.50786,-0.41434,471.77,0.3393,-0.8438,0.41578,196.64
    26176 
    26177 > ui mousemode right "rotate selected models"
    26178 
    26179 > view matrix models
    26180 > #3,-0.31072,0.047476,0.94931,49.418,-0.82644,-0.50685,-0.24516,453.98,0.46952,-0.86073,0.19672,215.61
    26181 
    26182 > view matrix models
    26183 > #3,-0.10594,-0.13924,0.98458,38.514,-0.92405,-0.35194,-0.1492,428.01,0.36729,-0.92561,-0.091386,295.82
    26184 
    26185 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
    26186 (#6) using 5602 atoms 
    26187 average map value = 0.08181, steps = 140 
    26188 shifted from previous position = 5.91 
    26189 rotated from previous position = 5.33 degrees 
    26190 atoms outside contour = 4112, contour level = 0.12 
    26191  
    26192 Position of D2NS1.pdb (#3) relative to
    26193 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    26194 Matrix rotation and translation 
    26195 0.96127167 0.06226622 -0.26847668 48.62307340 
    26196 -0.22542895 0.73805618 -0.63596769 218.36928771 
    26197 0.15855157 0.67186013 0.72350910 -87.31437189 
    26198 Axis 0.93048244 -0.30381850 -0.20468696 
    26199 Axis point 0.00000000 232.24708974 246.16405973 
    26200 Rotation angle (degrees) 44.64955765 
    26201 Shift along axis -3.22959992 
    26202  
    26203 
    26204 > view matrix models
    26205 > #3,-0.2167,-0.046006,0.97515,46.998,-0.825,-0.52541,-0.20812,455.06,0.52193,-0.8496,0.075903,227.93
    26206 
    26207 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
    26208 (#6) using 5602 atoms 
    26209 average map value = 0.08275, steps = 232 
    26210 shifted from previous position = 0.39 
    26211 rotated from previous position = 10.7 degrees 
    26212 atoms outside contour = 4141, contour level = 0.12 
    26213  
    26214 Position of D2NS1.pdb (#3) relative to
    26215 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    26216 Matrix rotation and translation 
    26217 0.94687496 0.16521963 -0.27591724 34.87295901 
    26218 -0.32111058 0.53311437 -0.78273693 296.77138746 
    26219 0.01777194 0.82975393 0.55784641 -59.68855935 
    26220 Axis 0.94317112 -0.17178339 -0.28446215 
    26221 Axis point 0.00000000 208.08374987 254.78468856 
    26222 Rotation angle (degrees) 58.74030833 
    26223 Shift along axis -1.11009298 
    26224  
    26225 
    26226 > view matrix models
    26227 > #3,-0.29357,0.29509,0.90925,14.248,-0.93223,-0.29887,-0.20399,435.37,0.21155,-0.90752,0.36283,240.41
    26228 
    26229 > view matrix models
    26230 > #3,-0.024736,0.33337,0.94247,-45.387,-0.98041,-0.19235,0.042305,382.05,0.19538,-0.92297,0.3316,251.41
    26231 
    26232 > ui mousemode right "translate selected models"
    26233 
    26234 > view matrix models
    26235 > #3,-0.024736,0.33337,0.94247,-50.647,-0.98041,-0.19235,0.042305,380.65,0.19538,-0.92297,0.3316,252
    26236 
    26237 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
    26238 (#6) using 5602 atoms 
    26239 average map value = 0.07754, steps = 124 
    26240 shifted from previous position = 0.984 
    26241 rotated from previous position = 11.7 degrees 
    26242 atoms outside contour = 4222, contour level = 0.12 
    26243  
    26244 Position of D2NS1.pdb (#3) relative to
    26245 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    26246 Matrix rotation and translation 
    26247 0.97038128 -0.18348442 -0.15714223 69.99792136 
    26248 -0.04643502 0.49668363 -0.86668864 273.08312267 
    26249 0.23707384 0.84831532 0.47345239 -88.46523910 
    26250 Axis 0.97164206 -0.22334462 0.07764586 
    26251 Axis point 0.00000000 220.43718489 187.11160518 
    26252 Rotation angle (degrees) 61.94891347 
    26253 Shift along axis 0.15231786 
    26254  
    26255 
    26256 > view matrix models
    26257 > #3,-0.16161,0.20679,0.96495,-7.8987,-0.94599,-0.31092,-0.091808,418.86,0.28103,-0.92767,0.24587,240.27
    26258 
    26259 > view matrix models
    26260 > #3,-0.16161,0.20679,0.96495,-7.6794,-0.94599,-0.31092,-0.091808,419.8,0.28103,-0.92767,0.24587,239.05
    26261 
    26262 > ui mousemode right "rotate selected models"
    26263 
    26264 > view matrix models
    26265 > #3,-0.065282,0.14337,0.98751,-17.979,-0.96082,-0.2762,-0.023418,404.39,0.26939,-0.95035,0.15578,260.96
    26266 
    26267 > view matrix models
    26268 > #3,0.11914,-0.22697,0.96659,15.581,-0.91769,-0.3968,0.019938,409.35,0.37901,-0.8894,-0.25556,304.72
    26269 
    26270 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
    26271 (#6) using 5602 atoms 
    26272 average map value = 0.082, steps = 232 
    26273 shifted from previous position = 14.3 
    26274 rotated from previous position = 15.8 degrees 
    26275 atoms outside contour = 4100, contour level = 0.12 
    26276  
    26277 Position of D2NS1.pdb (#3) relative to
    26278 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    26279 Matrix rotation and translation 
    26280 0.93730079 0.13375954 -0.32183172 47.54908073 
    26281 -0.32984053 0.63871002 -0.69516528 263.49850116 
    26282 0.11257216 0.75773210 0.64278271 -75.44380421 
    26283 Axis 0.91623198 -0.27394552 -0.29235734 
    26284 Axis point -0.00000000 224.55289345 259.75440758 
    26285 Rotation angle (degrees) 52.45410370 
    26286 Shift along axis -6.56169478 
    26287  
    26288 
    26289 > ui mousemode right "translate selected models"
    26290 
    26291 > view matrix models
    26292 > #3,-0.018323,-0.060034,0.99803,13.026,-0.84305,-0.53571,-0.047702,432.04,0.53752,-0.84226,-0.040796,240.98
    26293 
    26294 > ui mousemode right "rotate selected models"
    26295 
    26296 > view matrix models
    26297 > #3,-0.036597,-0.098259,0.99449,23.297,-0.80637,-0.58491,-0.087465,440.94,0.59028,-0.80513,-0.057828,228.49
    26298 
    26299 > view matrix models
    26300 > #3,-0.027477,-0.10288,0.99431,22.501,-0.77374,-0.6276,-0.086317,442.18,0.63291,-0.77171,-0.062357,216.18
    26301 
    26302 > view matrix models
    26303 > #3,-0.10002,-0.07995,0.99177,31.858,-0.93297,-0.33885,-0.12141,427.89,0.34577,-0.93744,-0.040699,290.69
    26304 
    26305 > view matrix models
    26306 > #3,-0.10077,-0.089813,0.99085,33.811,-0.91689,-0.37822,-0.12753,432.77,0.38621,-0.92135,-0.044236,281.5
    26307 
    26308 > view matrix models
    26309 > #3,-0.032685,-0.1875,0.98172,39.889,-0.92726,-0.36087,-0.099796,426.73,0.37298,-0.91357,-0.16207,303.51
    26310 
    26311 > volume #2 level 0.1688
    26312 
    26313 > hide #!2 models
    26314 
    26315 [Repeated 1 time(s)]
    26316 
    26317 > volume #6 level 0.1932
    26318 
    26319 > view matrix models
    26320 > #3,-0.15943,5.3271e-05,0.98721,29.667,-0.88694,0.43911,-0.14326,292.88,-0.4335,-0.89843,-0.06996,426.39
    26321 
    26322 > view matrix models
    26323 > #3,-0.23062,0.17059,0.95797,18.724,-0.93077,-0.3257,-0.16608,433.25,0.28369,-0.92996,0.23389,251.43
    26324 
    26325 > view matrix models
    26326 > #3,-0.029625,-0.49902,0.86608,112.33,-0.48854,-0.74869,-0.44809,476.83,0.87204,-0.43639,-0.22161,146.12
    26327 
    26328 > view matrix models
    26329 > #3,0.26982,-0.40253,0.87474,41.898,-0.5711,-0.79831,-0.1912,453.92,0.77527,-0.44797,-0.44528,204.93
    26330 
    26331 > view matrix models
    26332 > #3,-0.10768,-0.15758,0.98162,48.065,-0.99351,0.053323,-0.10043,368.86,-0.036518,-0.98607,-0.1623,387.76
    26333 
    26334 > view matrix models
    26335 > #3,-0.059748,-0.20275,0.97741,47.98,-0.99636,0.071795,-0.046014,356.56,-0.060844,-0.9766,-0.2063,398.29
    26336 
    26337 > view matrix models
    26338 > #3,-0.2527,-0.028861,0.96711,54.512,-0.96729,-0.015262,-0.2532,403,0.022068,-0.99947,-0.02406,355.08
    26339 
    26340 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    26341 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/4o6b_DV2NS1.pdb
    26342 
    26343 4o6b_DV2NS1.pdb title: 
    26344 Dengue TYPE2 virus non-structural protein 1 (NS1) form 1 crystal [more
    26345 info...] 
    26346  
    26347 Chain information for 4o6b_DV2NS1.pdb #7 
    26348 --- 
    26349 Chain | Description | UniProt 
    26350 A | NS1 | POLG_DEN26 
    26351 B | NS1 | POLG_DEN26 
    26352  
    26353 Non-standard residues in 4o6b_DV2NS1.pdb #7 
    26354 --- 
    26355 NAG — 2-acetamido-2-deoxy-β-D-glucopyranose 
    26356  
    26357 
    26358 > select #7
    26359 
    26360 5126 atoms, 5257 bonds, 5 pseudobonds, 644 residues, 2 models selected 
    26361 
    26362 > ui mousemode right "translate selected models"
    26363 
    26364 > view matrix models #7,1,0,0,195.73,0,1,0,55.756,0,0,1,0.30073
    26365 
    26366 > view matrix models #7,1,0,0,24.836,0,1,0,111.9,0,0,1,93.148
    26367 
    26368 > view matrix models #7,1,0,0,184.13,0,1,0,225.28,0,0,1,192.15
    26369 
    26370 > view matrix models #7,1,0,0,151.84,0,1,0,239.37,0,0,1,213.11
    26371 
    26372 > view matrix models #7,1,0,0,191.69,0,1,0,227.02,0,0,1,208.55
    26373 
    26374 > ui mousemode right "rotate selected models"
    26375 
    26376 > view matrix models
    26377 > #7,0.98804,-0.14623,0.048956,188.26,0.13002,0.61931,-0.7743,195.13,0.082905,0.77141,0.63092,223.81
    26378 
    26379 > view matrix models
    26380 > #7,0.99657,-0.079109,0.024224,189.79,0.063222,0.5393,-0.83974,190.38,0.053367,0.83839,0.54245,223.38
    26381 
    26382 > view matrix models
    26383 > #7,0.94783,-0.3073,0.084745,183.81,0.25252,0.5616,-0.78793,193.76,0.19454,0.76823,0.6099,223.91
    26384 
    26385 > view matrix models
    26386 > #7,0.59074,0.041726,0.80578,211.73,0.76522,0.28771,-0.57591,194.2,-0.25586,0.95681,0.13803,214.25
    26387 
    26388 > ui mousemode right "translate selected models"
    26389 
    26390 > view matrix models
    26391 > #7,0.59074,0.041726,0.80578,206.56,0.76522,0.28771,-0.57591,184.3,-0.25586,0.95681,0.13803,224.47
    26392 
    26393 > ui mousemode right "rotate selected models"
    26394 
    26395 > view matrix models
    26396 > #7,0.69999,-0.017723,0.71393,202.96,0.67927,0.32512,-0.65794,182.71,-0.22045,0.94551,0.23962,227.06
    26397 
    26398 > view matrix models
    26399 > #7,0.84135,0.059716,0.53718,201.67,0.50634,0.26057,-0.82202,175.1,-0.18906,0.96361,0.18899,226.5
    26400 
    26401 > view matrix models
    26402 > #7,0.91878,0.00070031,0.39477,196.52,0.37034,0.34484,-0.86252,175.78,-0.13674,0.93866,0.31658,229.47
    26403 
    26404 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    26405 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    26406 > sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J141_class_00_final_volume.mrc
    26407 
    26408 Opened cryosparc_P35_J141_class_00_final_volume.mrc as #8, grid size
    26409 128,128,128, pixel 2.79, shown at level 0.235, step 1, values float32 
    26410 
    26411 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    26412 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    26413 > sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J141_class_01_final_volume.mrc
    26414 
    26415 Opened cryosparc_P35_J141_class_01_final_volume.mrc as #10, grid size
    26416 128,128,128, pixel 2.79, shown at level 0.281, step 1, values float32 
    26417 
    26418 > select #10
    26419 
    26420 2 models selected 
    26421 
    26422 > view matrix models
    26423 > #10,-0.079171,0.66364,0.74385,-61.635,-0.22432,-0.73892,0.63536,232.1,0.97129,-0.11656,0.20737,-7.2572
    26424 
    26425 > view matrix models
    26426 > #10,-0.28893,0.313,0.90474,9.1948,-0.47663,-0.86662,0.1476,393.94,0.83026,-0.38858,0.39958,30.91
    26427 
    26428 > ~select #10
    26429 
    26430 Nothing selected 
    26431 
    26432 > select #8
    26433 
    26434 2 models selected 
    26435 
    26436 > view matrix models
    26437 > #8,0.27556,0.9224,0.27065,-84.292,-0.27059,-0.19574,0.94258,80.02,0.92241,-0.33297,0.19565,46.409
    26438 
    26439 > view matrix models
    26440 > #8,0.63638,0.51065,0.57815,-136.4,0.085328,0.6983,-0.7107,175.68,-0.76664,0.50161,0.40081,166.71
    26441 
    26442 > view matrix models
    26443 > #8,-0.3692,-0.17702,0.91234,105.18,-0.32493,-0.89515,-0.30518,456,0.8707,-0.40912,0.27296,54.461
    26444 
    26445 > view matrix models
    26446 > #8,-0.21183,0.1782,0.96092,3.7465,-0.32373,-0.94052,0.10305,384.86,0.92213,-0.28925,0.25692,26.817
    26447 
    26448 > color #10 #ffb2b270 models
    26449 
    26450 [Repeated 1 time(s)]
    26451 
    26452 > color #8 #ffb2ff56 models
    26453 
    26454 > color #8 #ffb2ff57 models
    26455 
    26456 > hide #4 models
    26457 
    26458 > hide #3 models
    26459 
    26460 > hide #!8 models
    26461 
    26462 > hide #9 models
    26463 
    26464 > show #9 models
    26465 
    26466 > hide #9 models
    26467 
    26468 > hide #!10 models
    26469 
    26470 > show #!8 models
    26471 
    26472 > view matrix models
    26473 > #8,0.27556,0.39667,0.87562,-107.73,0.79978,-0.59996,0.020098,134.95,0.53331,0.69477,-0.48257,65.706
    26474 
    26475 > view matrix models
    26476 > #8,0.27366,0.52314,0.80712,-116.65,0.91914,-0.38945,-0.059223,90.987,0.28335,0.75806,-0.58742,120.4
    26477 
    26478 > view matrix models
    26479 > #8,0.33758,0.53414,0.77507,-124.09,0.9382,-0.25771,-0.23103,97.287,0.076338,0.80516,-0.58813,149.98
    26480 
    26481 > view matrix models
    26482 > #8,0.45264,0.48026,0.75131,-130.92,0.89015,-0.19384,-0.41237,129.79,-0.052411,0.85544,-0.51524,150.44
    26483 
    26484 > view matrix models
    26485 > #8,0.65699,0.41807,0.62736,-133.2,0.73578,-0.1742,-0.65443,201.34,-0.16431,0.89156,-0.42206,146.43
    26486 
    26487 > ui mousemode right "translate selected models"
    26488 
    26489 > view matrix models
    26490 > #8,0.65699,0.41807,0.62736,-126.9,0.73578,-0.1742,-0.65443,207.73,-0.16431,0.89156,-0.42206,145.93
    26491 
    26492 > view matrix models
    26493 > #8,0.65699,0.41807,0.62736,-126.22,0.73578,-0.1742,-0.65443,209.21,-0.16431,0.89156,-0.42206,144.54
    26494 
    26495 > view matrix models
    26496 > #8,0.65699,0.41807,0.62736,-124.37,0.73578,-0.1742,-0.65443,208.1,-0.16431,0.89156,-0.42206,144.61
    26497 
    26498 > ui mousemode right "rotate selected models"
    26499 
    26500 > view matrix models
    26501 > #8,0.53344,-0.037486,0.84501,-62.766,0.5106,-0.78219,-0.35703,299.99,0.67434,0.62191,-0.39811,34.754
    26502 
    26503 > volume #8 level 0.8045
    26504 
    26505 > view matrix models
    26506 > #8,0.52401,-0.054439,0.84997,-58.961,0.47038,-0.81345,-0.3421,310.02,0.71003,0.57907,-0.40065,36.512
    26507 
    26508 > volume #8 level 0.3577
    26509 
    26510 > show #!10 models
    26511 
    26512 > hide #!8 models
    26513 
    26514 > view matrix models
    26515 > #8,0.60764,0.020079,0.79396,-76.868,0.73022,-0.40725,-0.54857,228.31,0.31232,0.9131,-0.26212,18.911
    26516 
    26517 > show #!8 models
    26518 
    26519 > view matrix models
    26520 > #8,0.37572,0.11623,0.91941,-75.961,0.70308,-0.68208,-0.20109,215.44,0.60375,0.72198,-0.33799,14.583
    26521 
    26522 Fit map cryosparc_P35_J141_class_01_final_volume.mrc in map
    26523 cryosparc_P35_J141_class_00_final_volume.mrc using 20957 points 
    26524 correlation = 0.9488, correlation about mean = 0.6585, overlap = 4385 
    26525 steps = 288, shift = 15.4, angle = 91.5 degrees 
    26526  
    26527 Position of cryosparc_P35_J141_class_01_final_volume.mrc (#10) relative to
    26528 cryosparc_P35_J141_class_00_final_volume.mrc (#8) coordinates: 
    26529 Matrix rotation and translation 
    26530 0.99679931 0.07719696 -0.02077903 -9.05098271 
    26531 -0.07875179 0.99291028 -0.08903553 30.04476737 
    26532 0.01375844 0.09038694 0.99581168 -19.54599107 
    26533 Axis 0.74691139 -0.14377477 -0.64919349 
    26534 Axis point 0.00000000 219.63678499 322.55619772 
    26535 Rotation angle (degrees) 6.89842857 
    26536 Shift along axis 1.60916844 
    26537  
    26538 
    26539 > volume #6 level 0.1566
    26540 
    26541 > volume #6 level 0.1346
    26542 
    26543 Fit map cryosparc_P35_J141_class_01_final_volume.mrc in map
    26544 cryosparc_P35_J90_005_volume_map_sharp.mrc using 20957 points 
    26545 correlation = 0.7294, correlation about mean = 0.2901, overlap = 713.6 
    26546 steps = 312, shift = 14.7, angle = 29.6 degrees 
    26547  
    26548 Position of cryosparc_P35_J141_class_01_final_volume.mrc (#10) relative to
    26549 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    26550 Matrix rotation and translation 
    26551 -0.81655312 0.57639109 -0.03184812 223.81505889 
    26552 -0.57200743 -0.81530920 -0.08987989 441.91818039 
    26553 -0.07777204 -0.05517435 0.99544327 24.62573349 
    26554 Axis 0.03018293 0.03993939 -0.99874613 
    26555 Axis point 182.23608880 186.02084504 0.00000000 
    26556 Rotation angle (degrees) 144.90596060 
    26557 Shift along axis -0.18951992 
    26558  
    26559 Fit map cryosparc_P35_J141_class_00_final_volume.mrc in map
    26560 cryosparc_P35_J90_005_volume_map_sharp.mrc using 13326 points 
    26561 correlation = 0.7531, correlation about mean = 0.2446, overlap = 614.5 
    26562 steps = 200, shift = 14.7, angle = 20.2 degrees 
    26563  
    26564 Position of cryosparc_P35_J141_class_00_final_volume.mrc (#8) relative to
    26565 cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates: 
    26566 Matrix rotation and translation 
    26567 -0.51114495 0.85836696 -0.04401141 122.12595771 
    26568 -0.83601173 -0.50841524 -0.20639360 453.44795134 
    26569 -0.19953752 -0.06870298 0.97747873 53.02558896 
    26570 Axis 0.08065933 0.09110739 -0.99256915 
    26571 Axis point 191.43391939 194.60207731 0.00000000 
    26572 Rotation angle (degrees) 121.40208746 
    26573 Shift along axis -1.46850799 
    26574  
    26575 
    26576 > volume #10 level 0.3562
    26577 
    26578 > volume #8 level 0.2852
    26579 
    26580 > volume #8 level 0.318
    26581 
    26582 > hide #!7 models
    26583 
    26584 > show #!7 models
    26585 
    26586 > select #7
    26587 
    26588 5126 atoms, 5257 bonds, 5 pseudobonds, 644 residues, 2 models selected 
    26589 
    26590 > ui mousemode right "translate selected models"
    26591 
    26592 > view matrix models
    26593 > #7,0.91878,0.00070031,0.39477,195.03,0.37034,0.34484,-0.86252,183.44,-0.13674,0.93866,0.31658,212.37
    26594 
    26595 > view matrix models
    26596 > #7,0.91878,0.00070031,0.39477,207.4,0.37034,0.34484,-0.86252,186.87,-0.13674,0.93866,0.31658,221.02
    26597 
    26598 > ui mousemode right "rotate selected models"
    26599 
    26600 > view matrix models
    26601 > #7,0.73404,-0.62761,0.2594,182.53,-0.25829,-0.61129,-0.74807,155.21,0.62806,0.48212,-0.61082,186.96
    26602 
    26603 > view matrix models
    26604 > #7,0.74989,-0.64446,0.14946,179.17,-0.33839,-0.56778,-0.75041,155.99,0.56846,0.51215,-0.64386,186.63
    26605 
    26606 > ui mousemode right "translate selected models"
    26607 
    26608 > view matrix models
    26609 > #7,0.74989,-0.64446,0.14946,177.57,-0.33839,-0.56778,-0.75041,160.17,0.56846,0.51215,-0.64386,189.52
    26610 
    26611 > view matrix models
    26612 > #7,0.74989,-0.64446,0.14946,178.16,-0.33839,-0.56778,-0.75041,160.58,0.56846,0.51215,-0.64386,182.7
    26613 
    26614 > view matrix models
    26615 > #7,0.74989,-0.64446,0.14946,177.56,-0.33839,-0.56778,-0.75041,162.27,0.56846,0.51215,-0.64386,183.32
    26616 
    26617 > view matrix models
    26618 > #7,0.74989,-0.64446,0.14946,179.58,-0.33839,-0.56778,-0.75041,162.74,0.56846,0.51215,-0.64386,180.3
    26619 
    26620 > ui mousemode right "rotate selected models"
    26621 
    26622 > view matrix models
    26623 > #7,0.69567,-0.70398,0.14302,177.14,-0.33345,-0.49279,-0.80372,163.74,0.63628,0.51144,-0.57756,182.51
    26624 
    26625 > view matrix models
    26626 > #7,0.76223,-0.64567,0.045974,176.86,-0.30995,-0.42641,-0.84977,164.78,0.56827,0.63347,-0.52515,187.33
    26627 
    26628 > view matrix models
    26629 > #7,0.78877,-0.61274,0.04891,178.17,-0.30035,-0.4536,-0.83907,164.27,0.53632,0.64714,-0.54182,187.1
    26630 
    26631 > view matrix models
    26632 > #7,0.6402,-0.76747,-0.033591,170.03,-0.27585,-0.18885,-0.94246,170.1,0.71697,0.61263,-0.33261,192.81
    26633 
    26634 > view matrix models
    26635 > #7,0.62699,-0.77647,0.063022,172.23,-0.19611,-0.23561,-0.95186,168.91,0.75394,0.58444,-0.3,193.04
    26636 
    26637 > view matrix models
    26638 > #7,0.75838,-0.62248,0.19333,181.51,-0.13362,-0.43878,-0.8886,164.56,0.63797,0.64807,-0.41594,191.18
    26639 
    26640 > view matrix models
    26641 > #7,0.70141,-0.70676,0.092259,175.74,-0.28093,-0.39309,-0.87553,165.35,0.65506,0.58819,-0.47427,187.83
    26642 
    26643 > view matrix models
    26644 > #7,0.69618,-0.71217,0.090246,175.48,-0.28016,-0.38529,-0.87924,165.51,0.66094,0.58683,-0.46775,188
    26645 
    26646 > view matrix models
    26647 > #7,0.68522,-0.72338,0.084779,174.9,-0.27616,-0.36576,-0.88879,165.9,0.67395,0.58561,-0.4504,188.52
    26648 
    26649 > view matrix models
    26650 > #7,0.74436,-0.66753,0.018223,175.3,-0.26396,-0.31919,-0.91019,166.9,0.61339,0.6727,-0.4138,191.85
    26651 
    26652 > view matrix models
    26653 > #7,0.77161,-0.63604,-0.0079224,175.8,-0.26676,-0.31226,-0.91177,167.06,0.57745,0.70565,-0.41062,192.74
    26654 
    26655 > view matrix models
    26656 > #7,0.73389,-0.66982,0.11293,177.69,-0.19652,-0.36852,-0.90861,165.83,0.65022,0.64462,-0.40208,191.52
    26657 
    26658 > ui mousemode right "translate selected models"
    26659 
    26660 > view matrix models
    26661 > #7,0.73389,-0.66982,0.11293,176.82,-0.19652,-0.36852,-0.90861,164.33,0.65022,0.64462,-0.40208,195.23
    26662 
    26663 > show #3 models
    26664 
    26665 > hide #3 models
    26666 
    26667 > show #!2 models
    26668 
    26669 > show #3 models
    26670 
    26671 > hide #!10 models
    26672 
    26673 > hide #!7 models
    26674 
    26675 Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
    26676 (#2) using 5602 atoms 
    26677 average map value = 0.1888, steps = 160 
    26678 shifted from previous position = 4.81 
    26679 rotated from previous position = 23.5 degrees 
    26680 atoms outside contour = 2712, contour level = 0.1688 
    26681  
    26682 Position of D2NS1.pdb (#3) relative to
    26683 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    26684 Matrix rotation and translation 
    26685 -0.55420887 0.78282865 -0.28289899 176.19297958 
    26686 -0.82333712 -0.46560234 0.32454654 303.63070097 
    26687 0.12234590 0.41278781 0.90257282 -106.76939213 
    26688 Axis 0.05319429 -0.24429289 -0.96824137 
    26689 Axis point 171.19224328 117.42998509 0.00000000 
    26690 Rotation angle (degrees) 123.96035927 
    26691 Shift along axis 38.57618189 
    26692  
    26693 
    26694 > close #10
    26695 
    26696 > show #9 models
    26697 
    26698 > hide #9 models
    26699 
    26700 > show #!7 models
    26701 
    26702 > view matrix models
    26703 > #7,0.73389,-0.66982,0.11293,170.79,-0.19652,-0.36852,-0.90861,155.22,0.65022,0.64462,-0.40208,205.07
    26704 
    26705 > ui mousemode right "rotate selected models"
    26706 
    26707 > view matrix models
    26708 > #7,0.90325,0.19269,0.38342,206.62,0.0001087,0.89341,-0.44925,208.99,-0.42912,0.40583,0.80695,222.37
    26709 
    26710 > view matrix models
    26711 > #7,0.91285,-0.26756,0.30841,190.03,0.40807,0.57317,-0.7106,194.6,0.013357,0.77453,0.6324,232.47
    26712 
    26713 > view matrix models
    26714 > #7,0.76546,-0.55709,0.32206,180.18,0.59967,0.43603,-0.67102,192.6,0.23339,0.70677,0.66784,232.76
    26715 
    26716 > view matrix models
    26717 > #7,0.49342,-0.33249,0.80373,198.32,0.86883,0.23191,-0.43745,194.17,-0.040945,0.91415,0.4033,230.43
    26718 
    26719 > view matrix models
    26720 > #7,0.61212,-0.26384,0.74546,199.76,0.7065,0.60592,-0.36567,206.88,-0.35521,0.7505,0.5573,227.19
    26721 
    26722 > ui mousemode right "translate selected models"
    26723 
    26724 > view matrix models
    26725 > #7,0.61212,-0.26384,0.74546,192.13,0.7065,0.60592,-0.36567,204.9,-0.35521,0.7505,0.5573,229.56
    26726 
    26727 Fit molecule 4o6b_DV2NS1.pdb (#7) to map
    26728 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 5126 atoms 
    26729 average map value = 0.1927, steps = 152 
    26730 shifted from previous position = 14.6 
    26731 rotated from previous position = 16.1 degrees 
    26732 atoms outside contour = 2452, contour level = 0.1688 
    26733  
    26734 Position of 4o6b_DV2NS1.pdb (#7) relative to
    26735 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    26736 Matrix rotation and translation 
    26737 0.34465485 -0.66063558 -0.66691350 125.14009286 
    26738 0.80909618 0.56930074 -0.14580812 154.59882031 
    26739 0.47600039 -0.48934370 0.73073000 156.62388255 
    26740 Axis -0.18145322 -0.60367956 0.77630260 
    26741 Axis point -61.23617800 251.69459436 0.00000000 
    26742 Rotation angle (degrees) 71.19533318 
    26743 Shift along axis 5.55230604 
    26744  
    26745 
    26746 > close #7
    26747 
    26748 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    26749 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
    26750 > sNS1-Fab56-2/cryosparc_P35_J130_004_volume_map_sharp.mrc
    26751 
    26752 Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
    26753 416,416,416, pixel 0.858, shown at level 0.0371, step 2, values float32 
    26754 
    26755 > volume #7 level 0.09025
    26756 
    26757 > lighting simple
    26758 
    26759 > hide #3 models
    26760 
    26761 > hide #!7 models
    26762 
    26763 > hide #!6 models
    26764 
    26765 > show #!7 models
    26766 
    26767 > show #3 models
    26768 
    26769 > show #!1 models
    26770 
    26771 > hide #!2 models
    26772 
    26773 > hide #3 models
    26774 
    26775 > select #7
    26776 
    26777 2 models selected 
    26778 
    26779 > ui mousemode right "rotate selected models"
    26780 
    26781 > view matrix models
    26782 > #7,0.24103,-0.29696,-0.92397,349.21,-0.038945,-0.95423,0.29653,285.57,-0.96974,-0.035487,-0.24156,398.71
    26783 
    26784 > view matrix models
    26785 > #7,-0.24983,0.23805,-0.93857,346.61,-0.30202,0.90179,0.30911,13.804,0.91998,0.3607,-0.1534,-14.399
    26786 
    26787 > view matrix models
    26788 > #7,-0.10249,0.16037,-0.98172,341.85,0.025379,0.98702,0.15858,-30.757,0.99441,-0.0086622,-0.10523,26.713
    26789 
    26790 > ui mousemode right "translate selected models"
    26791 
    26792 > view matrix models
    26793 > #7,-0.10249,0.16037,-0.98172,336.3,0.025379,0.98702,0.15858,-28.758,0.99441,-0.0086622,-0.10523,26.913
    26794 
    26795 > view matrix models
    26796 > #7,-0.10249,0.16037,-0.98172,337.29,0.025379,0.98702,0.15858,-28.672,0.99441,-0.0086622,-0.10523,28.197
    26797 
    26798 > ui mousemode right "rotate selected models"
    26799 
    26800 > view matrix models
    26801 > #7,-0.22211,-0.1265,-0.96678,404.24,-0.24639,0.96665,-0.069873,63.34,0.94338,0.22268,-0.24587,23.093
    26802 
    26803 > view matrix models
    26804 > #7,-0.19183,0.047993,-0.98025,371.72,-0.43799,0.88964,0.12927,74.05,0.87827,0.45414,-0.14964,-22.192
    26805 
    26806 > view matrix models
    26807 > #7,-0.34489,-0.073759,-0.93574,411.13,-0.53139,0.83711,0.12987,99.175,0.77374,0.54204,-0.32791,13.194
    26808 
    26809 > view matrix models
    26810 > #7,-0.36324,0.1037,-0.92591,382.4,-0.38069,0.89052,0.24908,42.339,0.85037,0.44296,-0.284,8.7541
    26811 
    26812 > view matrix models
    26813 > #7,-0.36165,0.10266,-0.92664,382.44,-0.38188,0.8904,0.24768,42.819,0.85051,0.44344,-0.28281,8.4329
    26814 
    26815 > view matrix models
    26816 > #7,-0.35715,0.16036,-0.92018,370.68,-0.43075,0.84586,0.3146,46.881,0.82879,0.50872,-0.23302,-7.8271
    26817 
    26818 > view matrix models
    26819 > #7,-0.37647,0.070708,-0.92373,389.93,-0.48903,0.83168,0.26297,68.754,0.78684,0.55073,-0.27853,0.54545
    26820 
    26821 > view matrix models
    26822 > #7,-0.21108,0.96488,-0.15637,71.026,-0.41939,0.055099,0.90613,72.864,0.88292,0.25684,0.39304,-87.108
    26823 
    26824 > view matrix models
    26825 > #7,-0.19093,-0.093424,0.97715,43.432,-0.59513,-0.78062,-0.19092,442.95,0.78062,-0.61798,0.093448,133.33
    26826 
    26827 > view matrix models
    26828 > #7,-0.25485,0.0071755,0.96696,39.327,0.96698,0.0034538,0.25483,-43.217,-0.0015111,0.99997,-0.0078187,13.125
    26829 
    26830 > view matrix models
    26831 > #7,-0.017228,0.34616,0.93802,-54.562,0.65851,0.70988,-0.24988,-18.615,-0.75238,0.61338,-0.24018,251.72
    26832 
    26833 > view matrix models
    26834 > #7,0.28808,0.16888,0.9426,-78.558,0.64678,0.69156,-0.32157,-0.5571,-0.70617,0.7023,0.089997,169.14
    26835 
    26836 > view matrix models
    26837 > #7,0.16326,0.14447,0.97595,-58.619,0.66325,0.71625,-0.21698,-26.446,-0.73037,0.68273,0.021113,189.08
    26838 
    26839 Fit map cryosparc_P35_J130_004_volume_map_sharp.mrc in map
    26840 cryosparc_P35_J96_006_volume_map_sharp.mrc using 19964 points 
    26841 correlation = 0.8354, correlation about mean = 0.6739, overlap = 929.1 
    26842 steps = 276, shift = 3.71, angle = 23.7 degrees 
    26843  
    26844 Position of cryosparc_P35_J130_004_volume_map_sharp.mrc (#7) relative to
    26845 cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: 
    26846 Matrix rotation and translation 
    26847 0.08559775 -0.03414562 -0.99574450 347.85846819 
    26848 0.92968539 -0.35664221 0.09214889 59.72132131 
    26849 -0.35827099 -0.93361685 0.00121691 410.96755552 
    26850 Axis -0.66385471 -0.41255988 0.62377181 
    26851 Axis point 0.00000000 67.86622584 347.54047210 
    26852 Rotation angle (degrees) 129.41358899 
    26853 Shift along axis 0.78387399 
    26854  
    26855 
    26856 > volume #1 level 0.09
    26857 
    26858 > volume #7 level 0.09
    26859 
    26860 > ~select #7
    26861 
    26862 Nothing selected 
    26863 
    26864 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    26865 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
    26866 > NS1ts.cxs" includeMaps true
    26867 
    26868 ——— End of log from Fri Mar 11 18:14:28 2022 ———
    26869 
    26870 opened ChimeraX session 
    26871 
    26872 > show #!2 models
    26873 
    26874 > hide #!2 models
    26875 
    26876 > show #!2 models
    26877 
    26878 > hide #!1 models
    26879 
    26880 > hide #!7 models
    26881 
    26882 > show #3 models
    26883 
    26884 > show #4 models
    26885 
    26886 > show #!8 models
    26887 
    26888 > hide #!8 models
    26889 
    26890 > close #8
    26891 
    26892 > show #!6 models
    26893 
    26894 > hide #!6 models
    26895 
    26896 > show #!6 models
    26897 
    26898 > hide #!6 models
    26899 
    26900 > close #6
    26901 
    26902 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    26903 > (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
    26904 > includeMaps true
    26905 
    26906 ——— End of log from Sat Mar 12 14:58:51 2022 ———
    26907 
    26908 opened ChimeraX session 
    26909 
    26910 > show #!1 models
    26911 
    26912 > hide #!1 models
    26913 
    26914 > open "/Users/alvinchew/Library/CloudStorage/OneDrive-
    26915 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P39_J166_002_volume_map_sharp
    26916 > (1).mrc"
    26917 
    26918 Opened cryosparc_P39_J166_002_volume_map_sharp (1).mrc as #6, grid size
    26919 416,416,416, pixel 0.85, shown at level 0.0339, step 2, values float32 
    26920 
    26921 > volume #6 level 0.05868
    26922 
    26923 > volume #6 step 1
    26924 
    26925 > ui mousemode right "translate selected models"
    26926 
    26927 > show #!7 models
    26928 
    26929 > hide #!7 models
    26930 
    26931 > show #9 models
    26932 
    26933 > hide #9 models
    26934 
    26935 > select #6
    26936 
    26937 2 models selected 
    26938 
    26939 > view matrix models #6,1,0,0,1.4767,0,1,0,-0.11126,0,0,1,17.894
    26940 
    26941 > view matrix models #6,1,0,0,2.5835,0,1,0,15.467,0,0,1,19.701
    26942 
    26943 > ui mousemode right "rotate selected models"
    26944 
    26945 > view matrix models
    26946 > #6,0.077918,0.99542,-0.055373,-3.5895,-0.96552,0.089183,0.24459,303.08,0.24841,0.034406,0.96804,-24.193
    26947 
    26948 > view matrix models
    26949 > #6,-0.62577,0.77732,-0.06471,158.15,-0.76968,-0.62881,-0.1104,452.92,-0.12651,-0.019279,0.99178,46.339
    26950 
    26951 > view matrix models
    26952 > #6,-0.49195,0.83765,-0.23731,152.38,-0.80175,-0.32963,0.49855,307.08,0.33939,0.43553,0.83375,-88.641
    26953 
    26954 > view matrix models
    26955 > #6,-0.43603,0.58765,-0.68157,258.71,-0.82618,0.03888,0.56206,236.26,0.3568,0.80818,0.46855,-97.873
    26956 
    26957 > view matrix models
    26958 > #6,0.17544,0.72595,-0.66499,125.79,-0.86837,0.43236,0.24289,226.23,0.46384,0.53485,0.70625,-106.96
    26959 
    26960 > view matrix models
    26961 > #6,-0.010663,0.39041,-0.92058,258.46,-0.28789,0.88046,0.37672,25.213,0.95761,0.26904,0.103,-47.908
    26962 
    26963 > ui mousemode right "translate selected models"
    26964 
    26965 > view matrix models
    26966 > #6,-0.010663,0.39041,-0.92058,281.12,-0.28789,0.88046,0.37672,26.602,0.95761,0.26904,0.103,-46.122
    26967 
    26968 > ui mousemode right "rotate selected models"
    26969 
    26970 > view matrix models
    26971 > #6,0.14635,0.34874,-0.92572,262.07,-0.39341,0.87913,0.26899,62.599,0.90764,0.32483,0.26586,-73.695
    26972 
    26973 > view matrix models
    26974 > #6,0.12836,0.25158,-0.95929,287.7,-0.38687,0.90336,0.18515,70.814,0.91316,0.34735,0.21329,-70.077
    26975 
    26976 > view matrix models
    26977 > #6,0.14119,0.15753,-0.97737,304.94,-0.41649,0.90509,0.085709,91.778,0.89811,0.39496,0.1934,-72.61
    26978 
    26979 > view matrix models
    26980 > #6,0.16148,0.39933,-0.90248,246.79,-0.45122,0.84317,0.29235,75.141,0.87768,0.36001,0.31634,-82.878
    26981 
    26982 > view matrix models
    26983 > #6,0.26156,0.1615,-0.95158,279.21,-0.12782,0.98301,0.1317,20.613,0.95669,0.087181,0.27776,-42.368
    26984 
    26985 > ui mousemode right "translate selected models"
    26986 
    26987 > view matrix models
    26988 > #6,0.26156,0.1615,-0.95158,282.66,-0.12782,0.98301,0.1317,9.0483,0.95669,0.087181,0.27776,-38.201
    26989 
    26990 > ui mousemode right "rotate selected models"
    26991 
    26992 > view matrix models
    26993 > #6,0.13471,0.17399,-0.97549,306.32,-0.19051,0.97064,0.14682,19.629,0.9724,0.16606,0.1639,-36.307
    26994 
    26995 > view matrix models
    26996 > #6,0.1878,0.10849,-0.9762,308.75,-0.44957,0.89315,0.012769,99.878,0.87328,0.43647,0.21651,-75.185
    26997 
    26998 > view matrix models
    26999 > #6,0.28328,0.3407,-0.89648,238.47,-0.3572,0.905,0.23106,46.37,0.89003,0.25476,0.37807,-72.377
    27000 
    27001 > volume #6 level 0.169
    27002 
    27003 > volume #6 level 0.05336
    27004 
    27005 > ui tool show "Fit in Map"
    27006 
    27007 Fit map cryosparc_P39_J166_002_volume_map_sharp (1).mrc in map
    27008 cryosparc_P47_J20_004_volume_map_sharp.mrc using 331401 points 
    27009 correlation = 0.898, correlation about mean = 0.6711, overlap = 6198 
    27010 steps = 152, shift = 5.34, angle = 16.7 degrees 
    27011  
    27012 Position of cryosparc_P39_J166_002_volume_map_sharp (1).mrc (#6) relative to
    27013 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    27014 Matrix rotation and translation 
    27015 -0.92297785 -0.38455624 0.01511101 379.01804384 
    27016 -0.38212566 0.91106400 -0.15473309 83.70405585 
    27017 0.04573648 -0.14858952 -0.98784072 344.43723548 
    27018 Axis 0.19609203 -0.97751177 0.07757998 
    27019 Axis point 196.53062877 0.00000000 177.04366349 
    27020 Rotation angle (degrees) 179.10242404 
    27021 Shift along axis 19.22215351 
    27022  
    27023 
    27024 > volume #6 level 0.05037
    27025 
    27026 > volume #6 level 0.03372
    27027 
    27028 > volume #6 level 0.02603
    27029 
    27030 > volume #2 level 0.1649
    27031 
    27032 > volume #2 level 0.1496
    27033 
    27034 > show #9 models
    27035 
    27036 > volume #6 color #bf9d9e
    27037 
    27038 > volume #6 color #bf9d9e57
    27039 
    27040 > volume #6 level 0.05379
    27041 
    27042 > volume #6 level 0.06874
    27043 
    27044 > volume #2 level 0.1649
    27045 
    27046 > volume #2 level 0.17
    27047 
    27048 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    27049 > University/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig4_E2.png"
    27050 > width 1326 height 850 supersample 3 transparentBackground true
    27051 
    27052 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27053 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220125_NTU-K2_NS1-WT_Fab/cryosparc_P36_J32_002_volume_map_sharp.mrc
    27054 
    27055 Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
    27056 416,416,416, pixel 0.85, shown at level 0.0324, step 2, values float32 
    27057 
    27058 > select #8
    27059 
    27060 2 models selected 
    27061 
    27062 > view matrix models
    27063 > #8,0.93452,-0.21005,-0.2873,102.16,-0.33903,-0.27981,-0.8982,451.28,0.10828,0.93679,-0.3327,69.288
    27064 
    27065 > view matrix models
    27066 > #8,-0.43794,-0.41147,0.79931,176.41,-0.88911,0.32976,-0.31738,334,-0.13299,-0.84967,-0.51026,455.34
    27067 
    27068 > view matrix models
    27069 > #8,-0.13025,-0.70515,0.697,191.9,-0.98813,0.15007,-0.032822,329.17,-0.081457,-0.693,-0.71632,457.81
    27070 
    27071 > close #8
    27072 
    27073 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27074 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220125_NTU-K2_NS1-WT_Fab/cryosparc_P36_J32_002_volume_map_sharp.mrc
    27075 
    27076 Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
    27077 416,416,416, pixel 0.85, shown at level 0.0324, step 2, values float32 
    27078 
    27079 > color #8 #fff5c5 models transparency 0
    27080 
    27081 > select #8
    27082 
    27083 2 models selected 
    27084 
    27085 > view matrix models
    27086 > #8,-0.37477,-0.5067,0.77641,186,-0.92653,0.23447,-0.29422,352.81,-0.032965,-0.82963,-0.55734,442.95
    27087 
    27088 > view matrix models
    27089 > #8,-0.40741,-0.58403,0.70209,219.21,-0.91262,0.28892,-0.28924,339.96,-0.033924,-0.75857,-0.6507,448.38
    27090 
    27091 > view matrix models
    27092 > #8,-0.26337,-0.46915,0.84293,147.17,-0.95679,0.23865,-0.16612,333.34,-0.12323,-0.85026,-0.51174,453.98
    27093 
    27094 > ui mousemode right zoom
    27095 
    27096 > ui mousemode right "translate selected models"
    27097 
    27098 > view matrix models
    27099 > #8,-0.26337,-0.46915,0.84293,164.19,-0.95679,0.23865,-0.16612,339.86,-0.12323,-0.85026,-0.51174,459.4
    27100 
    27101 > color #8 #fff5c592 models
    27102 
    27103 > color #8 #fff5c591 models
    27104 
    27105 > view matrix models
    27106 > #8,-0.26337,-0.46915,0.84293,164.75,-0.95679,0.23865,-0.16612,339.53,-0.12323,-0.85026,-0.51174,460.75
    27107 
    27108 > ui mousemode right "rotate selected models"
    27109 
    27110 > view matrix models
    27111 > #8,-0.30728,0.18959,0.93254,41.475,-0.40778,0.85919,-0.30905,161.27,-0.85982,-0.47524,-0.1867,465.45
    27112 
    27113 > view matrix models
    27114 > #8,-0.48566,0.40603,0.77413,65.486,-0.39669,0.68678,-0.60908,245.69,-0.77896,-0.60289,-0.17248,470.53
    27115 
    27116 > view matrix models
    27117 > #8,-0.49722,0.30467,0.81237,77.911,-0.61559,0.53594,-0.57777,304.85,-0.61141,-0.78737,-0.078928,455.12
    27118 
    27119 > view matrix models
    27120 > #8,0.06302,-0.34884,0.93506,68.532,-0.69818,-0.6849,-0.20846,461.65,0.71314,-0.63971,-0.28672,233.22
    27121 
    27122 > view matrix models
    27123 > #8,0.26213,-0.7558,0.60005,166.78,-0.96461,-0.18676,0.18614,348.34,-0.028616,-0.62761,-0.778,455.47
    27124 
    27125 > view matrix models
    27126 > #8,-0.37994,0.023033,0.92472,84.739,-0.51716,0.82356,-0.233,172.57,-0.76693,-0.56676,-0.301,486.33
    27127 
    27128 > view matrix models
    27129 > #8,0.19338,0.23275,0.95312,-58.871,-0.72187,0.69166,-0.022445,192.18,-0.66446,-0.68369,0.30177,374.89
    27130 
    27131 > view matrix models
    27132 > #8,-0.21084,0.47884,0.85221,-10.689,-0.12039,0.85245,-0.50876,148.96,-0.97008,-0.20987,-0.12208,426.87
    27133 
    27134 > view matrix models
    27135 > #8,-0.41196,0.43496,0.80069,42.367,-0.11525,0.84679,-0.51929,151.02,-0.90389,-0.30621,-0.29871,465.07
    27136 
    27137 > view matrix models
    27138 > #8,-0.47775,0.38326,0.79049,64.945,-0.089881,0.87377,-0.47796,134.05,-0.87389,-0.29939,-0.38299,474.43
    27139 
    27140 > ui mousemode right "translate selected models"
    27141 
    27142 > view matrix models
    27143 > #8,-0.47775,0.38326,0.79049,62.298,-0.089881,0.87377,-0.47796,139.19,-0.87389,-0.29939,-0.38299,469.27
    27144 
    27145 > ui mousemode right "rotate selected models"
    27146 
    27147 [Repeated 1 time(s)]
    27148 
    27149 > view matrix models
    27150 > #8,-0.62887,0.14228,0.76438,135.85,-0.3807,0.80086,-0.46227,200.57,-0.67794,-0.5817,-0.44947,495.91
    27151 
    27152 > view matrix models
    27153 > #8,-0.68532,0.11195,0.71959,159.58,-0.34754,0.81805,-0.45826,190.94,-0.63997,-0.56414,-0.52172,499.72
    27154 
    27155 > view matrix models
    27156 > #8,-0.62799,-0.10151,0.77157,176.61,-0.55751,0.75043,-0.35503,220.55,-0.54297,-0.65311,-0.52785,499.06
    27157 
    27158 > ui tool show "Fit in Map"
    27159 
    27160 Fit map cryosparc_P36_J32_002_volume_map_sharp.mrc in map
    27161 cryosparc_P47_J20_004_volume_map_sharp.mrc using 89910 points 
    27162 correlation = 0.5947, correlation about mean = 0.2353, overlap = 907.9 
    27163 steps = 260, shift = 8.79, angle = 25 degrees 
    27164  
    27165 Position of cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) relative to
    27166 cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates: 
    27167 Matrix rotation and translation 
    27168 0.83017657 0.55542318 0.04808244 -106.08230735 
    27169 -0.55722739 0.82397862 0.10274640 83.33490981 
    27170 0.01744883 -0.11209051 0.99354477 -6.27353855 
    27171 Axis -0.18951476 0.02702292 -0.98150594 
    27172 Axis point 82.90354713 206.61275632 0.00000000 
    27173 Rotation angle (degrees) 34.52792807 
    27174 Shift along axis 28.51363138 
    27175  
    27176 
    27177 > volume #8 level 0.03877
    27178 
    27179 > volume #8 step 1
    27180 
    27181 > volume #8 level 0.05098
    27182 
    27183 > volume #8 level 0.08193
    27184 
    27185 > volume #8 level 0.07541
    27186 
    27187 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    27188 > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-23_NS1wt-Ab-Fab-
    27189 > ApoAI_hdl.cxs" includeMaps true
    27190 
    27191 ——— End of log from Thu Mar 24 12:02:48 2022 ———
    27192 
    27193 opened ChimeraX session 
    27194 
    27195 > ui tool show "Volume Viewer"
    27196 
    27197 > show #!1 models
    27198 
    27199 > close #1
    27200 
    27201 > show #!2 models
    27202 
    27203 > hide #!8 models
    27204 
    27205 > show #!8 models
    27206 
    27207 > hide #!8 models
    27208 
    27209 > show #!8 models
    27210 
    27211 > hide #!2 models
    27212 
    27213 > show #!2 models
    27214 
    27215 > rename #2 sNS1wt-Ab562.mrc
    27216 
    27217 > show #!6 models
    27218 
    27219 > hide #!6 models
    27220 
    27221 > show #!6 models
    27222 
    27223 > hide #!6 models
    27224 
    27225 > hide #!2 models
    27226 
    27227 > hide #3 models
    27228 
    27229 > show #3 models
    27230 
    27231 > hide #4 models
    27232 
    27233 > show #4 models
    27234 
    27235 > show #5 models
    27236 
    27237 > hide #5 models
    27238 
    27239 > show #!6 models
    27240 
    27241 > hide #!6 models
    27242 
    27243 > show #!6 models
    27244 
    27245 > show #!2 models
    27246 
    27247 > hide #!2 models
    27248 
    27249 > show #!2 models
    27250 
    27251 > hide #!2 models
    27252 
    27253 > hide #!8 models
    27254 
    27255 > volume #6 level 0.0595
    27256 
    27257 > show #!2 models
    27258 
    27259 > hide #!6 models
    27260 
    27261 > show #!6 models
    27262 
    27263 > hide #!2 models
    27264 
    27265 > show #!2 models
    27266 
    27267 > close #6
    27268 
    27269 > show #!7 models
    27270 
    27271 > hide #!2 models
    27272 
    27273 > show #!2 models
    27274 
    27275 > close #7
    27276 
    27277 > show #5 models
    27278 
    27279 > show #!8 models
    27280 
    27281 > hide #9 models
    27282 
    27283 > show #9 models
    27284 
    27285 > hide #!2 models
    27286 
    27287 > show #!2 models
    27288 
    27289 > hide #!2 models
    27290 
    27291 > hide #3 models
    27292 
    27293 > show #3 models
    27294 
    27295 > hide #3 models
    27296 
    27297 > hide #4 models
    27298 
    27299 > show #4 models
    27300 
    27301 > hide #4 models
    27302 
    27303 > hide #5 models
    27304 
    27305 > show #5 models
    27306 
    27307 > hide #!8 models
    27308 
    27309 > show #!8 models
    27310 
    27311 > hide #9 models
    27312 
    27313 > select add #5
    27314 
    27315 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    27316 
    27317 > ui mousemode right select
    27318 
    27319 > ui mousemode right zoom
    27320 
    27321 > ui mousemode right "translate selected models"
    27322 
    27323 > view matrix models
    27324 > #5,0.911,-0.19028,-0.36588,158.81,-0.385,-0.71042,-0.58914,511.26,-0.14783,0.67757,-0.72045,241.26
    27325 
    27326 > ui mousemode right "rotate selected models"
    27327 
    27328 > view matrix models
    27329 > #5,0.033091,0.22459,0.97389,-84.329,0.17148,0.9587,-0.22691,18.38,-0.98463,0.17451,-0.006788,310.39
    27330 
    27331 > ui mousemode right "translate selected models"
    27332 
    27333 > view matrix models
    27334 > #5,0.033091,0.22459,0.97389,-41.613,0.17148,0.9587,-0.22691,17.858,-0.98463,0.17451,-0.006788,323.69
    27335 
    27336 > ui mousemode right "rotate selected models"
    27337 
    27338 > view matrix models
    27339 > #5,-0.027159,0.41704,0.90848,-51.291,0.63529,0.70888,-0.30642,2.4644,-0.77179,0.56883,-0.2842,279.48
    27340 
    27341 > view matrix models
    27342 > #5,-0.080191,0.31482,0.94576,-31.96,0.72243,0.67208,-0.16247,-40.126,-0.68678,0.67022,-0.28133,245.19
    27343 
    27344 > view matrix models
    27345 > #5,-0.13135,0.33964,0.93134,-24.234,0.71868,0.67973,-0.14652,-44.687,-0.68283,0.65008,-0.33337,260.62
    27346 
    27347 > view matrix models
    27348 > #5,-0.11889,0.37005,0.92137,-29.677,0.7114,0.6791,-0.18095,-35.108,-0.69266,0.63395,-0.34399,267.86
    27349 
    27350 > view matrix models
    27351 > #5,0.045939,0.59116,0.80525,-71.763,0.70283,0.55371,-0.44659,52.881,-0.70988,0.58646,-0.39004,290.63
    27352 
    27353 > view matrix models
    27354 > #5,0.084841,0.56745,0.81902,-77.41,0.67501,0.57189,-0.46615,59,-0.73291,0.5924,-0.33452,280.32
    27355 
    27356 > view matrix models
    27357 > #5,-0.13391,0.55975,0.81777,-37.622,0.55097,0.72796,-0.40805,37.78,-0.82371,0.39592,-0.40589,349.58
    27358 
    27359 > view matrix models
    27360 > #5,-0.09912,0.51183,0.85335,-43.247,0.59183,0.71973,-0.36294,21.462,-0.79994,0.46907,-0.37425,324.33
    27361 
    27362 > view matrix models
    27363 > #5,-0.11178,0.47533,0.87268,-38.868,0.59167,0.73739,-0.32585,9.3844,-0.79839,0.47992,-0.36367,319.53
    27364 
    27365 > view matrix models
    27366 > #5,-0.22153,0.44542,0.86748,-12.986,0.53956,0.79699,-0.27144,-5.5629,-0.81228,0.40793,-0.41688,347.98
    27367 
    27368 > ui mousemode right "translate selected models"
    27369 
    27370 > view matrix models
    27371 > #5,-0.22153,0.44542,0.86748,-14.111,0.53956,0.79699,-0.27144,-5.3645,-0.81228,0.40793,-0.41688,348.49
    27372 
    27373 > select add #8
    27374 
    27375 3401 atoms, 3493 bonds, 442 residues, 3 models selected 
    27376 
    27377 > fitmap #5 inMap #8
    27378 
    27379 Fit molecule F562b.pdb (#5) to map cryosparc_P36_J32_002_volume_map_sharp.mrc
    27380 (#8) using 3401 atoms 
    27381 average map value = 0.09851, steps = 108 
    27382 shifted from previous position = 1.67 
    27383 rotated from previous position = 17.3 degrees 
    27384 atoms outside contour = 1366, contour level = 0.075413 
    27385  
    27386 Position of F562b.pdb (#5) relative to
    27387 cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) coordinates: 
    27388 Matrix rotation and translation 
    27389 0.45238682 -0.88366144 -0.12036870 287.11798101 
    27390 0.88783684 0.43349946 0.15435016 -99.22400613 
    27391 -0.08421352 -0.17669374 0.98065662 40.64404116 
    27392 Axis -0.18365545 -0.02005805 0.98278601 
    27393 Axis point 227.81128239 181.49795933 0.00000000 
    27394 Rotation angle (degrees) 64.32464577 
    27395 Shift along axis -10.79614671 
    27396  
    27397 
    27398 > fitmap #5 inMap #8
    27399 
    27400 Fit molecule F562b.pdb (#5) to map cryosparc_P36_J32_002_volume_map_sharp.mrc
    27401 (#8) using 3401 atoms 
    27402 average map value = 0.09851, steps = 44 
    27403 shifted from previous position = 0.00416 
    27404 rotated from previous position = 0.0187 degrees 
    27405 atoms outside contour = 1367, contour level = 0.075413 
    27406  
    27407 Position of F562b.pdb (#5) relative to
    27408 cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) coordinates: 
    27409 Matrix rotation and translation 
    27410 0.45231009 -0.88373711 -0.12010123 287.08058767 
    27411 0.88785087 0.43341968 0.15449342 -99.24674165 
    27412 -0.08447733 -0.17651091 0.98066686 40.65823137 
    27413 Axis -0.18362633 -0.01976254 0.98279744 
    27414 Axis point 227.80088638 181.42728547 0.00000000 
    27415 Rotation angle (degrees) 64.32929481 
    27416 Shift along axis -10.79538196 
    27417  
    27418 
    27419 > show #3 models
    27420 
    27421 > hide #3 models
    27422 
    27423 > show #3 models
    27424 
    27425 > color #8 #d7fef991 models
    27426 
    27427 > color #8 #c5fef791 models
    27428 
    27429 > color #8 #c4fbfe91 models
    27430 
    27431 > color #8 #c3fef791 models
    27432 
    27433 > rename #8 sNS1wt-Fab562.mrc
    27434 
    27435 > select subtract #5
    27436 
    27437 2 models selected 
    27438 
    27439 > select subtract #8
    27440 
    27441 Nothing selected 
    27442 
    27443 > show #4 models
    27444 
    27445 > show #!2 models
    27446 
    27447 > rename #4 F562a-FL.pdb
    27448 
    27449 > show #9 models
    27450 
    27451 > color #2 #c4a1924d models
    27452 
    27453 [Repeated 1 time(s)]
    27454 
    27455 > hide #!2 models
    27456 
    27457 > hide #4 models
    27458 
    27459 > ui mousemode right zoom
    27460 
    27461 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    27462 > (1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM Maps_docked
    27463 > structures/EDEN2 sNS1wt-Fab562/20220323_NS1wt-Ab-Fab-ApoAI_hdl.cxs"
    27464 > includeMaps true
    27465 
    27466 ——— End of log from Sat Nov 19 10:30:44 2022 ———
    27467 
    27468 opened ChimeraX session 
    27469 
    27470 > volume #8 color #dbfdf891
    27471 
    27472 > volume #8 color #c5fdf891
    27473 
    27474 > volume #8 color #c5fdf849
    27475 
    27476 > volume #8 color #c5fdf84c
    27477 
    27478 > select add #3
    27479 
    27480 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    27481 
    27482 > select subtract #3
    27483 
    27484 Nothing selected 
    27485 
    27486 > rename #3 eden2ns1.pdb
    27487 
    27488 > ui tool show "Show Sequence Viewer"
    27489 
    27490 > sequence chain #3/B #3/C
    27491 
    27492 Alignment identifier is 1 
    27493 
    27494 > select #3/B-C:2
    27495 
    27496 12 atoms, 10 bonds, 2 residues, 1 model selected 
    27497 
    27498 > select #3/B-C:2-75
    27499 
    27500 1174 atoms, 1200 bonds, 148 residues, 1 model selected 
    27501 
    27502 > select #3/B-C:172
    27503 
    27504 18 atoms, 16 bonds, 2 residues, 1 model selected 
    27505 
    27506 > select #3/B-C:172-178
    27507 
    27508 118 atoms, 116 bonds, 14 residues, 1 model selected 
    27509 
    27510 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27511 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    27512 
    27513 Line 8 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr is either
    27514 not of the form 'name: value' or is missing initial tab 
    27515 
    27516 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27517 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    27518 
    27519 Data line 8 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr not of
    27520 the form: <tab> atomspec <tab> value 
    27521 
    27522 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27523 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    27524 
    27525 Line 43 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr is either
    27526 not of the form 'name: value' or is missing initial tab 
    27527 
    27528 > color #3/A-B dimgray
    27529 
    27530 > hide #3 models
    27531 
    27532 > show #3 models
    27533 
    27534 > select add #3
    27535 
    27536 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    27537 
    27538 > select subtract #3
    27539 
    27540 Nothing selected 
    27541 
    27542 > select add #3
    27543 
    27544 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    27545 
    27546 > color #3 dimgray
    27547 
    27548 > ui tool show "Change Chain IDs"
    27549 
    27550 > changechains C A
    27551 
    27552 Proposed chain ID change would produce multiple residues with the samechain-
    27553 ID/number/insertion-code combo (A/1/) 
    27554 
    27555 > changechains C A
    27556 
    27557 Proposed chain ID change would produce multiple residues with the samechain-
    27558 ID/number/insertion-code combo (A/1/) 
    27559 
    27560 > changechains sel C A
    27561 
    27562 Chain IDs of 352 residues changed 
    27563 
    27564 > ui tool show "Show Sequence Viewer"
    27565 
    27566 > sequence chain #3/B #3/A
    27567 
    27568 Alignment identifier is 1 
    27569 
    27570 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27571 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    27572 
    27573 Summary of feedback from opening
    27574 /Users/alvinchew/Library/CloudStorage/OneDrive-
    27575 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    27576 --- 
    27577 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 1097
    27578 residues using match mode: any 
    27579  
    27580 
    27581 > ui tool show "Show Sequence Viewer"
    27582 
    27583 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27584 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    27585 
    27586 Summary of feedback from opening
    27587 /Users/alvinchew/Library/CloudStorage/OneDrive-
    27588 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    27589 --- 
    27590 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 1097
    27591 residues using match mode: any 
    27592  
    27593 
    27594 > byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key true
    27595 > bluered noValueColor gray
    27596 
    27597 Unknown command: byattribute relative_deuterium_uptake_NS1c_10min
    27598 #3/A-B:174-361 key true bluered noValueColor gray 
    27599 
    27600 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27601 > true bluered noValueColor gray
    27602 
    27603 Expected a keyword 
    27604 
    27605 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27606 > true palette bluered noValueColor gray
    27607 
    27608 > key blue-white-red :-0.98 :-0.47 :0.04 showTool true
    27609 
    27610 > ui mousemode right "color key"
    27611 
    27612 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27613 -0.98 to 0.04 
    27614 
    27615 > key blue-white-red :-0.98 :-0.47 :1
    27616 
    27617 > key blue-white-red :-2 :-0.47 :1
    27618 
    27619 > key blue-white-red :-2 :0 :1
    27620 
    27621 > hide #5 models
    27622 
    27623 > hide #9 models
    27624 
    27625 > hide #!8 models
    27626 
    27627 > hide #8.1 models
    27628 
    27629 > key pos 0.636108,0.370379 size 0.0013699,0.146465
    27630 
    27631 > undo
    27632 
    27633 > key pos 0.479592,0.196551 size 0.329083,0.0401247
    27634 
    27635 > ui mousemode right zoom
    27636 
    27637 > select subtract #3
    27638 
    27639 Nothing selected 
    27640 
    27641 > ui mousemode right "translate selected models"
    27642 
    27643 > ui mousemode right zoom
    27644 
    27645 > select #3/B,A:212-213
    27646 
    27647 34 atoms, 32 bonds, 4 residues, 1 model selected 
    27648 
    27649 > select #3/B,A:212-217
    27650 
    27651 96 atoms, 96 bonds, 12 residues, 1 model selected 
    27652 
    27653 > select #3/B,A:216
    27654 
    27655 12 atoms, 10 bonds, 2 residues, 1 model selected 
    27656 
    27657 > select #3/B,A:212-216
    27658 
    27659 74 atoms, 72 bonds, 10 residues, 1 model selected 
    27660 
    27661 > select #3/B,A:211
    27662 
    27663 18 atoms, 16 bonds, 2 residues, 1 model selected 
    27664 
    27665 > select #3/B,A:211-216
    27666 
    27667 92 atoms, 90 bonds, 12 residues, 1 model selected 
    27668 
    27669 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27670 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    27671 
    27672 Summary of feedback from opening
    27673 /Users/alvinchew/Library/CloudStorage/OneDrive-
    27674 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    27675 --- 
    27676 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 984
    27677 residues using match mode: any 
    27678  
    27679 
    27680 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27681 > true palette bluered noValueColor gray
    27682 
    27683 > key blue-white-red :-0.98 :-0.47 :0.04 showTool true
    27684 
    27685 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27686 -0.98 to 0.04 
    27687 
    27688 > undo
    27689 
    27690 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27691 > true palette bluered noValueColor gray
    27692 
    27693 > key blue-white-red :-0.98 :-0.47 :0.04 showTool true
    27694 
    27695 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27696 -0.98 to 0.04 
    27697 
    27698 > undo
    27699 
    27700 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27701 > true palette bluered noValueColor grey
    27702 
    27703 > key blue-white-red :-0.98 :-0.47 :0.04 showTool true
    27704 
    27705 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27706 -0.98 to 0.04 
    27707 
    27708 > ui tool show "Selection Inspector"
    27709 
    27710 > toolshed show
    27711 
    27712 > view sel
    27713 
    27714 > key blue-white-red :-0.98 :-0.47 :1
    27715 
    27716 > key blue-white-red :- :-0.47 :1
    27717 
    27718 > key blue-white-red :-2 :-0.47 :1
    27719 
    27720 > key colorTreatment distinct
    27721 
    27722 > key colorTreatment blended
    27723 
    27724 > attributes available
    27725 
    27726 Unknown command: attributes available 
    27727 
    27728 > info attributes
    27729 
    27730 Expected a models specifier or a keyword 
    27731 
    27732 > info resattr
    27733 
    27734 resattr alt_loc 
    27735 resattr alt_locs 
    27736 resattr atoms 
    27737 resattr atomspec 
    27738 resattr center 
    27739 resattr chain 
    27740 resattr chain_id 
    27741 resattr chi1 
    27742 resattr chi2 
    27743 resattr chi3 
    27744 resattr chi4 
    27745 resattr cpp_pointer 
    27746 resattr custom_attrs 
    27747 resattr deleted 
    27748 resattr description 
    27749 resattr has_custom_attrs 
    27750 resattr insertion_code 
    27751 resattr is_helix 
    27752 resattr is_strand 
    27753 resattr label_one_letter_code 
    27754 resattr label_specifier 
    27755 resattr mmcif_chain_id 
    27756 resattr name 
    27757 resattr neighbors 
    27758 resattr num_atoms 
    27759 resattr number 
    27760 resattr omega 
    27761 resattr one_letter_code 
    27762 resattr phi 
    27763 resattr polymer_type 
    27764 resattr principal_atom 
    27765 resattr psi 
    27766 resattr relative_deuterium_uptake_NS1c_10min 
    27767 resattr ribbon_adjust 
    27768 resattr ribbon_color 
    27769 resattr ribbon_display 
    27770 resattr ribbon_hide_backbone 
    27771 resattr ring_color 
    27772 resattr ring_display 
    27773 resattr selected 
    27774 resattr seq_conservation 
    27775 resattr session 
    27776 resattr ss_id 
    27777 resattr ss_type 
    27778 resattr standard_aa_name 
    27779 resattr structure 
    27780 resattr sym_chi1 
    27781 resattr sym_chi2 
    27782 resattr sym_chi3 
    27783 resattr sym_chi4 
    27784 resattr thin_rings 
    27785 
    27786 > select #3/B,A:181
    27787 
    27788 12 atoms, 10 bonds, 2 residues, 1 model selected 
    27789 
    27790 > select #3/B,A:181-198
    27791 
    27792 268 atoms, 268 bonds, 36 residues, 1 model selected 
    27793 
    27794 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27795 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    27796 
    27797 Summary of feedback from opening
    27798 /Users/alvinchew/Library/CloudStorage/OneDrive-
    27799 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    27800 --- 
    27801 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
    27802 residues using match mode: any 
    27803  
    27804 
    27805 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27806 > true palette bluered noValueColor grey
    27807 
    27808 > key blue-white-red :-0.98 :-0.47 :0.04 showTool true
    27809 
    27810 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27811 -0.98 to 0.04 
    27812 
    27813 > select #3/B,A:299-300
    27814 
    27815 36 atoms, 34 bonds, 4 residues, 1 model selected 
    27816 
    27817 > select #3/B,A:299-301
    27818 
    27819 50 atoms, 48 bonds, 6 residues, 1 model selected 
    27820 
    27821 > key red-white-blue :0.04 :-0.47 :-0.98
    27822 
    27823 > key blue-white-red :-0.98 :-0.47 :0.04
    27824 
    27825 > key red-white-blue :0.04 :-0.47 :-0.98
    27826 
    27827 > key blue-white-red :-0.98 :-0.47 :0.04
    27828 
    27829 > key blue-white-red :- :-0.47 :0.04
    27830 
    27831 > key blue-white-red :-2 :-0.47 :0.04
    27832 
    27833 > key blue-white-red :-2 :-0.47 :1
    27834 
    27835 > key blue-white-red :-2 :0 :1
    27836 
    27837 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27838 > true palette bluered range -2:1 noValueColor grey
    27839 
    27840 Invalid "range" argument: Expected some numbers or 'full' 
    27841 
    27842 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27843 > true palette bluered range -2,1 noValueColor grey
    27844 
    27845 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27846 
    27847 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27848 -0.98 to 0.04 
    27849 
    27850 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27851 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    27852 
    27853 Summary of feedback from opening
    27854 /Users/alvinchew/Library/CloudStorage/OneDrive-
    27855 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    27856 --- 
    27857 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
    27858 residues using match mode: any 
    27859  
    27860 
    27861 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27862 > true palette bluered range -2,1 noValueColor grey
    27863 
    27864 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27865 
    27866 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27867 -1.98 to 0.04 
    27868 
    27869 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27870 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
    27871 
    27872 Summary of feedback from opening
    27873 /Users/alvinchew/Library/CloudStorage/OneDrive-
    27874 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr 
    27875 --- 
    27876 note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
    27877 residues using match mode: any 
    27878  
    27879 
    27880 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27881 > true palette bluered range -2,1 noValueColor grey
    27882 
    27883 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27884 
    27885 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27886 -1.98 to 0.04 
    27887 
    27888 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27889 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
    27890 
    27891 Summary of feedback from opening
    27892 /Users/alvinchew/Library/CloudStorage/OneDrive-
    27893 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr 
    27894 --- 
    27895 note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
    27896 residues using match mode: any 
    27897  
    27898 
    27899 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27900 > true palette bluered range -2,1 noValueColor grey
    27901 
    27902 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27903 
    27904 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27905 -1.98 to 0.04 
    27906 
    27907 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27908 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    27909 
    27910 Summary of feedback from opening
    27911 /Users/alvinchew/Library/CloudStorage/OneDrive-
    27912 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    27913 --- 
    27914 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
    27915 residues using match mode: any 
    27916  
    27917 
    27918 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27919 > true palette bluered range -2,1 noValueColor grey
    27920 
    27921 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27922 
    27923 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27924 -1.98 to 0.04 
    27925 
    27926 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27927 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
    27928 
    27929 Summary of feedback from opening
    27930 /Users/alvinchew/Library/CloudStorage/OneDrive-
    27931 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr 
    27932 --- 
    27933 note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 866
    27934 residues using match mode: any 
    27935  
    27936 
    27937 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27938 > true palette bluered range -2,1 noValueColor grey
    27939 
    27940 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27941 
    27942 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27943 -1.98 to 0.04 
    27944 
    27945 > undo
    27946 
    27947 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27948 > true palette bluered range -2,1 noValueColor grey
    27949 
    27950 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27951 
    27952 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27953 -1.98 to 0.04 
    27954 
    27955 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    27956 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
    27957 
    27958 Summary of feedback from opening
    27959 /Users/alvinchew/Library/CloudStorage/OneDrive-
    27960 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr 
    27961 --- 
    27962 note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
    27963 residues using match mode: any 
    27964  
    27965 
    27966 > color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27967 > true palette bluered range -2,1 noValueColor grey
    27968 
    27969 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27970 
    27971 2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
    27972 -1.98 to 0.04 
    27973 
    27974 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27975 > true palette bluered range -2,1 noValueColor grey
    27976 
    27977 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27978 
    27979 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    27980 -1.03 to 0 
    27981 
    27982 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27983 > true palette bluered range -2,1 noValueColor grey
    27984 
    27985 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27986 
    27987 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    27988 -1.03 to 0 
    27989 
    27990 > undo
    27991 
    27992 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    27993 > true palette bluered range -2,1 noValueColor grey
    27994 
    27995 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    27996 
    27997 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    27998 -1.03 to 0 
    27999 
    28000 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    28001 > true palette bluered range -2,1 noValueColor grey
    28002 
    28003 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    28004 
    28005 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    28006 -1.03 to 0 
    28007 
    28008 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    28009 > true palette bluered range -2,1 noValueColor grey
    28010 
    28011 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    28012 
    28013 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    28014 -1.03 to 0 
    28015 
    28016 > color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
    28017 > true palette bluered range -2,1 noValueColor grey
    28018 
    28019 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    28020 
    28021 2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
    28022 -1.03 to 0 
    28023 
    28024 > select #3/B,A:175
    28025 
    28026 18 atoms, 16 bonds, 2 residues, 1 model selected 
    28027 
    28028 > select #3/B,A:175-178
    28029 
    28030 60 atoms, 58 bonds, 8 residues, 1 model selected 
    28031 
    28032 > ui mousemode right translate
    28033 
    28034 > ui mousemode right zoom
    28035 
    28036 > select #3/B,A:172
    28037 
    28038 18 atoms, 16 bonds, 2 residues, 1 model selected 
    28039 
    28040 > select #3/B,A:172-174
    28041 
    28042 58 atoms, 56 bonds, 6 residues, 1 model selected 
    28043 
    28044 > select #3/B,A:174-175
    28045 
    28046 40 atoms, 38 bonds, 4 residues, 1 model selected 
    28047 
    28048 > select #3/B,A:174-178
    28049 
    28050 82 atoms, 80 bonds, 10 residues, 1 model selected 
    28051 
    28052 > ui tool show "Color Actions"
    28053 
    28054 > color sel #cbdbffff
    28055 
    28056 > color sel #c1d2ffff
    28057 
    28058 > color sel #c1d1ffff
    28059 
    28060 > color sel #c2d2ffff
    28061 
    28062 [Repeated 1 time(s)]
    28063 
    28064 > color sel #c3d3ffff
    28065 
    28066 > color sel #c4d3ffff
    28067 
    28068 > color sel #c4d4ffff
    28069 
    28070 > color sel #c4d5ffff
    28071 
    28072 > color sel #c5d6ffff
    28073 
    28074 > color sel #c5d5ffff
    28075 
    28076 > color sel #c4d4ffff
    28077 
    28078 > color sel #c4d3ffff
    28079 
    28080 [Repeated 1 time(s)]
    28081 
    28082 > color sel #c3d2ffff
    28083 
    28084 > color sel #c3d1ffff
    28085 
    28086 > color sel #c2d0ffff
    28087 
    28088 [Repeated 1 time(s)]
    28089 
    28090 > color sel #c1cfffff
    28091 
    28092 > color sel #c1ceffff
    28093 
    28094 > color sel #c1cdffff
    28095 
    28096 > color sel #c0cdffff
    28097 
    28098 > color sel #c0ccffff
    28099 
    28100 > color sel #c1cdffff
    28101 
    28102 [Repeated 1 time(s)]
    28103 
    28104 > color sel #c1ceffff
    28105 
    28106 > color sel #c2cfffff
    28107 
    28108 > color sel #b8c2ffff
    28109 
    28110 > color sel #aebdffff
    28111 
    28112 > select #3/B,A:179
    28113 
    28114 12 atoms, 10 bonds, 2 residues, 1 model selected 
    28115 
    28116 > select #3/B,A:179-187
    28117 
    28118 122 atoms, 120 bonds, 18 residues, 1 model selected 
    28119 
    28120 > color sel #c4cfffff
    28121 
    28122 > select #3/B,A:188
    28123 
    28124 16 atoms, 14 bonds, 2 residues, 1 model selected 
    28125 
    28126 > select #3/B,A:188-198
    28127 
    28128 174 atoms, 174 bonds, 22 residues, 1 model selected 
    28129 
    28130 > color sel #b1bbffff
    28131 
    28132 > select #3/B,A:199
    28133 
    28134 8 atoms, 6 bonds, 2 residues, 1 model selected 
    28135 
    28136 > select #3/B,A:199-200
    28137 
    28138 32 atoms, 32 bonds, 4 residues, 1 model selected 
    28139 
    28140 > color sel #99b0ffff
    28141 
    28142 > color sel #96baffff
    28143 
    28144 > color sel #92b4ffff
    28145 
    28146 > color sel #6a97ffff
    28147 
    28148 > select #3/B,A:201-202
    28149 
    28150 44 atoms, 46 bonds, 4 residues, 1 model selected 
    28151 
    28152 > select #3/B,A:201-211
    28153 
    28154 192 atoms, 198 bonds, 22 residues, 1 model selected 
    28155 
    28156 > color sel #91acffff
    28157 
    28158 > select #3/B,A:212
    28159 
    28160 16 atoms, 14 bonds, 2 residues, 1 model selected 
    28161 
    28162 > select #3/B,A:212-217
    28163 
    28164 96 atoms, 96 bonds, 12 residues, 1 model selected 
    28165 
    28166 > color sel #aabeffff
    28167 
    28168 > color sel #bfcfffff
    28169 
    28170 [Repeated 1 time(s)]
    28171 
    28172 > color sel #bfceffff
    28173 
    28174 > color sel #beceffff
    28175 
    28176 > color sel #becdffff
    28177 
    28178 > color sel #bdcdffff
    28179 
    28180 > select #3/B,A:218
    28181 
    28182 16 atoms, 14 bonds, 2 residues, 1 model selected 
    28183 
    28184 > select #3/B,A:218-219
    28185 
    28186 34 atoms, 32 bonds, 4 residues, 1 model selected 
    28187 
    28188 > color sel #adc4ffff
    28189 
    28190 > select #3/B,A:220
    28191 
    28192 14 atoms, 12 bonds, 2 residues, 1 model selected 
    28193 
    28194 > select #3/B,A:220-231
    28195 
    28196 198 atoms, 206 bonds, 24 residues, 1 model selected 
    28197 
    28198 > color sel #88a5ffff
    28199 
    28200 > color sel #83a2ffff
    28201 
    28202 > color sel #7fa0ffff
    28203 
    28204 > select #3/B,A:232
    28205 
    28206 28 atoms, 30 bonds, 2 residues, 1 model selected 
    28207 
    28208 > select #3/B,A:232-240
    28209 
    28210 142 atoms, 144 bonds, 18 residues, 1 model selected 
    28211 
    28212 > color sel #98b0ffff
    28213 
    28214 > select #3/B,A:231
    28215 
    28216 16 atoms, 14 bonds, 2 residues, 1 model selected 
    28217 
    28218 > select #3/B,A:220-231
    28219 
    28220 198 atoms, 206 bonds, 24 residues, 1 model selected 
    28221 
    28222 > color sel #8da3edff
    28223 
    28224 > color sel #8da3ecff
    28225 
    28226 [Repeated 1 time(s)]
    28227 
    28228 > color sel #8ca2ecff
    28229 
    28230 > color sel #8ca2ebff
    28231 
    28232 > color sel #8ba1eaff
    28233 
    28234 > color sel #8ba0e9ff
    28235 
    28236 > color sel #889ee5ff
    28237 
    28238 > color sel #869be0ff
    28239 
    28240 > color sel #8397dcff
    28241 
    28242 > color sel #8195d9ff
    28243 
    28244 > color sel #8094d7ff
    28245 
    28246 > color sel #7f93d6ff
    28247 
    28248 > color sel #7f93d5ff
    28249 
    28250 > color sel #7e92d4ff
    28251 
    28252 > color sel #7d90d2ff
    28253 
    28254 > color sel #7b8eceff
    28255 
    28256 > color sel #798cccff
    28257 
    28258 > color sel #788bc9ff
    28259 
    28260 > color sel #778ac8ff
    28261 
    28262 [Repeated 1 time(s)]
    28263 
    28264 > color sel #7689c7ff
    28265 
    28266 > color sel #7688c6ff
    28267 
    28268 > color sel #7587c5ff
    28269 
    28270 > color sel #7587c4ff
    28271 
    28272 > color sel #7487c3ff
    28273 
    28274 > color sel #7486c3ff
    28275 
    28276 > color sel #7081bcff
    28277 
    28278 > color sel #6878afff
    28279 
    28280 > color sel #6272a5ff
    28281 
    28282 > color sel #576592ff
    28283 
    28284 > color sel #4c5880ff
    28285 
    28286 > color sel #444f73ff
    28287 
    28288 > color sel #414b6dff
    28289 
    28290 > color sel #404a6cff
    28291 
    28292 > color sel #404a6bff
    28293 
    28294 > color sel #3f4969ff
    28295 
    28296 > color sel #3d4666ff
    28297 
    28298 > color sel #3b4463ff
    28299 
    28300 > color sel #38415fff
    28301 
    28302 > color sel #343c57ff
    28303 
    28304 > color sel #2e364eff
    28305 
    28306 > color sel #2c3249ff
    28307 
    28308 > color sel #2b3148ff
    28309 
    28310 > color sel #2a3146ff
    28311 
    28312 [Repeated 1 time(s)]
    28313 
    28314 > color sel #2a3147ff
    28315 
    28316 > color sel #2c334bff
    28317 
    28318 > color sel #2f364fff
    28319 
    28320 > color sel #343c58ff
    28321 
    28322 > color sel #3a4361ff
    28323 
    28324 > color sel #404a6cff
    28325 
    28326 > color sel #475277ff
    28327 
    28328 > color sel #4d5981ff
    28329 
    28330 > color sel #55638fff
    28331 
    28332 > color sel #596796ff
    28333 
    28334 > color sel #5d6b9cff
    28335 
    28336 > color sel #606fa1ff
    28337 
    28338 > color sel #6272a5ff
    28339 
    28340 > color sel #6878afff
    28341 
    28342 > color sel #6b7bb3ff
    28343 
    28344 > color sel #7082bcff
    28345 
    28346 > color sel #7284c0ff
    28347 
    28348 > color sel #7486c3ff
    28349 
    28350 > color sel #7587c5ff
    28351 
    28352 > color sel #7688c6ff
    28353 
    28354 > color sel #7689c6ff
    28355 
    28356 > color sel #778ac8ff
    28357 
    28358 > color sel #788ac9ff
    28359 
    28360 > color sel #788bcaff
    28361 
    28362 > color sel #798cccff
    28363 
    28364 > color sel #7a8dcdff
    28365 
    28366 > color sel #7b8eceff
    28367 
    28368 > color sel #7c8fcfff
    28369 
    28370 > color sel #7c90d0ff
    28371 
    28372 > color sel #7d90d1ff
    28373 
    28374 > color sel #7d91d2ff
    28375 
    28376 > color sel #7e91d3ff
    28377 
    28378 > color sel #7e92d4ff
    28379 
    28380 > color sel #7f93d5ff
    28381 
    28382 [Repeated 1 time(s)]
    28383 
    28384 > color sel #7f93d6ff
    28385 
    28386 > color sel #8094d7ff
    28387 
    28388 > color sel #8296daff
    28389 
    28390 > color sel #859ae0ff
    28391 
    28392 > color sel #879ce2ff
    28393 
    28394 > color sel #899ee5ff
    28395 
    28396 > color sel #899ee6ff
    28397 
    28398 [Repeated 1 time(s)]
    28399 
    28400 > color sel #899fe6ff
    28401 
    28402 > color sel #899fe7ff
    28403 
    28404 > color sel #8aa0e8ff
    28405 
    28406 > color sel #8ca2ebff
    28407 
    28408 > color sel #8da3ecff
    28409 
    28410 > color sel #8da3edff
    28411 
    28412 > color sel #8da4edff
    28413 
    28414 > color sel #8ea5efff
    28415 
    28416 > color sel #90a6f1ff
    28417 
    28418 > color sel #91a7f3ff
    28419 
    28420 > color sel #92a9f5ff
    28421 
    28422 > color sel #92a9f6ff
    28423 
    28424 > color sel #94abf8ff
    28425 
    28426 > color sel #95acfaff
    28427 
    28428 [Repeated 1 time(s)]
    28429 
    28430 > color sel #95adfbff
    28431 
    28432 > color sel #96aefcff
    28433 
    28434 > color sel #97affeff
    28435 
    28436 > color sel #98b0ffff
    28437 
    28438 [Repeated 1 time(s)]
    28439 
    28440 > color sel #97affeff
    28441 
    28442 > color sel #94abf9ff
    28443 
    28444 > color sel #92a9f6ff
    28445 
    28446 > color sel #92a8f4ff
    28447 
    28448 > color sel #91a8f4ff
    28449 
    28450 > color sel #91a7f3ff
    28451 
    28452 > color sel #90a7f2ff
    28453 
    28454 > color sel #91a7f3ff
    28455 
    28456 > color sel #91a8f4ff
    28457 
    28458 > color sel #92a9f5ff
    28459 
    28460 > color sel #92a9f6ff
    28461 
    28462 > color sel #93aaf7ff
    28463 
    28464 > color sel #94abf8ff
    28465 
    28466 > color sel #94abf9ff
    28467 
    28468 > color sel #6492f9ff
    28469 
    28470 > color sel #4f5af9ff
    28471 
    28472 > color sel #505df9ff
    28473 
    28474 > color sel #505ef9ff
    28475 
    28476 > color sel #515ff9ff
    28477 
    28478 [Repeated 1 time(s)]
    28479 
    28480 > color sel #5260f9ff
    28481 
    28482 > color sel #5362f9ff
    28483 
    28484 > color sel #5363f9ff
    28485 
    28486 [Repeated 1 time(s)]
    28487 
    28488 > color sel #5465f9ff
    28489 
    28490 > color sel #5567f9ff
    28491 
    28492 > color sel #5667f9ff
    28493 
    28494 > color sel #5668f9ff
    28495 
    28496 > color sel #5568f9ff
    28497 
    28498 > color sel #5569f9ff
    28499 
    28500 [Repeated 1 time(s)]
    28501 
    28502 > color sel #5469f9ff
    28503 
    28504 [Repeated 2 time(s)]
    28505 
    28506 > color sel #5369f9ff
    28507 
    28508 > color sel #536af9ff
    28509 
    28510 > color sel #546bf9ff
    28511 
    28512 > color sel #546cf9ff
    28513 
    28514 [Repeated 1 time(s)]
    28515 
    28516 > color sel #556df9ff
    28517 
    28518 > color sel #556ef9ff
    28519 
    28520 > color sel #556ff9ff
    28521 
    28522 > color sel #5670f9ff
    28523 
    28524 [Repeated 2 time(s)]
    28525 
    28526 > color sel #5671f9ff
    28527 
    28528 > color sel #5772f9ff
    28529 
    28530 > color sel #5672f9ff
    28531 
    28532 > color sel #5671f9ff
    28533 
    28534 [Repeated 1 time(s)]
    28535 
    28536 > color sel #5570f9ff
    28537 
    28538 > color sel #556ff9ff
    28539 
    28540 > color sel #546ef9ff
    28541 
    28542 [Repeated 1 time(s)]
    28543 
    28544 > color sel #536df9ff
    28545 
    28546 [Repeated 1 time(s)]
    28547 
    28548 > color sel #526cf9ff
    28549 
    28550 [Repeated 1 time(s)]
    28551 
    28552 > color sel #526bf9ff
    28553 
    28554 > color sel #516af9ff
    28555 
    28556 > color sel #5169f9ff
    28557 
    28558 > color sel #5069f9ff
    28559 
    28560 > color sel #5068f9ff
    28561 
    28562 > color sel #4f67f9ff
    28563 
    28564 > color sel #4f66f9ff
    28565 
    28566 > color sel #4f65f9ff
    28567 
    28568 > color sel #5069f9ff
    28569 
    28570 > color sel #516af9ff
    28571 
    28572 [Repeated 1 time(s)]
    28573 
    28574 > color sel #516bf9ff
    28575 
    28576 > color sel #536cf9ff
    28577 
    28578 > color sel #536df9ff
    28579 
    28580 > color sel #546df9ff
    28581 
    28582 > color sel #546ef9ff
    28583 
    28584 > color sel #556ff9ff
    28585 
    28586 > color sel #5670f9ff
    28587 
    28588 [Repeated 1 time(s)]
    28589 
    28590 > color sel #5770f9ff
    28591 
    28592 > color sel #5771f9ff
    28593 
    28594 > color sel #5872f9ff
    28595 
    28596 [Repeated 2 time(s)]
    28597 
    28598 > color sel #5972f9ff
    28599 
    28600 > color sel #5973f9ff
    28601 
    28602 > color sel #5a73f9ff
    28603 
    28604 [Repeated 1 time(s)]
    28605 
    28606 > color sel #5a74f9ff
    28607 
    28608 > color sel #5b73f9ff
    28609 
    28610 [Repeated 1 time(s)]
    28611 
    28612 > color sel #5c74f9ff
    28613 
    28614 [Repeated 2 time(s)]
    28615 
    28616 > color sel #5d74f9ff
    28617 
    28618 [Repeated 1 time(s)]
    28619 
    28620 > color sel #5e73f9ff
    28621 
    28622 > color sel #5e74f9ff
    28623 
    28624 [Repeated 1 time(s)]
    28625 
    28626 > select #3/B,A:241
    28627 
    28628 16 atoms, 14 bonds, 2 residues, 1 model selected 
    28629 
    28630 > select #3/B,A:241
    28631 
    28632 16 atoms, 14 bonds, 2 residues, 1 model selected 
    28633 
    28634 > color sel #8897f9ff
    28635 
    28636 > color sel #b4bff9ff
    28637 
    28638 > color sel #becff9ff
    28639 
    28640 > color sel #bdcff9ff
    28641 
    28642 [Repeated 1 time(s)]
    28643 
    28644 > color sel #bccff9ff
    28645 
    28646 [Repeated 1 time(s)]
    28647 
    28648 > color sel #bbcff9ff
    28649 
    28650 [Repeated 2 time(s)]
    28651 
    28652 > color sel #bbd0f9ff
    28653 
    28654 > color sel #bbcff9ff
    28655 
    28656 > color sel #bacff9ff
    28657 
    28658 > color sel #bacef9ff
    28659 
    28660 > color sel #b9cdf9ff
    28661 
    28662 > color sel #b9ccf9ff
    28663 
    28664 [Repeated 1 time(s)]
    28665 
    28666 > color sel #b8cbf9ff
    28667 
    28668 [Repeated 1 time(s)]
    28669 
    28670 > color sel #b7caf9ff
    28671 
    28672 [Repeated 1 time(s)]
    28673 
    28674 > color sel #b7c9f9ff
    28675 
    28676 > color sel #b5c8f9ff
    28677 
    28678 > color sel #b5c7f9ff
    28679 
    28680 > color sel #b5c6f9ff
    28681 
    28682 > color sel #b4c6f9ff
    28683 
    28684 [Repeated 1 time(s)]
    28685 
    28686 > color sel #b3c5f9ff
    28687 
    28688 > color sel #b3c4f9ff
    28689 
    28690 > color sel #b2c4f9ff
    28691 
    28692 > color sel #b2c3f9ff
    28693 
    28694 > color sel #b1c2f9ff
    28695 
    28696 > color sel #b1c1f9ff
    28697 
    28698 > color sel #b0c1f9ff
    28699 
    28700 > color sel #b0c0f9ff
    28701 
    28702 > color sel #afbff9ff
    28703 
    28704 [Repeated 1 time(s)]
    28705 
    28706 > color sel #aebef9ff
    28707 
    28708 > color sel #aebdf9ff
    28709 
    28710 > select #3/B,A:242
    28711 
    28712 16 atoms, 14 bonds, 2 residues, 1 model selected 
    28713 
    28714 > select #3/B,A:242-247
    28715 
    28716 102 atoms, 104 bonds, 12 residues, 1 model selected 
    28717 
    28718 > color sel #909df9ff
    28719 
    28720 > select #3/B,A:248-249
    28721 
    28722 18 atoms, 16 bonds, 4 residues, 1 model selected 
    28723 
    28724 > select #3/B,A:248-253
    28725 
    28726 76 atoms, 76 bonds, 12 residues, 1 model selected 
    28727 
    28728 > color sel #9fabf9ff
    28729 
    28730 > select #3/B,A:254-255
    28731 
    28732 36 atoms, 36 bonds, 4 residues, 1 model selected 
    28733 
    28734 > select #3/B,A:254-262
    28735 
    28736 162 atoms, 170 bonds, 18 residues, 1 model selected 
    28737 
    28738 > color sel #92a1f9ff
    28739 
    28740 > select #3/B,A:263-264
    28741 
    28742 32 atoms, 30 bonds, 4 residues, 1 model selected 
    28743 
    28744 > select #3/B,A:263-265
    28745 
    28746 42 atoms, 40 bonds, 6 residues, 1 model selected 
    28747 
    28748 > color sel #acbbf9ff
    28749 
    28750 [Repeated 1 time(s)]
    28751 
    28752 > color sel #abbaf9ff
    28753 
    28754 > color sel #abb9f9ff
    28755 
    28756 > select #3/B,A:266-267
    28757 
    28758 22 atoms, 22 bonds, 4 residues, 1 model selected 
    28759 
    28760 > select #3/B,A:266-267
    28761 
    28762 22 atoms, 22 bonds, 4 residues, 1 model selected 
    28763 
    28764 > color sel #7a98f9ff
    28765 
    28766 > color sel #6689f9ff
    28767 
    28768 > color sel #698bf9ff
    28769 
    28770 > color sel #698cf9ff
    28771 
    28772 > color sel #6a8cf9ff
    28773 
    28774 > color sel #6b8cf9ff
    28775 
    28776 > color sel #6c8df9ff
    28777 
    28778 > color sel #6c8ef9ff
    28779 
    28780 > color sel #6d8ef9ff
    28781 
    28782 > color sel #6e8ef9ff
    28783 
    28784 > color sel #6e8ff9ff
    28785 
    28786 > color sel #6f90f9ff
    28787 
    28788 > color sel #6f8ff9ff
    28789 
    28790 > color sel #6284f9ff
    28791 
    28792 > select #3/B,A:268-269
    28793 
    28794 48 atoms, 52 bonds, 4 residues, 1 model selected 
    28795 
    28796 > select #3/B,A:268-273
    28797 
    28798 110 atoms, 114 bonds, 12 residues, 1 model selected 
    28799 
    28800 > color sel #86abf9ff
    28801 
    28802 > select #3/B,A:274-275
    28803 
    28804 34 atoms, 32 bonds, 4 residues, 1 model selected 
    28805 
    28806 > select #3/B,A:274-275
    28807 
    28808 34 atoms, 32 bonds, 4 residues, 1 model selected 
    28809 
    28810 > color sel #5584f9ff
    28811 
    28812 > color sel #5684f9ff
    28813 
    28814 > color sel #5785f9ff
    28815 
    28816 > color sel #5886f9ff
    28817 
    28818 > color sel #5986f9ff
    28819 
    28820 > color sel #5b87f9ff
    28821 
    28822 > color sel #5c88f9ff
    28823 
    28824 [Repeated 1 time(s)]
    28825 
    28826 > color sel #5c89f9ff
    28827 
    28828 > color sel #5d89f9ff
    28829 
    28830 > color sel #5e8af9ff
    28831 
    28832 > color sel #5e8bf9ff
    28833 
    28834 > color sel #5f8bf9ff
    28835 
    28836 > color sel #5f8cf9ff
    28837 
    28838 > color sel #608df9ff
    28839 
    28840 > color sel #618df9ff
    28841 
    28842 > color sel #618ef9ff
    28843 
    28844 [Repeated 1 time(s)]
    28845 
    28846 > color sel #628ff9ff
    28847 
    28848 > color sel #638ff9ff
    28849 
    28850 > color sel #6390f9ff
    28851 
    28852 > color sel #6592f9ff
    28853 
    28854 > color sel #6994f9ff
    28855 
    28856 > color sel #6a96f9ff
    28857 
    28858 > color sel #6b96f9ff
    28859 
    28860 > color sel #6c97f9ff
    28861 
    28862 [Repeated 1 time(s)]
    28863 
    28864 > select #3/B,A:276-277
    28865 
    28866 38 atoms, 38 bonds, 4 residues, 1 model selected 
    28867 
    28868 > select #3/B,A:276-277
    28869 
    28870 38 atoms, 38 bonds, 4 residues, 1 model selected 
    28871 
    28872 > color sel #89aef9ff
    28873 
    28874 > select #3/B,A:278
    28875 
    28876 16 atoms, 14 bonds, 2 residues, 1 model selected 
    28877 
    28878 > select #3/B,A:278-285
    28879 
    28880 118 atoms, 118 bonds, 16 residues, 1 model selected 
    28881 
    28882 > select #3/B,A:286-287
    28883 
    28884 28 atoms, 26 bonds, 4 residues, 1 model selected 
    28885 
    28886 > select #3/B,A:286-287
    28887 
    28888 28 atoms, 26 bonds, 4 residues, 1 model selected 
    28889 
    28890 > select #3/B,A:286
    28891 
    28892 14 atoms, 12 bonds, 2 residues, 1 model selected 
    28893 
    28894 > select #3/B,A:286-299
    28895 
    28896 206 atoms, 206 bonds, 28 residues, 1 model selected 
    28897 
    28898 > color sel #7c9df9ff
    28899 
    28900 > color sel #798df9ff
    28901 
    28902 > select #3/B,A:300
    28903 
    28904 14 atoms, 12 bonds, 2 residues, 1 model selected 
    28905 
    28906 > select #3/B,A:300-309
    28907 
    28908 136 atoms, 134 bonds, 20 residues, 1 model selected 
    28909 
    28910 > color sel #527af9ff
    28911 
    28912 > color sel #3a5af9ff
    28913 
    28914 > select #3/B,A:310
    28915 
    28916 18 atoms, 16 bonds, 2 residues, 1 model selected 
    28917 
    28918 > select #3/B,A:310
    28919 
    28920 18 atoms, 16 bonds, 2 residues, 1 model selected 
    28921 
    28922 > color sel #526af9ff
    28923 
    28924 > select #3/B,A:311
    28925 
    28926 28 atoms, 30 bonds, 2 residues, 1 model selected 
    28927 
    28928 > select #3/B,A:311-333
    28929 
    28930 378 atoms, 392 bonds, 46 residues, 1 model selected 
    28931 
    28932 > color sel #c6c6f3ff
    28933 
    28934 > color sel #b6b4f3ff
    28935 
    28936 > select #3/B,A:334-335
    28937 
    28938 34 atoms, 32 bonds, 4 residues, 1 model selected 
    28939 
    28940 > select #3/B,A:334-335
    28941 
    28942 34 atoms, 32 bonds, 4 residues, 1 model selected 
    28943 
    28944 > color sel #9c98f3ff
    28945 
    28946 > select #3/B,A:336-337
    28947 
    28948 36 atoms, 36 bonds, 4 residues, 1 model selected 
    28949 
    28950 > select #3/B,A:336-341
    28951 
    28952 106 atoms, 106 bonds, 12 residues, 1 model selected 
    28953 
    28954 > color sel #a7acf3ff
    28955 
    28956 > select #3/B,A:341-342
    28957 
    28958 36 atoms, 34 bonds, 4 residues, 1 model selected 
    28959 
    28960 > select #3/B,A:341-350
    28961 
    28962 158 atoms, 156 bonds, 20 residues, 1 model selected 
    28963 
    28964 > color sel #6b69f3ff
    28965 
    28966 > color sel #6b6af3ff
    28967 
    28968 > color sel #6b6bf3ff
    28969 
    28970 > color sel #6d6ef3ff
    28971 
    28972 > color sel #6f70f3ff
    28973 
    28974 > color sel #7273f3ff
    28975 
    28976 > color sel #7274f3ff
    28977 
    28978 > color sel #7375f3ff
    28979 
    28980 > color sel #7476f3ff
    28981 
    28982 > color sel #7477f3ff
    28983 
    28984 > color sel #7578f3ff
    28985 
    28986 > color sel #7579f3ff
    28987 
    28988 > color sel #7679f3ff
    28989 
    28990 > color sel #777af3ff
    28991 
    28992 > color sel #787cf3ff
    28993 
    28994 > color sel #777bf3ff
    28995 
    28996 > color sel #777af3ff
    28997 
    28998 > color sel #7679f3ff
    28999 
    29000 > color sel #7072f3ff
    29001 
    29002 > select add #3
    29003 
    29004 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    29005 
    29006 > select subtract #3
    29007 
    29008 Nothing selected 
    29009 
    29010 > select #3/B,A:300
    29011 
    29012 14 atoms, 12 bonds, 2 residues, 1 model selected 
    29013 
    29014 > select #3/B,A:300-309
    29015 
    29016 136 atoms, 134 bonds, 20 residues, 1 model selected 
    29017 
    29018 > color sel #4c4ef3ff
    29019 
    29020 > color sel #4242f3ff
    29021 
    29022 > select add #3
    29023 
    29024 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    29025 
    29026 > select subtract #3
    29027 
    29028 Nothing selected 
    29029 
    29030 > select #3/B,A:1-2
    29031 
    29032 28 atoms, 26 bonds, 4 residues, 1 model selected 
    29033 
    29034 > select #3/B,A:1-171
    29035 
    29036 2732 atoms, 2798 bonds, 342 residues, 1 model selected 
    29037 
    29038 > color sel #edeff3ff
    29039 
    29040 > color sel #c7c9ccff
    29041 
    29042 > color sel #c7c8ccff
    29043 
    29044 > color sel #c2c4c7ff
    29045 
    29046 > color sel #c1c2c6ff
    29047 
    29048 > color sel #c0c2c5ff
    29049 
    29050 > color sel #bfc0c4ff
    29051 
    29052 > color sel #bdbec2ff
    29053 
    29054 > color sel #bcbdc0ff
    29055 
    29056 > color sel #babcbfff
    29057 
    29058 > color sel #babbbeff
    29059 
    29060 > color sel #b9bbbeff
    29061 
    29062 > color sel #b9babeff
    29063 
    29064 > color sel #b6b7bbff
    29065 
    29066 > color sel #b2b3b6ff
    29067 
    29068 > color sel #afb0b3ff
    29069 
    29070 > color sel #abacafff
    29071 
    29072 > color sel #a6a7abff
    29073 
    29074 > color sel #a3a4a7ff
    29075 
    29076 > color sel #a1a2a5ff
    29077 
    29078 > color sel #9fa0a3ff
    29079 
    29080 > color sel #9c9da0ff
    29081 
    29082 > color sel #999a9cff
    29083 
    29084 > color sel #96979aff
    29085 
    29086 [Repeated 1 time(s)]
    29087 
    29088 > color sel #949597ff
    29089 
    29090 > color sel #919295ff
    29091 
    29092 > color sel #8b8b8eff
    29093 
    29094 > color sel #87888aff
    29095 
    29096 > color sel #7e7f81ff
    29097 
    29098 > color sel #727375ff
    29099 
    29100 > color sel #68686aff
    29101 
    29102 > color sel #616264ff
    29103 
    29104 > color sel #59595bff
    29105 
    29106 > color sel #545556ff
    29107 
    29108 > color sel #4d4e4fff
    29109 
    29110 > color sel #464748ff
    29111 
    29112 > color sel #444446ff
    29113 
    29114 > color sel #424244ff
    29115 
    29116 > color sel #3f3f40ff
    29117 
    29118 > color sel #3e3e3fff
    29119 
    29120 > color sel #3c3d3eff
    29121 
    29122 [Repeated 1 time(s)]
    29123 
    29124 > color sel #414243ff
    29125 
    29126 > color sel #4d4e4fff
    29127 
    29128 > color sel #565658ff
    29129 
    29130 > color sel #606162ff
    29131 
    29132 > color sel #656668ff
    29133 
    29134 > color sel #6a6b6dff
    29135 
    29136 > color sel #717274ff
    29137 
    29138 > color sel #737476ff
    29139 
    29140 > color sel #78797bff
    29141 
    29142 > color sel #7b7b7eff
    29143 
    29144 > color sel #818285ff
    29145 
    29146 > color sel #858689ff
    29147 
    29148 > color sel #88898cff
    29149 
    29150 > color sel #8b8c8eff
    29151 
    29152 > color sel #8c8d90ff
    29153 
    29154 > color sel #8f8f92ff
    29155 
    29156 > color sel #919295ff
    29157 
    29158 > color sel #959699ff
    29159 
    29160 > color sel #9a9b9eff
    29161 
    29162 > color sel #9e9fa2ff
    29163 
    29164 > color sel #a1a2a5ff
    29165 
    29166 > color sel #a5a6a9ff
    29167 
    29168 > color sel #a7a8abff
    29169 
    29170 > color sel #a8a9adff
    29171 
    29172 > color sel #a9aaaeff
    29173 
    29174 > color sel #aaabaeff
    29175 
    29176 [Repeated 1 time(s)]
    29177 
    29178 > color sel #adaeb1ff
    29179 
    29180 > color sel #afb0b3ff
    29181 
    29182 [Repeated 1 time(s)]
    29183 
    29184 > color sel #b0b1b4ff
    29185 
    29186 > color sel #b1b2b5ff
    29187 
    29188 > color sel #b2b3b6ff
    29189 
    29190 [Repeated 1 time(s)]
    29191 
    29192 > color sel #b2b3b6fa
    29193 
    29194 > color sel #b2b3b6f5
    29195 
    29196 > color sel #b2b3b6f3
    29197 
    29198 > color sel #b2b3b6ee
    29199 
    29200 [Repeated 2 time(s)]
    29201 
    29202 > color sel #b2b3b6ed
    29203 
    29204 [Repeated 1 time(s)]
    29205 
    29206 > color sel #b2b3b6eb
    29207 
    29208 [Repeated 1 time(s)]
    29209 
    29210 > color sel #b2b3b6ea
    29211 
    29212 > color sel #b2b3b6e9
    29213 
    29214 > color sel #b2b3b6e8
    29215 
    29216 [Repeated 1 time(s)]
    29217 
    29218 > color sel #b2b3b6e7
    29219 
    29220 [Repeated 1 time(s)]
    29221 
    29222 > color sel #b2b3b6e6
    29223 
    29224 > color sel #b2b3b6e5
    29225 
    29226 > color sel #b2b3b6e3
    29227 
    29228 > color sel #b2b3b6e2
    29229 
    29230 > color sel #b2b3b6e1
    29231 
    29232 > color sel #b2b3b6e0
    29233 
    29234 > color sel #b2b3b6df
    29235 
    29236 [Repeated 1 time(s)]
    29237 
    29238 > color sel #b2b3b6de
    29239 
    29240 > color sel #b2b3b6dd
    29241 
    29242 > color sel #b2b3b6dc
    29243 
    29244 > color sel #b2b3b6db
    29245 
    29246 > color sel #b2b3b6da
    29247 
    29248 [Repeated 1 time(s)]
    29249 
    29250 > color sel #b2b3b6d9
    29251 
    29252 > color sel #b2b3b6d8
    29253 
    29254 [Repeated 1 time(s)]
    29255 
    29256 > color sel #b2b3b6d7
    29257 
    29258 [Repeated 1 time(s)]
    29259 
    29260 > color sel #b2b3b6d6
    29261 
    29262 > color sel #b2b3b6d5
    29263 
    29264 > color sel #b2b3b6d4
    29265 
    29266 > color sel #b2b3b6d2
    29267 
    29268 > color sel #b2b3b6d1
    29269 
    29270 > color sel #b2b3b6d0
    29271 
    29272 [Repeated 1 time(s)]
    29273 
    29274 > color sel #b2b3b6cf
    29275 
    29276 > color sel #b2b3b6cd
    29277 
    29278 [Repeated 1 time(s)]
    29279 
    29280 > color sel #b1b3b6cd
    29281 
    29282 > color sel #b1b2b6cd
    29283 
    29284 > color sel #b1b2b5cd
    29285 
    29286 [Repeated 1 time(s)]
    29287 
    29288 > select add #3
    29289 
    29290 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    29291 
    29292 > select subtract #3
    29293 
    29294 Nothing selected 
    29295 
    29296 > select #3/B,A:1
    29297 
    29298 16 atoms, 14 bonds, 2 residues, 1 model selected 
    29299 
    29300 > select #3/B,A:1-171
    29301 
    29302 2732 atoms, 2798 bonds, 342 residues, 1 model selected 
    29303 
    29304 > color sel #b1b2b5cc
    29305 
    29306 > color sel #b1b2b5c8
    29307 
    29308 > color sel #b1b2b5c6
    29309 
    29310 > color sel #b1b2b5c5
    29311 
    29312 > color sel #b1b2b5c1
    29313 
    29314 > color sel #b1b2b5be
    29315 
    29316 > color sel #b1b2b5bb
    29317 
    29318 > color sel #b1b2b5b7
    29319 
    29320 > color sel #b1b2b5b5
    29321 
    29322 > color sel #b1b2b5b1
    29323 
    29324 > color sel #b1b2b5ad
    29325 
    29326 > color sel #b1b2b5aa
    29327 
    29328 > color sel #b1b2b5a7
    29329 
    29330 > color sel #b1b2b5a4
    29331 
    29332 > color sel #b1b2b5a0
    29333 
    29334 > color sel #b1b2b599
    29335 
    29336 > color sel #b1b2b592
    29337 
    29338 > color sel #b1b2b58c
    29339 
    29340 > color sel #b1b2b586
    29341 
    29342 > color sel #b1b2b576
    29343 
    29344 > color sel #b1b2b573
    29345 
    29346 > color sel #b1b2b56e
    29347 
    29348 > color sel #b1b2b56a
    29349 
    29350 > color sel #b1b2b568
    29351 
    29352 > color sel #b1b2b567
    29353 
    29354 > color sel #b1b2b565
    29355 
    29356 > color sel #b1b2b563
    29357 
    29358 [Repeated 1 time(s)]
    29359 
    29360 > color sel #b1b2b565
    29361 
    29362 > color sel #b1b2b569
    29363 
    29364 > color sel #b1b2b56c
    29365 
    29366 > color sel #b1b2b572
    29367 
    29368 > color sel #b1b2b575
    29369 
    29370 > color sel #b1b2b57b
    29371 
    29372 > color sel #b1b2b581
    29373 
    29374 > color sel #b1b2b587
    29375 
    29376 > color sel #b1b2b589
    29377 
    29378 > color sel #b1b2b58a
    29379 
    29380 [Repeated 1 time(s)]
    29381 
    29382 > color sel #b1b2b58d
    29383 
    29384 > color sel #b1b2b590
    29385 
    29386 > color sel #b1b2b591
    29387 
    29388 > color sel #b1b2b594
    29389 
    29390 > color sel #b1b2b596
    29391 
    29392 [Repeated 2 time(s)]
    29393 
    29394 > color sel #b1b2b597
    29395 
    29396 > color sel #b1b2b598
    29397 
    29398 [Repeated 1 time(s)]
    29399 
    29400 > color sel #b1b2b599
    29401 
    29402 > color sel #b1b2b59a
    29403 
    29404 > color sel #b1b2b59c
    29405 
    29406 > color sel #b1b2b59d
    29407 
    29408 > color sel #b1b2b59c
    29409 
    29410 [Repeated 1 time(s)]
    29411 
    29412 > color sel #b1b2b59b
    29413 
    29414 [Repeated 1 time(s)]
    29415 
    29416 > color sel #b1b2b59a
    29417 
    29418 [Repeated 1 time(s)]
    29419 
    29420 > color sel #b1b2b599
    29421 
    29422 [Repeated 1 time(s)]
    29423 
    29424 > color sel #b1b2b598
    29425 
    29426 > select add #3
    29427 
    29428 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    29429 
    29430 > select subtract #3
    29431 
    29432 Nothing selected 
    29433 
    29434 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    29435 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/sNS1wt-Ab562_EM-HDX.cxs"
    29436 > includeMaps true
    29437 
    29438 > show #!2 models
    29439 
    29440 > color #2 #cfbabb4d models
    29441 
    29442 > color #2 #c1acae4d models
    29443 
    29444 > color #2 #c1acae2e models
    29445 
    29446 > color #2 #c1acae34 models
    29447 
    29448 > show #!8 models
    29449 
    29450 > show #4 models
    29451 
    29452 > select add #4
    29453 
    29454 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    29455 
    29456 > ui mousemode right "translate selected models"
    29457 
    29458 > view matrix models
    29459 > #4,0.25081,-0.17578,-0.95194,337.54,0.94086,0.27565,0.19699,-69.227,0.22777,-0.94505,0.23452,277.17
    29460 
    29461 > view matrix models
    29462 > #4,0.25081,-0.17578,-0.95194,337.61,0.94086,0.27565,0.19699,-68.962,0.22777,-0.94505,0.23452,277.21
    29463 
    29464 > view matrix models
    29465 > #4,0.25081,-0.17578,-0.95194,338.3,0.94086,0.27565,0.19699,-67.778,0.22777,-0.94505,0.23452,276.56
    29466 
    29467 > ui mousemode right "rotate selected models"
    29468 
    29469 > view matrix models
    29470 > #4,0.28381,-0.20491,-0.93673,335.61,0.93973,0.25368,0.22923,-67.38,0.19066,-0.94534,0.26456,280.03
    29471 
    29472 > view matrix models
    29473 > #4,0.29033,-0.1329,-0.94765,322.58,0.93808,0.23513,0.25442,-66.671,0.18901,-0.96284,0.19293,291.98
    29474 
    29475 > view matrix models
    29476 > #4,0.35013,-0.063779,-0.93453,297.24,0.92612,0.17313,0.33516,-62.689,0.14042,-0.98283,0.11968,313.39
    29477 
    29478 > view matrix models
    29479 > #4,0.28929,-0.083154,-0.95362,314.43,0.94763,0.16569,0.27303,-58.03,0.1353,-0.98267,0.12673,313.48
    29480 
    29481 > view matrix models
    29482 > #4,0.29468,-0.086777,-0.95165,313.84,0.94725,0.15789,0.27892,-57.235,0.12605,-0.98364,0.12873,315.16
    29483 
    29484 > view matrix models
    29485 > #4,0.36145,-0.11336,-0.92548,303.06,0.89859,0.30718,0.31332,-79.332,0.24877,-0.94488,0.21289,275.15
    29486 
    29487 > hide #!2 models
    29488 
    29489 > view matrix models
    29490 > #4,0.75588,-0.11899,-0.6438,196.83,0.49521,0.74715,0.44333,-99.072,0.42827,-0.65392,0.62368,140.02
    29491 
    29492 > view matrix models
    29493 > #4,0.79244,-0.19913,-0.57652,196.6,0.59732,0.44467,0.66744,-89.678,0.12346,-0.87328,0.47133,255.09
    29494 
    29495 > show #!2 models
    29496 
    29497 > view matrix models
    29498 > #4,0.84088,0.043539,-0.53947,139,0.20748,0.89468,0.3956,-66.307,0.49988,-0.44458,0.74328,74.375
    29499 
    29500 > view matrix models
    29501 > #4,0.61732,-0.23939,-0.7494,257.2,0.45462,0.88598,0.091476,-75.144,0.64205,-0.39716,0.65577,49.425
    29502 
    29503 > view matrix models
    29504 > #4,0.38724,0.030398,-0.92148,271.6,0.61211,0.73893,0.28161,-100.4,0.68947,-0.6731,0.26753,136.6
    29505 
    29506 > view matrix models
    29507 > #4,0.32928,0.15127,-0.93204,261.73,0.67479,0.65276,0.34434,-103.89,0.66048,-0.74231,0.11286,172.9
    29508 
    29509 > view matrix models
    29510 > #4,0.83345,-0.16899,-0.52612,177.48,0.33798,0.90914,0.24338,-75.428,0.43719,-0.38066,0.81484,66.051
    29511 
    29512 > view matrix models
    29513 > #4,0.73197,-0.15661,-0.6631,210.44,0.61773,0.56316,0.54888,-101.05,0.28747,-0.81137,0.50895,208.62
    29514 
    29515 > view matrix models
    29516 > #4,0.70748,-0.11472,-0.69736,211.46,0.67078,0.41972,0.61146,-92.303,0.22255,-0.90037,0.3739,252.95
    29517 
    29518 > view matrix models
    29519 > #4,0.50475,-0.22825,-0.83254,286.11,0.80219,0.4803,0.35468,-97.631,0.31892,-0.84689,0.42553,219.04
    29520 
    29521 > view matrix models
    29522 > #4,0.43321,-0.14625,-0.88935,291.32,0.79138,0.53394,0.29769,-98.629,0.43133,-0.83278,0.34705,204.67
    29523 
    29524 > view matrix models
    29525 > #4,0.39985,-0.22492,-0.88856,311.79,0.73762,0.65442,0.16627,-94.936,0.54409,-0.7219,0.42757,153.83
    29526 
    29527 > hide #!8 models
    29528 
    29529 > view matrix models
    29530 > #4,0.40534,-0.24527,-0.88065,313.53,0.76932,0.61189,0.18368,-95.2,0.49381,-0.75196,0.43671,167.65
    29531 
    29532 > view matrix models
    29533 > #4,0.25068,-0.40305,-0.88017,371.18,0.81823,0.57411,-0.029862,-72.272,0.51736,-0.7127,0.47371,151.72
    29534 
    29535 > view matrix models
    29536 > #4,0.3665,-0.39401,-0.84287,343.41,0.8386,0.5323,0.11581,-85.696,0.40303,-0.74927,0.5255,173.7
    29537 
    29538 > view matrix models
    29539 > #4,0.48359,-0.37777,-0.78957,312.2,0.85036,0.41655,0.32152,-91.15,0.20743,-0.82691,0.52268,224.84
    29540 
    29541 > view matrix models
    29542 > #4,0.44767,-0.35695,-0.81986,318.73,0.84619,0.46549,0.25939,-91.93,0.28905,-0.80988,0.51043,207.88
    29543 
    29544 > show #5 models
    29545 
    29546 > hide #4 models
    29547 
    29548 > show #!8 models
    29549 
    29550 > hide #!2 models
    29551 
    29552 > ui tool show "Show Sequence Viewer"
    29553 
    29554 > sequence chain #5/B
    29555 
    29556 Alignment identifier is 5/B 
    29557 
    29558 > sequence chain #5/C
    29559 
    29560 Alignment identifier is 5/C 
    29561 
    29562 > ui tool show "Change Chain IDs"
    29563 
    29564 > select #5/C:1
    29565 
    29566 5 atoms, 4 bonds, 1 residue, 1 model selected 
    29567 
    29568 > select #5/C
    29569 
    29570 1632 atoms, 1668 bonds, 214 residues, 1 model selected 
    29571 
    29572 > changechains sel C L
    29573 
    29574 Chain IDs of 214 residues changed 
    29575 
    29576 > changechains sel C L
    29577 
    29578 No residues specified have any of the 'from' chain IDs 
    29579 
    29580 > ui tool show "Show Sequence Viewer"
    29581 
    29582 > sequence chain #5/L
    29583 
    29584 Alignment identifier is 5/L 
    29585 
    29586 > ui tool show "Change Chain IDs"
    29587 
    29588 > select
    29589 > #5/B:5-9,20-27,36-42,48-54,60-62,70-75,80-85,94-101,118-120,131-135,146-156,161-165,174-176,187-196,205-211,216-222
    29590 
    29591 837 atoms, 847 bonds, 101 residues, 1 model selected 
    29592 
    29593 > select #5/B:228
    29594 
    29595 8 atoms, 7 bonds, 1 residue, 1 model selected 
    29596 
    29597 > select #5/B
    29598 
    29599 1769 atoms, 1825 bonds, 228 residues, 1 model selected 
    29600 
    29601 > ui tool show "Change Chain IDs"
    29602 
    29603 > changechains sel B H
    29604 
    29605 Chain IDs of 228 residues changed 
    29606 
    29607 > ui tool show "Show Sequence Viewer"
    29608 
    29609 > sequence chain #5/H
    29610 
    29611 Alignment identifier is 5/H 
    29612 
    29613 > select #5/H:1
    29614 
    29615 5 atoms, 4 bonds, 1 residue, 1 model selected 
    29616 
    29617 > select #5/H:1
    29618 
    29619 5 atoms, 4 bonds, 1 residue, 1 model selected 
    29620 
    29621 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    29622 > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/Fab562_HDXMS_RelativeDchange_10min_recolored.defattr
    29623 
    29624 Summary of feedback from opening
    29625 /Users/alvinchew/Library/CloudStorage/OneDrive-
    29626 NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/Fab562_HDXMS_RelativeDchange_10min_recolored.defattr 
    29627 --- 
    29628 note | Assigned attribute 'fab562_10min_relative_deuterium_uptake' to 1126
    29629 residues using match mode: any 
    29630  
    29631 
    29632 > color byattribute fab562_10min_relative_deuterium_uptake #3/A-B:174-361 key
    29633 > true palette bluered range -2.0,1.0 noValueColor grey
    29634 
    29635 All 'fab562_10min_relative_deuterium_uptake' values are None 
    29636 
    29637 > color byattribute fab562_10min_relative_deuterium_uptake #5 key true palette
    29638 > bluered range -2.0,1.0 noValueColor grey
    29639 
    29640 > key blue-white-red :-2.0 :-0.5 :1.0 showTool true
    29641 
    29642 3401 atoms, 442 residues, atom fab562_10min_relative_deuterium_uptake range
    29643 -1.18 to 0.73 
    29644 
    29645 > hide #!8 models
    29646 
    29647 > select add #5
    29648 
    29649 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    29650 
    29651 > select subtract #5
    29652 
    29653 Nothing selected 
    29654 
    29655 > ui mousemode right zoom
    29656 
    29657 > select #5/H:1-2
    29658 
    29659 13 atoms, 12 bonds, 2 residues, 1 model selected 
    29660 
    29661 > select #5/H:1-3
    29662 
    29663 22 atoms, 21 bonds, 3 residues, 1 model selected 
    29664 
    29665 > select add #5
    29666 
    29667 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    29668 
    29669 > select subtract #5
    29670 
    29671 Nothing selected 
    29672 
    29673 > select add #5
    29674 
    29675 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    29676 
    29677 > select subtract #5
    29678 
    29679 Nothing selected 
    29680 
    29681 > select #5/H:5
    29682 
    29683 9 atoms, 8 bonds, 1 residue, 1 model selected 
    29684 
    29685 > select #5/H:5-14
    29686 
    29687 71 atoms, 71 bonds, 10 residues, 1 model selected 
    29688 
    29689 > color sel #ddddffff
    29690 
    29691 > color sel #aab4ffff
    29692 
    29693 > color sel #8390ffff
    29694 
    29695 > select #5/H:15
    29696 
    29697 9 atoms, 8 bonds, 1 residue, 1 model selected 
    29698 
    29699 > select #5/H:15-29
    29700 
    29701 120 atoms, 124 bonds, 15 residues, 1 model selected 
    29702 
    29703 > color sel #ffe6e6ff
    29704 
    29705 > color sel #ffe2ddff
    29706 
    29707 > color sel #ffe1ddff
    29708 
    29709 > color sel #ffe0dcff
    29710 
    29711 [Repeated 2 time(s)]
    29712 
    29713 > color sel #ffe0dbff
    29714 
    29715 > color sel #ffdfdaff
    29716 
    29717 [Repeated 1 time(s)]
    29718 
    29719 > color sel #ffdedaff
    29720 
    29721 > color sel #ffddd9ff
    29722 
    29723 [Repeated 1 time(s)]
    29724 
    29725 > color sel #ffdcd8ff
    29726 
    29727 > select #5/H:30
    29728 
    29729 6 atoms, 5 bonds, 1 residue, 1 model selected 
    29730 
    29731 > select #5/H:30-35
    29732 
    29733 43 atoms, 43 bonds, 6 residues, 1 model selected 
    29734 
    29735 > ui tool show "Color Actions"
    29736 
    29737 > color sel #6f70ffff
    29738 
    29739 > color sel #4449ffff
    29740 
    29741 > color sel #1f28ffff
    29742 
    29743 > color sel #1f29ffff
    29744 
    29745 > color sel #202affff
    29746 
    29747 > color sel #212cffff
    29748 
    29749 > color sel #222cffff
    29750 
    29751 > color sel #222dffff
    29752 
    29753 > color sel #232effff
    29754 
    29755 > color sel #242fffff
    29756 
    29757 [Repeated 2 time(s)]
    29758 
    29759 > color sel #2531ffff
    29760 
    29761 > color sel #2631ffff
    29762 
    29763 > color sel #2632ffff
    29764 
    29765 > color sel #2732ffff
    29766 
    29767 > color sel #2733ffff
    29768 
    29769 > color sel #2935ffff
    29770 
    29771 > color sel #2a35ffff
    29772 
    29773 > color sel #2a36ffff
    29774 
    29775 > color sel #2b37ffff
    29776 
    29777 > select #5/H:36
    29778 
    29779 12 atoms, 12 bonds, 1 residue, 1 model selected 
    29780 
    29781 > select #5/H:36-47
    29782 
    29783 115 atoms, 120 bonds, 12 residues, 1 model selected 
    29784 
    29785 > color sel #ffcfe1ff
    29786 
    29787 > color sel #ffdddeff
    29788 
    29789 [Repeated 1 time(s)]
    29790 
    29791 > color sel #ffdddfff
    29792 
    29793 > color sel #ffdde2ff
    29794 
    29795 > color sel #ffdde3ff
    29796 
    29797 > color sel #ffdde5ff
    29798 
    29799 > color sel #ffdde8ff
    29800 
    29801 > color sel #ffdde9ff
    29802 
    29803 > color sel #ffdceaff
    29804 
    29805 [Repeated 1 time(s)]
    29806 
    29807 > color sel #ffdce9ff
    29808 
    29809 > color sel #ffdae7ff
    29810 
    29811 > color sel #ffd9e4ff
    29812 
    29813 > color sel #ffd8e2ff
    29814 
    29815 > color sel #ffd7e0ff
    29816 
    29817 > color sel #ffd7dfff
    29818 
    29819 > color sel #ffd6dcff
    29820 
    29821 > color sel #ffd5dbff
    29822 
    29823 > color sel #ffd3daff
    29824 
    29825 > color sel #ffd3d9ff
    29826 
    29827 > color sel #ffd2d7ff
    29828 
    29829 [Repeated 1 time(s)]
    29830 
    29831 > color sel #ffd1d6ff
    29832 
    29833 > color sel #ffd0d5ff
    29834 
    29835 > select #5/H:48
    29836 
    29837 8 atoms, 7 bonds, 1 residue, 1 model selected 
    29838 
    29839 > select #5/H:48-61
    29840 
    29841 120 atoms, 123 bonds, 14 residues, 1 model selected 
    29842 
    29843 > color sel #6277ffff
    29844 
    29845 > select #5/H:62-63
    29846 
    29847 20 atoms, 20 bonds, 2 residues, 1 model selected 
    29848 
    29849 > select #5/H:62-72
    29850 
    29851 91 atoms, 92 bonds, 11 residues, 1 model selected 
    29852 
    29853 > color sel #ff7f7fff
    29854 
    29855 > color sel #ff9b9aff
    29856 
    29857 > select #5/H:79-80
    29858 
    29859 17 atoms, 16 bonds, 2 residues, 1 model selected 
    29860 
    29861 > select #5/H:79-81
    29862 
    29863 28 atoms, 28 bonds, 3 residues, 1 model selected 
    29864 
    29865 > select #5/H:78
    29866 
    29867 9 atoms, 8 bonds, 1 residue, 1 model selected 
    29868 
    29869 > select #5/H:78-95
    29870 
    29871 142 atoms, 144 bonds, 18 residues, 1 model selected 
    29872 
    29873 > color sel #a9b9ffff
    29874 
    29875 > select #5/H:96
    29876 
    29877 12 atoms, 12 bonds, 1 residue, 1 model selected 
    29878 
    29879 > select #5/H:96-103
    29880 
    29881 75 atoms, 78 bonds, 8 residues, 1 model selected 
    29882 
    29883 > color sel #8493ffff
    29884 
    29885 > color sel #88a0ffff
    29886 
    29887 > select #5/H:104
    29888 
    29889 12 atoms, 12 bonds, 1 residue, 1 model selected 
    29890 
    29891 > select #5/H:104-112
    29892 
    29893 73 atoms, 78 bonds, 9 residues, 1 model selected 
    29894 
    29895 > color sel #8296ffff
    29896 
    29897 > color sel #8297ffff
    29898 
    29899 > color sel #8398ffff
    29900 
    29901 > color sel #8499ffff
    29902 
    29903 > color sel #849affff
    29904 
    29905 > color sel #849bffff
    29906 
    29907 > color sel #859cffff
    29908 
    29909 > color sel #859dffff
    29910 
    29911 [Repeated 1 time(s)]
    29912 
    29913 > color sel #869effff
    29914 
    29915 > color sel #869fffff
    29916 
    29917 > color sel #87a0ffff
    29918 
    29919 > color sel #88a1ffff
    29920 
    29921 > color sel #88a2ffff
    29922 
    29923 > color sel #89a3ffff
    29924 
    29925 [Repeated 1 time(s)]
    29926 
    29927 > color sel #8aa4ffff
    29928 
    29929 > color sel #8aa5ffff
    29930 
    29931 > select #5/H:113-114
    29932 
    29933 26 atoms, 28 bonds, 2 residues, 1 model selected 
    29934 
    29935 > select #5/H:113-120
    29936 
    29937 65 atoms, 67 bonds, 8 residues, 1 model selected 
    29938 
    29939 > color sel #aab4ffff
    29940 
    29941 > select #5/H:120-121
    29942 
    29943 14 atoms, 13 bonds, 2 residues, 1 model selected 
    29944 
    29945 > select #5/H:120-121
    29946 
    29947 14 atoms, 13 bonds, 2 residues, 1 model selected 
    29948 
    29949 > select #5/H:120
    29950 
    29951 7 atoms, 6 bonds, 1 residue, 1 model selected 
    29952 
    29953 > select #5/H:120
    29954 
    29955 7 atoms, 6 bonds, 1 residue, 1 model selected 
    29956 
    29957 > color sel #7e95ffff
    29958 
    29959 > select #5/H:121
    29960 
    29961 7 atoms, 6 bonds, 1 residue, 1 model selected 
    29962 
    29963 > select #5/H:121-123
    29964 
    29965 25 atoms, 25 bonds, 3 residues, 1 model selected 
    29966 
    29967 > select #5/H:121
    29968 
    29969 7 atoms, 6 bonds, 1 residue, 1 model selected 
    29970 
    29971 > select #5/H:121-122
    29972 
    29973 14 atoms, 13 bonds, 2 residues, 1 model selected 
    29974 
    29975 > color sel #eceeffff
    29976 
    29977 > color sel #73747cff
    29978 
    29979 [Repeated 1 time(s)]
    29980 
    29981 > color sel #74747dff
    29982 
    29983 > color sel #74757dff
    29984 
    29985 [Repeated 1 time(s)]
    29986 
    29987 > color sel #75757eff
    29988 
    29989 [Repeated 1 time(s)]
    29990 
    29991 > color sel #75767eff
    29992 
    29993 > undo
    29994 
    29995 [Repeated 1 time(s)]
    29996 
    29997 > select #5/H:123-124
    29998 
    29999 16 atoms, 16 bonds, 2 residues, 1 model selected 
    30000 
    30001 > select #5/H:123-145
    30002 
    30003 153 atoms, 157 bonds, 23 residues, 1 model selected 
    30004 
    30005 > color sel #6c6c7eff
    30006 
    30007 > color sel #dad8feff
    30008 
    30009 > color sel #d9d8fdff
    30010 
    30011 [Repeated 1 time(s)]
    30012 
    30013 > color sel #d8d7fcff
    30014 
    30015 > color sel #d6d5f9ff
    30016 
    30017 > color sel #d5d4f8ff
    30018 
    30019 > color sel #d4d3f7ff
    30020 
    30021 > color sel #d4d2f7ff
    30022 
    30023 > color sel #d3d2f6ff
    30024 
    30025 > color sel #d3d1f5ff
    30026 
    30027 > color sel #d2d1f5ff
    30028 
    30029 > color sel #d1d0f4ff
    30030 
    30031 > color sel #cbcaecff
    30032 
    30033 > color sel #c7c6e8ff
    30034 
    30035 > color sel #c5c4e6ff
    30036 
    30037 > color sel #b3c3e6ff
    30038 
    30039 > color sel #b6bee6ff
    30040 
    30041 > select #5/H:146-193
    30042 
    30043 349 atoms, 358 bonds, 48 residues, 1 model selected 
    30044 
    30045 > select #5/H:146-156
    30046 
    30047 79 atoms, 79 bonds, 11 residues, 1 model selected 
    30048 
    30049 > color sel #e6ced9ff
    30050 
    30051 > color sel #e6bfbaff
    30052 
    30053 > select #5/H:157-159
    30054 
    30055 27 atoms, 28 bonds, 3 residues, 1 model selected 
    30056 
    30057 > select #5/H:157-168
    30058 
    30059 93 atoms, 97 bonds, 12 residues, 1 model selected 
    30060 
    30061 > color sel #e6b7aeff
    30062 
    30063 > select #5/H:169-171
    30064 
    30065 20 atoms, 19 bonds, 3 residues, 1 model selected 
    30066 
    30067 > select #5/H:169-176
    30068 
    30069 54 atoms, 54 bonds, 8 residues, 1 model selected 
    30070 
    30071 > color sel #c1c4e6ff
    30072 
    30073 > select #5/H:177
    30074 
    30075 11 atoms, 11 bonds, 1 residue, 1 model selected 
    30076 
    30077 > select #5/H:177
    30078 
    30079 11 atoms, 11 bonds, 1 residue, 1 model selected 
    30080 
    30081 > color sel #e6d7dbff
    30082 
    30083 > color sel #e6bfc0ff
    30084 
    30085 > select #5/H:181
    30086 
    30087 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30088 
    30089 > select #5/H:181-184
    30090 
    30091 29 atoms, 28 bonds, 4 residues, 1 model selected 
    30092 
    30093 > select #5/H:180
    30094 
    30095 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30096 
    30097 > color sel #e6ced4ff
    30098 
    30099 > select #5/H:181
    30100 
    30101 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30102 
    30103 > select #5/H:181-186
    30104 
    30105 41 atoms, 40 bonds, 6 residues, 1 model selected 
    30106 
    30107 > color sel #e6c9cdff
    30108 
    30109 > color sel #e6c2c5ff
    30110 
    30111 [Repeated 1 time(s)]
    30112 
    30113 > color sel #e6c3c5ff
    30114 
    30115 > color sel #e6c3c6ff
    30116 
    30117 > color sel #e6c4c7ff
    30118 
    30119 [Repeated 1 time(s)]
    30120 
    30121 > color sel #e6c5c8ff
    30122 
    30123 > color sel #e6c5c7ff
    30124 
    30125 > color sel #e6c5c8ff
    30126 
    30127 > color sel #e6c6c8ff
    30128 
    30129 [Repeated 1 time(s)]
    30130 
    30131 > select #5/H:188
    30132 
    30133 6 atoms, 5 bonds, 1 residue, 1 model selected 
    30134 
    30135 > select #5/H:188-198
    30136 
    30137 73 atoms, 73 bonds, 11 residues, 1 model selected 
    30138 
    30139 > color sel #b4b7e6ff
    30140 
    30141 > select #5/H:199-200
    30142 
    30143 14 atoms, 13 bonds, 2 residues, 1 model selected 
    30144 
    30145 > select #5/H:199-208
    30146 
    30147 75 atoms, 76 bonds, 10 residues, 1 model selected 
    30148 
    30149 > color sel #8999e6ff
    30150 
    30151 > color sel #7b90e6ff
    30152 
    30153 > color sel #7083e6ff
    30154 
    30155 > select #5/H:209
    30156 
    30157 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30158 
    30159 > select #5/H:209-212
    30160 
    30161 34 atoms, 34 bonds, 4 residues, 1 model selected 
    30162 
    30163 > color sel #95a4e6ff
    30164 
    30165 > color sel #b0b6e6ff
    30166 
    30167 > select #5/H:213-214
    30168 
    30169 13 atoms, 13 bonds, 2 residues, 1 model selected 
    30170 
    30171 > select #5/H:213-223
    30172 
    30173 86 atoms, 86 bonds, 11 residues, 1 model selected 
    30174 
    30175 > color sel #93a0e6ff
    30176 
    30177 > select #5/L:1
    30178 
    30179 5 atoms, 4 bonds, 1 residue, 1 model selected 
    30180 
    30181 > select #5/L:1-6
    30182 
    30183 45 atoms, 44 bonds, 6 residues, 1 model selected 
    30184 
    30185 > select #5/L:7-8
    30186 
    30187 15 atoms, 14 bonds, 2 residues, 1 model selected 
    30188 
    30189 > select #5/L:7-14
    30190 
    30191 58 atoms, 58 bonds, 8 residues, 1 model selected 
    30192 
    30193 > color sel #9daae6ff
    30194 
    30195 > select #5/L:15
    30196 
    30197 6 atoms, 5 bonds, 1 residue, 1 model selected 
    30198 
    30199 > select #5/L:15-21
    30200 
    30201 47 atoms, 46 bonds, 7 residues, 1 model selected 
    30202 
    30203 > color sel #e6c2caff
    30204 
    30205 > color sel #e6c3c3ff
    30206 
    30207 > select #5/L:22-23
    30208 
    30209 15 atoms, 14 bonds, 2 residues, 1 model selected 
    30210 
    30211 > select #5/L:22-26
    30212 
    30213 36 atoms, 35 bonds, 5 residues, 1 model selected 
    30214 
    30215 > color sel #e6cdceff
    30216 
    30217 > select #5/L:27-28
    30218 
    30219 11 atoms, 10 bonds, 2 residues, 1 model selected 
    30220 
    30221 > select #5/L:27-28
    30222 
    30223 11 atoms, 10 bonds, 2 residues, 1 model selected 
    30224 
    30225 > color sel #a5bbe6ff
    30226 
    30227 > color sel #a5b6e6ff
    30228 
    30229 > select #5/L:29-30
    30230 
    30231 12 atoms, 11 bonds, 2 residues, 1 model selected 
    30232 
    30233 > select #5/L:29-35
    30234 
    30235 51 atoms, 51 bonds, 7 residues, 1 model selected 
    30236 
    30237 > color sel #c4c6e6ff
    30238 
    30239 > color sel #d0d4e6ff
    30240 
    30241 > select #5/L:36-37
    30242 
    30243 24 atoms, 26 bonds, 2 residues, 1 model selected 
    30244 
    30245 > select #5/L:36
    30246 
    30247 10 atoms, 10 bonds, 1 residue, 1 model selected 
    30248 
    30249 > color sel #c7cfe6ff
    30250 
    30251 > select #5/L:37
    30252 
    30253 14 atoms, 15 bonds, 1 residue, 1 model selected 
    30254 
    30255 > select #5/L:37-38
    30256 
    30257 26 atoms, 28 bonds, 2 residues, 1 model selected 
    30258 
    30259 > color sel #b2bde6ff
    30260 
    30261 > color sel #abbae6ff
    30262 
    30263 > color sel #abbbe6ff
    30264 
    30265 > color sel #abbce6ff
    30266 
    30267 > color sel #acbce6ff
    30268 
    30269 > color sel #acbde6ff
    30270 
    30271 > color sel #adbee6ff
    30272 
    30273 [Repeated 1 time(s)]
    30274 
    30275 > color sel #adbfe6ff
    30276 
    30277 [Repeated 1 time(s)]
    30278 
    30279 > color sel #adc0e6ff
    30280 
    30281 > color sel #aec0e6ff
    30282 
    30283 > color sel #aec1e6ff
    30284 
    30285 > color sel #aec2e6ff
    30286 
    30287 > color sel #afc2e6ff
    30288 
    30289 > color sel #afc3e6ff
    30290 
    30291 > color sel #afc2e6ff
    30292 
    30293 > color sel #aec2e6ff
    30294 
    30295 > color sel #aec1e6ff
    30296 
    30297 > color sel #aec0e6ff
    30298 
    30299 [Repeated 1 time(s)]
    30300 
    30301 > color sel #aebfe6ff
    30302 
    30303 > color sel #adbee6ff
    30304 
    30305 > color sel #b0c3e6ff
    30306 
    30307 [Repeated 1 time(s)]
    30308 
    30309 > color sel #b0c2e6ff
    30310 
    30311 > color sel #b0c1e6ff
    30312 
    30313 [Repeated 2 time(s)]
    30314 
    30315 > color sel #b0c0e6ff
    30316 
    30317 [Repeated 2 time(s)]
    30318 
    30319 > color sel #b0bfe6ff
    30320 
    30321 [Repeated 1 time(s)]
    30322 
    30323 > color sel #b1bfe6ff
    30324 
    30325 [Repeated 2 time(s)]
    30326 
    30327 > color sel #b1bee6ff
    30328 
    30329 [Repeated 1 time(s)]
    30330 
    30331 > color sel #b2bee6ff
    30332 
    30333 > select #5/L:39
    30334 
    30335 9 atoms, 8 bonds, 1 residue, 1 model selected 
    30336 
    30337 > select #5/L:39-48
    30338 
    30339 74 atoms, 74 bonds, 10 residues, 1 model selected 
    30340 
    30341 > color sel #abbbe6ff
    30342 
    30343 > select #5/L:49
    30344 
    30345 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30346 
    30347 > color sel #a1ace6ff
    30348 
    30349 > color sel #a1ade6ff
    30350 
    30351 > color sel #a0b1e6ff
    30352 
    30353 > color sel #a1b1e6ff
    30354 
    30355 > select #5/L:50
    30356 
    30357 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30358 
    30359 > select #5/L:50-55
    30360 
    30361 47 atoms, 47 bonds, 6 residues, 1 model selected 
    30362 
    30363 > color sel #6a88e6ff
    30364 
    30365 > color sel #5b80e6ff
    30366 
    30367 > color sel #5176e6ff
    30368 
    30369 > color sel #426be6ff
    30370 
    30371 > color sel #3b67e6ff
    30372 
    30373 > color sel #315ae6ff
    30374 
    30375 > select #5/L:56
    30376 
    30377 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30378 
    30379 > select #5/L:56
    30380 
    30381 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30382 
    30383 > color sel #3f64e6ff
    30384 
    30385 > select #5/L:57
    30386 
    30387 5 atoms, 4 bonds, 1 residue, 1 model selected 
    30388 
    30389 > select #5/L:57
    30390 
    30391 5 atoms, 4 bonds, 1 residue, 1 model selected 
    30392 
    30393 > color sel #b3b7e6ff
    30394 
    30395 > select #5/L:58
    30396 
    30397 6 atoms, 5 bonds, 1 residue, 1 model selected 
    30398 
    30399 > select #5/L:58-69
    30400 
    30401 78 atoms, 79 bonds, 12 residues, 1 model selected 
    30402 
    30403 > color sel #b0b2e6ff
    30404 
    30405 > select #5/L:70-71
    30406 
    30407 11 atoms, 10 bonds, 2 residues, 1 model selected 
    30408 
    30409 > select #5/L:70-73
    30410 
    30411 34 atoms, 35 bonds, 4 residues, 1 model selected 
    30412 
    30413 > color sel #a9ace6ff
    30414 
    30415 > select #5/L:74-75
    30416 
    30417 14 atoms, 13 bonds, 2 residues, 1 model selected 
    30418 
    30419 > select #5/L:74-79
    30420 
    30421 41 atoms, 40 bonds, 6 residues, 1 model selected 
    30422 
    30423 > color sel #9eaae6ff
    30424 
    30425 > select #5/L:80
    30426 
    30427 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30428 
    30429 > select #5/L:80-82
    30430 
    30431 21 atoms, 20 bonds, 3 residues, 1 model selected 
    30432 
    30433 > color sel #d3cbe6ff
    30434 
    30435 > color sel #e6ced1ff
    30436 
    30437 > select #5/L:83
    30438 
    30439 9 atoms, 8 bonds, 1 residue, 1 model selected 
    30440 
    30441 > select #5/L:83
    30442 
    30443 9 atoms, 8 bonds, 1 residue, 1 model selected 
    30444 
    30445 > select #5/L:82
    30446 
    30447 5 atoms, 4 bonds, 1 residue, 1 model selected 
    30448 
    30449 > select #5/L:82-83
    30450 
    30451 14 atoms, 13 bonds, 2 residues, 1 model selected 
    30452 
    30453 > volume #8 level 0.09283
    30454 
    30455 > color sel #b7bbe6ff
    30456 
    30457 > select #5/L:84
    30458 
    30459 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30460 
    30461 > select #5/L:84-87
    30462 
    30463 26 atoms, 25 bonds, 4 residues, 1 model selected 
    30464 
    30465 > color sel #d9cce6ff
    30466 
    30467 > color sel #e6d9e4ff
    30468 
    30469 > color sel #e6d2d0ff
    30470 
    30471 > select #5/L:98-99
    30472 
    30473 15 atoms, 15 bonds, 2 residues, 1 model selected 
    30474 
    30475 > select #5/L:98-100
    30476 
    30477 19 atoms, 19 bonds, 3 residues, 1 model selected 
    30478 
    30479 > select #5/L:97
    30480 
    30481 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30482 
    30483 > select #5/L:97
    30484 
    30485 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30486 
    30487 > color sel #d0d1e6ff
    30488 
    30489 > select #5/L:98-99
    30490 
    30491 15 atoms, 15 bonds, 2 residues, 1 model selected 
    30492 
    30493 > select #5/L:98-105
    30494 
    30495 56 atoms, 56 bonds, 8 residues, 1 model selected 
    30496 
    30497 > color sel #a9aee6ff
    30498 
    30499 > select #5/L:114-115
    30500 
    30501 13 atoms, 12 bonds, 2 residues, 1 model selected 
    30502 
    30503 > select #5/L:114-125
    30504 
    30505 97 atoms, 100 bonds, 12 residues, 1 model selected 
    30506 
    30507 > color sel #a8ace6ff
    30508 
    30509 > select #5/L:128-129
    30510 
    30511 11 atoms, 10 bonds, 2 residues, 1 model selected 
    30512 
    30513 > select #5/L:128-131
    30514 
    30515 22 atoms, 21 bonds, 4 residues, 1 model selected 
    30516 
    30517 > color sel #ccccffff
    30518 
    30519 > select #5/L:132
    30520 
    30521 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30522 
    30523 > select #5/L:132-137
    30524 
    30525 44 atoms, 43 bonds, 6 residues, 1 model selected 
    30526 
    30527 > color sel #ffeefaff
    30528 
    30529 > color sel #ffe4e2ff
    30530 
    30531 > color sel #ffe7ddff
    30532 
    30533 > color sel #ffe7dcff
    30534 
    30535 [Repeated 2 time(s)]
    30536 
    30537 > color sel #ffe7dbff
    30538 
    30539 [Repeated 1 time(s)]
    30540 
    30541 > color sel #ffe8daff
    30542 
    30543 > color sel #ffe7daff
    30544 
    30545 > color sel #ffe3d2ff
    30546 
    30547 > color sel #ffe1cdff
    30548 
    30549 > color sel #ffe2cdff
    30550 
    30551 > color sel #ffdbc2ff
    30552 
    30553 > color sel #ffdac2ff
    30554 
    30555 > color sel #ffd5c2ff
    30556 
    30557 > select #5/L:138
    30558 
    30559 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30560 
    30561 > select #5/L:138-146
    30562 
    30563 79 atoms, 81 bonds, 9 residues, 1 model selected 
    30564 
    30565 > color sel #d0d6ffff
    30566 
    30567 > color sel #c1c6ffff
    30568 
    30569 > color sel #b1bdffff
    30570 
    30571 > select #5/L:147
    30572 
    30573 9 atoms, 8 bonds, 1 residue, 1 model selected 
    30574 
    30575 > select #5/L:147-158
    30576 
    30577 95 atoms, 96 bonds, 12 residues, 1 model selected 
    30578 
    30579 > color sel #ff5b5bff
    30580 
    30581 > color sel #ff484dff
    30582 
    30583 > color sel #ff4347ff
    30584 
    30585 > color sel #ff4247ff
    30586 
    30587 > color sel #ff4146ff
    30588 
    30589 > color sel #ff4145ff
    30590 
    30591 > color sel #ff4045ff
    30592 
    30593 > color sel #ff4044ff
    30594 
    30595 > color sel #ff3f43ff
    30596 
    30597 > color sel #ff3e43ff
    30598 
    30599 > color sel #ff3e42ff
    30600 
    30601 > color sel #ff3d42ff
    30602 
    30603 > color sel #ff3c41ff
    30604 
    30605 > color sel #ff3c40ff
    30606 
    30607 > color sel #ff3b40ff
    30608 
    30609 > color sel #ff3c40ff
    30610 
    30611 [Repeated 2 time(s)]
    30612 
    30613 > color sel #ff3d40ff
    30614 
    30615 > color sel #ff3e40ff
    30616 
    30617 [Repeated 1 time(s)]
    30618 
    30619 > color sel #ff3e41ff
    30620 
    30621 > color sel #ff3f41ff
    30622 
    30623 > color sel #ff3f40ff
    30624 
    30625 > color sel #ff4040ff
    30626 
    30627 [Repeated 2 time(s)]
    30628 
    30629 > color sel #ff3f3aff
    30630 
    30631 > color sel #ff3e39ff
    30632 
    30633 [Repeated 2 time(s)]
    30634 
    30635 > color sel #ff3e38ff
    30636 
    30637 [Repeated 1 time(s)]
    30638 
    30639 > select #5/L:159-160
    30640 
    30641 15 atoms, 14 bonds, 2 residues, 1 model selected 
    30642 
    30643 > select #5/L:159-160
    30644 
    30645 15 atoms, 14 bonds, 2 residues, 1 model selected 
    30646 
    30647 > select #5/L:161-162
    30648 
    30649 15 atoms, 14 bonds, 2 residues, 1 model selected 
    30650 
    30651 > select #5/L:161-179
    30652 
    30653 144 atoms, 144 bonds, 19 residues, 1 model selected 
    30654 
    30655 > select #5/L:180-181
    30656 
    30657 15 atoms, 14 bonds, 2 residues, 1 model selected 
    30658 
    30659 > select #5/L:180-182
    30660 
    30661 21 atoms, 20 bonds, 3 residues, 1 model selected 
    30662 
    30663 > select #5/L:183
    30664 
    30665 9 atoms, 8 bonds, 1 residue, 1 model selected 
    30666 
    30667 > select #5/L:183-204
    30668 
    30669 176 atoms, 180 bonds, 22 residues, 1 model selected 
    30670 
    30671 > color sel #6f7bffff
    30672 
    30673 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    30674 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
    30675 
    30676 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    30677 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
    30678 > includeMaps true
    30679 
    30680 > show #!8 models
    30681 
    30682 > select add #5
    30683 
    30684 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    30685 
    30686 > select subtract #5
    30687 
    30688 Nothing selected 
    30689 
    30690 > hide #!8 models
    30691 
    30692 > select add #8
    30693 
    30694 2 models selected 
    30695 
    30696 > select subtract #8
    30697 
    30698 Nothing selected 
    30699 
    30700 > color #8 #c5fdf81a models
    30701 
    30702 > show #!8 models
    30703 
    30704 > ui tool show "Show Sequence Viewer"
    30705 
    30706 > sequence chain #3/B
    30707 
    30708 Alignment identifier is 3/B 
    30709 
    30710 > select #3/B:111
    30711 
    30712 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30713 
    30714 > select #3/B:111-271
    30715 
    30716 1300 atoms, 1342 bonds, 161 residues, 1 model selected 
    30717 
    30718 > select #3/B:302
    30719 
    30720 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30721 
    30722 > select #3/B:302-304
    30723 
    30724 18 atoms, 17 bonds, 3 residues, 1 model selected 
    30725 
    30726 > select #3/B:301-302
    30727 
    30728 14 atoms, 13 bonds, 2 residues, 1 model selected 
    30729 
    30730 > select #3/B:301-310
    30731 
    30732 70 atoms, 69 bonds, 10 residues, 1 model selected 
    30733 
    30734 > hide #5 models
    30735 
    30736 > show #5 models
    30737 
    30738 > select add #5
    30739 
    30740 3471 atoms, 3562 bonds, 452 residues, 2 models selected 
    30741 
    30742 > select subtract #5
    30743 
    30744 70 atoms, 69 bonds, 10 residues, 1 model selected 
    30745 
    30746 > select add #3
    30747 
    30748 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    30749 
    30750 > select subtract #3
    30751 
    30752 Nothing selected 
    30753 
    30754 > select add #5
    30755 
    30756 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    30757 
    30758 > select #3/B:301
    30759 
    30760 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30761 
    30762 > select #3/B:301-313
    30763 
    30764 96 atoms, 97 bonds, 13 residues, 1 model selected 
    30765 
    30766 > select add #5
    30767 
    30768 3497 atoms, 3590 bonds, 455 residues, 2 models selected 
    30769 
    30770 > select add #3
    30771 
    30772 9003 atoms, 9237 bonds, 1146 residues, 2 models selected 
    30773 
    30774 > select subtract #3
    30775 
    30776 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    30777 
    30778 > ui mousemode right "translate selected models"
    30779 
    30780 > view matrix models
    30781 > #5,-0.17857,0.27184,0.94563,-4.5206,0.69023,0.71954,-0.076505,-64.572,-0.70121,0.63904,-0.31613,263.65
    30782 
    30783 > view matrix models
    30784 > #5,-0.17857,0.27184,0.94563,-4.1095,0.69023,0.71954,-0.076505,-65.814,-0.70121,0.63904,-0.31613,263.22
    30785 
    30786 > view matrix models
    30787 > #5,-0.17857,0.27184,0.94563,-4.2566,0.69023,0.71954,-0.076505,-65.556,-0.70121,0.63904,-0.31613,262.84
    30788 
    30789 > view matrix models
    30790 > #5,-0.17857,0.27184,0.94563,-3.5932,0.69023,0.71954,-0.076505,-65.573,-0.70121,0.63904,-0.31613,263.6
    30791 
    30792 > view matrix models
    30793 > #5,-0.17857,0.27184,0.94563,6.1172,0.69023,0.71954,-0.076505,-64.318,-0.70121,0.63904,-0.31613,265.1
    30794 
    30795 > view matrix models
    30796 > #5,-0.17857,0.27184,0.94563,6.2366,0.69023,0.71954,-0.076505,-63.955,-0.70121,0.63904,-0.31613,264.58
    30797 
    30798 > ui mousemode right "rotate selected models"
    30799 
    30800 > view matrix models
    30801 > #5,-0.50511,0.42112,0.75334,81.099,-0.58382,-0.80958,0.061111,408.82,0.63563,-0.40895,0.65478,-4.5259
    30802 
    30803 > view matrix models
    30804 > #5,-0.71614,0.48271,0.50412,165.69,-0.55355,-0.83274,0.011012,419.78,0.42512,-0.27117,0.86356,-43.167
    30805 
    30806 > view matrix models
    30807 > #5,-0.85245,0.30633,0.42367,241.3,-0.43531,-0.86468,-0.25067,467.41,0.28955,-0.39811,0.87044,2.3483
    30808 
    30809 > view matrix models
    30810 > #5,-0.93915,0.14358,0.31205,313.16,-0.24014,-0.924,-0.29757,455.63,0.24561,-0.3544,0.90226,-5.6943
    30811 
    30812 > ui mousemode right "translate selected models"
    30813 
    30814 > view matrix models
    30815 > #5,-0.93915,0.14358,0.31205,310.36,-0.24014,-0.924,-0.29757,454.57,0.24561,-0.3544,0.90226,-10.513
    30816 
    30817 > ui mousemode right "rotate selected models"
    30818 
    30819 > view matrix models
    30820 > #5,-0.92978,0.12057,0.3478,304.49,-0.25511,-0.89219,-0.3727,469.15,0.26537,-0.43526,0.86031,11.045
    30821 
    30822 > ui mousemode right "translate selected models"
    30823 
    30824 > view matrix models
    30825 > #5,-0.92978,0.12057,0.3478,301.55,-0.25511,-0.89219,-0.3727,465.8,0.26537,-0.43526,0.86031,10.049
    30826 
    30827 > ui mousemode right "rotate selected models"
    30828 
    30829 > view matrix models
    30830 > #5,-0.96388,-0.016383,0.26582,352.42,-0.11335,-0.87796,-0.46513,460.49,0.241,-0.47846,0.84439,26.097
    30831 
    30832 > view matrix models
    30833 > #5,-0.91826,0.06169,0.39115,300.16,-0.36231,-0.52952,-0.76703,510.97,0.15981,-0.84605,0.50859,188.38
    30834 
    30835 > view matrix models
    30836 > #5,-0.92676,0.077675,0.36753,304.3,-0.31305,-0.70047,-0.64136,504.23,0.20763,-0.70944,0.67349,115.46
    30837 
    30838 > view matrix models
    30839 > #5,-0.9834,-0.04765,0.17507,383.22,-0.094665,-0.6884,-0.71913,482.5,0.15478,-0.72376,0.67247,127.55
    30840 
    30841 > view matrix models
    30842 > #5,-0.95001,-0.19011,0.24767,386.58,-0.077458,-0.62494,-0.77682,481.46,0.30246,-0.75717,0.57898,130.31
    30843 
    30844 > view matrix models
    30845 > #5,-0.94393,-0.018851,0.3296,334.23,-0.26473,-0.55329,-0.7898,503.83,0.19725,-0.83277,0.51728,177.33
    30846 
    30847 > view matrix models
    30848 > #5,-0.84008,0.30007,0.45192,227.84,-0.54043,-0.53518,-0.64924,514.98,0.047043,-0.78964,0.61176,172.97
    30849 
    30850 > view matrix models
    30851 > #5,-0.90734,0.12615,0.40102,283.95,-0.29751,-0.86665,-0.40051,475.05,0.29702,-0.48271,0.82388,22.022
    30852 
    30853 > view matrix models
    30854 > #5,-0.89414,0.12288,0.43059,275.22,-0.30852,-0.866,-0.39353,475.19,0.32453,-0.48472,0.81224,20.379
    30855 
    30856 > view matrix models
    30857 > #5,-0.89988,0.10062,0.42437,281.83,-0.22953,-0.93663,-0.26465,443.88,0.37085,-0.33556,0.86595,-28.153
    30858 
    30859 > view matrix models
    30860 > #5,-0.91467,-0.052744,0.40075,318.49,-0.021786,-0.98358,-0.17917,396.11,0.40362,-0.17262,0.8985,-71.851
    30861 
    30862 > view matrix models
    30863 > #5,-0.83178,-0.098166,0.54635,277.86,0.12592,-0.99195,0.013478,326.12,0.54063,0.080008,0.83745,-128.06
    30864 
    30865 > view matrix models
    30866 > #5,-0.63629,-0.24728,0.73074,227.64,0.13032,-0.96808,-0.21411,375.09,0.76036,-0.041004,0.6482,-98.781
    30867 
    30868 > view matrix models
    30869 > #5,-0.61952,-0.21214,0.75577,212.25,0.091718,-0.97576,-0.19871,379.56,0.7796,-0.05379,0.62396,-93.986
    30870 
    30871 > view matrix models
    30872 > #5,-0.75135,-0.11146,0.65042,241.56,0.10086,-0.99345,-0.053733,346.75,0.65215,0.025229,0.75767,-118.3
    30873 
    30874 > view matrix models
    30875 > #5,-0.66332,-0.23987,0.70885,236.18,0.33554,-0.94201,-0.0047814,284.72,0.6689,0.23468,0.70534,-147.64
    30876 
    30877 > view matrix models
    30878 > #5,-0.7722,0.036461,0.63433,221.56,0.075095,-0.98612,0.1481,301.84,0.63093,0.162,0.75874,-140.25
    30879 
    30880 > view matrix models
    30881 > #5,-0.77412,-0.056826,0.63048,240.13,0.10514,-0.99367,0.039532,323.85,0.62424,0.096891,0.7752,-130.92
    30882 
    30883 > view matrix models
    30884 > #5,-0.82608,-0.15163,0.54277,287.64,0.13237,-0.98838,-0.074658,345.31,0.54779,0.010175,0.83655,-116.13
    30885 
    30886 > ui mousemode right "translate selected models"
    30887 
    30888 > view matrix models
    30889 > #5,-0.82608,-0.15163,0.54277,287.24,0.13237,-0.98838,-0.074658,345.43,0.54779,0.010175,0.83655,-116.45
    30890 
    30891 > view matrix models
    30892 > #5,-0.82608,-0.15163,0.54277,287.21,0.13237,-0.98838,-0.074658,345.17,0.54779,0.010175,0.83655,-116.29
    30893 
    30894 > select subtract #5
    30895 
    30896 Nothing selected 
    30897 
    30898 > select #3/B:301
    30899 
    30900 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30901 
    30902 > select #3/B:301-313
    30903 
    30904 96 atoms, 97 bonds, 13 residues, 1 model selected 
    30905 
    30906 > select #3/B:310
    30907 
    30908 9 atoms, 8 bonds, 1 residue, 1 model selected 
    30909 
    30910 > select #3/B:300-310
    30911 
    30912 77 atoms, 76 bonds, 11 residues, 1 model selected 
    30913 
    30914 > ui mousemode right "rotate selected models"
    30915 
    30916 > select add #5
    30917 
    30918 3478 atoms, 3569 bonds, 453 residues, 2 models selected 
    30919 
    30920 > select add #3
    30921 
    30922 9003 atoms, 9237 bonds, 1146 residues, 2 models selected 
    30923 
    30924 > select subtract #3
    30925 
    30926 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    30927 
    30928 > view matrix models
    30929 > #5,-0.57941,0.69777,0.4212,115.54,-0.37625,0.22943,-0.89766,403.45,-0.723,-0.67859,0.1296,400.92
    30930 
    30931 > view matrix models
    30932 > #5,-0.42133,0.73627,0.52952,55.111,0.43201,0.67631,-0.59663,108.23,-0.7974,-0.022616,-0.60303,466.45
    30933 
    30934 > view matrix models
    30935 > #5,-0.21413,0.8577,0.46743,11.295,0.513,0.50597,-0.69341,148.79,-0.83125,0.091314,-0.54835,438.17
    30936 
    30937 > view matrix models
    30938 > #5,-0.1885,0.67264,0.71556,-17.862,0.29998,0.73323,-0.61023,123.87,-0.93514,0.09963,-0.33999,405.12
    30939 
    30940 > log thumbnail
    30941 
    30942 ![](data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAABkCAIAAAD/gAIDAAAXEklEQVR4nO1deZgdVZX/1Xuvu9NJ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%0AaB9Y06B9YE2D9oE1Dfo/aRiVuzY0Nb4AAAAASUVORK5CYII=%0A) 
    30943 
    30944 > view matrix models
    30945 > #5,-0.31715,0.77532,0.54617,25.775,0.1619,0.61171,-0.77434,209.51,-0.93445,-0.15716,-0.31953,447.8
    30946 
    30947 > view matrix models
    30948 > #5,-0.32237,0.77028,0.55023,26.653,0.15917,0.61709,-0.77062,208.1,-0.93313,-0.16085,-0.32154,448.73
    30949 
    30950 > view matrix models
    30951 > #5,-0.35979,0.63359,0.68492,26.481,0.1023,0.75644,-0.64601,162.47,-0.92741,-0.16236,-0.33698,451.69
    30952 
    30953 > select subtract #5
    30954 
    30955 Nothing selected 
    30956 
    30957 > select add #5
    30958 
    30959 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    30960 
    30961 > view matrix models
    30962 > #5,-0.22546,0.76745,0.60016,-1.5674,0.19788,0.63926,-0.7431,190.7,-0.95395,-0.048776,-0.29599,425.47
    30963 
    30964 > view matrix models
    30965 > #5,0.070979,0.66168,0.74642,-68.315,0.16435,0.73032,-0.66304,160.57,-0.98385,0.16974,-0.056909,333.2
    30966 
    30967 > view matrix models
    30968 > #5,0.11489,0.59902,0.79245,-75.277,0.39981,0.70238,-0.5889,107.15,-0.90937,0.38449,-0.1588,304.63
    30969 
    30970 > view matrix models
    30971 > #5,0.18754,0.5726,0.7981,-84.357,0.35537,0.71792,-0.59858,114.3,-0.91572,0.39588,-0.068839,282.21
    30972 
    30973 > view matrix models
    30974 > #5,0.12973,0.70112,0.70114,-75.082,0.32499,0.63799,-0.6981,158.11,-0.93678,0.31843,-0.14509,318.4
    30975 
    30976 > view matrix models
    30977 > #5,0.012151,0.66827,0.74382,-58.685,0.27803,0.71228,-0.64448,139.73,-0.9605,0.21463,-0.17714,349.42
    30978 
    30979 > view matrix models
    30980 > #5,0.087714,-0.77021,0.63174,221.89,0.82852,-0.29568,-0.47553,190.87,0.55305,0.56511,0.61219,-166.83
    30981 
    30982 > view matrix models
    30983 > #5,-0.33436,-0.81985,0.46481,344.26,0.68971,-0.54897,-0.47216,261.24,0.64227,0.16271,0.74901,-140.21
    30984 
    30985 > view matrix models
    30986 > #5,-0.44895,-0.57242,0.68614,265.59,0.52883,-0.78916,-0.31235,295.78,0.72027,0.22263,0.657,-143
    30987 
    30988 > view matrix models
    30989 > #5,-0.4442,-0.59383,0.67086,272.37,0.54224,-0.77427,-0.32633,294.01,0.7132,0.21881,0.66593,-143.19
    30990 
    30991 > view matrix models
    30992 > #5,-0.46401,-0.4815,0.74354,237.67,0.47306,-0.84435,-0.25157,301.26,0.74894,0.23501,0.61957,-141.38
    30993 
    30994 > view matrix models
    30995 > #5,-0.44441,-0.50908,0.73711,240.91,0.50441,-0.8222,-0.26373,294.59,0.74031,0.25461,0.62218,-144.14
    30996 
    30997 > ui mousemode right "translate selected models"
    30998 
    30999 > view matrix models
    31000 > #5,-0.44441,-0.50908,0.73711,237.62,0.50441,-0.8222,-0.26373,296.55,0.74031,0.25461,0.62218,-146.91
    31001 
    31002 > ui mousemode right "rotate selected models"
    31003 
    31004 > view matrix models
    31005 > #5,-0.60143,-0.49924,0.62373,290.1,0.509,-0.8412,-0.18249,279.94,0.61579,0.20772,0.76004,-149.35
    31006 
    31007 > view matrix models
    31008 > #5,-0.74827,-0.24752,0.61549,270.87,0.3197,-0.94749,0.0076404,287.36,0.58128,0.20249,0.78811,-149.06
    31009 
    31010 > view matrix models
    31011 > #5,-0.81926,-0.51039,0.26136,416.31,0.4815,-0.85984,-0.1698,285.16,0.31139,-0.013269,0.95019,-100.62
    31012 
    31013 > view matrix models
    31014 > #5,-0.8197,-0.3099,0.48172,326.72,0.29937,-0.94878,-0.10096,316.98,0.48834,0.061452,0.87049,-126.31
    31015 
    31016 > view matrix models
    31017 > #5,-0.74081,-0.34591,0.57581,297.29,0.14449,-0.91921,-0.3663,401.59,0.65599,-0.18816,0.73094,-75.929
    31018 
    31019 > view matrix models
    31020 > #5,-0.81757,-0.07895,0.57039,262.37,-0.070004,-0.96958,-0.23455,416.9,0.57155,-0.23169,0.78718,-66.543
    31021 
    31022 > view matrix models
    31023 > #5,-0.91951,-0.12462,0.37278,335.62,0.063486,-0.98304,-0.17204,381.3,0.3879,-0.13453,0.91183,-82.295
    31024 
    31025 > view matrix models
    31026 > #5,-0.90793,0.0064486,0.41907,298.25,-0.059509,-0.99174,-0.11367,390.42,0.41488,-0.12814,0.90081,-85.551
    31027 
    31028 > view matrix models
    31029 > #5,-0.91351,-0.073219,0.40017,318.51,-0.028011,-0.97001,-0.24143,411.31,0.40585,-0.23176,0.88407,-60.76
    31030 
    31031 > view matrix models
    31032 > #5,-0.89133,0.0016103,0.45335,288.11,-0.071877,-0.98785,-0.13781,397.59,0.44762,-0.15542,0.88062,-81.377
    31033 
    31034 > view matrix models
    31035 > #5,-0.88255,0.076297,0.46398,270.18,-0.18199,-0.96527,-0.18743,424.37,0.43356,-0.24986,0.86579,-57.872
    31036 
    31037 > ui mousemode right select
    31038 
    31039 > select clear
    31040 
    31041 > ui mousemode right "translate selected models"
    31042 
    31043 > ui mousemode right "rotate selected models"
    31044 
    31045 > select add #5
    31046 
    31047 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    31048 
    31049 > view matrix models
    31050 > #5,-0.90173,0.066834,0.42711,284.05,-0.16494,-0.96643,-0.197,423.89,0.3996,-0.24809,0.88248,-56.263
    31051 
    31052 > view matrix models
    31053 > #5,-0.91899,-0.040079,0.39223,315.2,-0.062389,-0.9675,-0.24504,417.68,0.3893,-0.24966,0.88663,-55.168
    31054 
    31055 > ui mousemode right "translate selected models"
    31056 
    31057 > view matrix models
    31058 > #5,-0.91899,-0.040079,0.39223,315,-0.062389,-0.9675,-0.24504,417.81,0.3893,-0.24966,0.88663,-53.939
    31059 
    31060 > view matrix models
    31061 > #5,-0.91899,-0.040079,0.39223,318.19,-0.062389,-0.9675,-0.24504,417.19,0.3893,-0.24966,0.88663,-52.686
    31062 
    31063 > view matrix models
    31064 > #5,-0.91899,-0.040079,0.39223,318.14,-0.062389,-0.9675,-0.24504,417.21,0.3893,-0.24966,0.88663,-52.699
    31065 
    31066 > view matrix models
    31067 > #5,-0.91899,-0.040079,0.39223,317.71,-0.062389,-0.9675,-0.24504,417.12,0.3893,-0.24966,0.88663,-52.726
    31068 
    31069 > view matrix models
    31070 > #5,-0.91899,-0.040079,0.39223,317.53,-0.062389,-0.9675,-0.24504,417.02,0.3893,-0.24966,0.88663,-52.524
    31071 
    31072 > ui mousemode right "rotate selected models"
    31073 
    31074 > view matrix models
    31075 > #5,-0.94446,-0.024801,0.32768,334.49,-0.074776,-0.95477,-0.28779,426.99,0.31999,-0.29631,0.89989,-34.96
    31076 
    31077 > view matrix models
    31078 > #5,-0.9387,-0.13701,0.31634,357.02,0.018467,-0.93629,-0.35073,422.31,0.34424,-0.32339,0.88143,-29.758
    31079 
    31080 > view matrix models
    31081 > #5,-0.97606,-0.21236,0.047016,441.6,0.10357,-0.64388,-0.75808,450.17,0.19126,-0.73506,0.65046,128.25
    31082 
    31083 > view matrix models
    31084 > #5,-0.97665,-0.2075,0.055729,438.73,0.092906,-0.64173,-0.76128,452.39,0.19373,-0.73832,0.64603,129.48
    31085 
    31086 > view matrix models
    31087 > #5,-0.9734,-0.14293,0.17908,396.82,-0.057279,-0.60498,-0.79418,479.52,0.22185,-0.78331,0.5807,148.49
    31088 
    31089 > view matrix models
    31090 > #5,-0.9046,-0.16174,0.39438,337.11,-0.12194,-0.78835,-0.60302,479.32,0.40844,-0.59359,0.69342,53.977
    31091 
    31092 > view matrix models
    31093 > #5,-0.88062,-0.11723,0.45909,309.27,-0.22079,-0.75576,-0.61651,493.68,0.41923,-0.64427,0.63965,74.305
    31094 
    31095 > view matrix models
    31096 > #5,-0.77365,-0.13721,0.61857,256.41,-0.084758,-0.94508,-0.31565,433.55,0.62792,-0.29663,0.71954,-45.551
    31097 
    31098 > view matrix models
    31099 > #5,-0.73239,-0.017561,0.68065,212.25,-0.29602,-0.89204,-0.34153,466.62,0.61317,-0.45162,0.64812,2.7847
    31100 
    31101 > view matrix models
    31102 > #5,-0.75559,0.045501,0.65347,211.04,-0.31215,-0.90204,-0.29812,460.96,0.57589,-0.42924,0.69578,-6.2267
    31103 
    31104 > ui mousemode right select
    31105 
    31106 > select clear
    31107 
    31108 > volume #8 level 0.04382
    31109 
    31110 > select add #5
    31111 
    31112 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    31113 
    31114 > ui mousemode right "translate selected models"
    31115 
    31116 > ui mousemode right "rotate selected models"
    31117 
    31118 > view matrix models
    31119 > #5,-0.81035,-0.039349,0.58462,252.71,-0.22376,-0.90134,-0.37083,462.75,0.54153,-0.43132,0.7216,-6.0096
    31120 
    31121 > view matrix models
    31122 > #5,-0.75411,-0.09465,0.64989,237.66,-0.18462,-0.9191,-0.34808,453.83,0.63026,-0.38248,0.67563,-19.574
    31123 
    31124 > view matrix models
    31125 > #5,-0.82045,-0.19006,0.5392,293.25,-0.01249,-0.93694,-0.34926,427.47,0.57158,-0.29329,0.76634,-47.509
    31126 
    31127 > view matrix models
    31128 > #5,-0.8334,-0.14541,0.5332,288.65,-0.074442,-0.92644,-0.36901,441,0.54764,-0.34723,0.76127,-32.123
    31129 
    31130 > view matrix models
    31131 > #5,-0.86676,-0.2008,0.45651,322.99,-0.01989,-0.90071,-0.43396,442.19,0.49833,-0.38522,0.77671,-20.166
    31132 
    31133 > view matrix models
    31134 > #5,-0.91778,-0.012999,0.39688,311.19,-0.033872,-0.99326,-0.11086,384.91,0.39565,-0.11519,0.91115,-84.427
    31135 
    31136 > view matrix models
    31137 > #5,-0.92008,-0.092652,0.38063,330.24,0.036985,-0.98783,-0.15106,381.14,0.38999,-0.12491,0.91231,-81.914
    31138 
    31139 > view matrix models
    31140 > #5,-0.92081,-0.14037,0.36387,343.22,0.070303,-0.97744,-0.19917,384.86,0.38362,-0.15781,0.90991,-74.125
    31141 
    31142 > view matrix models
    31143 > #5,-0.90137,-0.23742,0.36216,358.26,0.18937,-0.96821,-0.16341,353.92,0.38944,-0.078707,0.91768,-91.674
    31144 
    31145 > view matrix models
    31146 > #5,-0.91318,-0.21739,0.34475,360.74,0.15071,-0.96603,-0.20993,371.32,0.37867,-0.13975,0.91492,-77.812
    31147 
    31148 > view matrix models
    31149 > #5,-0.79261,-0.38378,0.47381,339.94,0.3287,-0.92343,-0.1981,329.62,0.51355,-0.0012739,0.85806,-113.45
    31150 
    31151 > view matrix models
    31152 > #5,-0.82527,-0.3527,0.44105,347.65,0.32765,-0.93514,-0.13475,316.9,0.45997,0.033307,0.88731,-117.51
    31153 
    31154 > view matrix models
    31155 > #5,-0.84093,-0.3241,0.43335,346.89,0.26592,-0.94495,-0.1907,342.78,0.4713,-0.045133,0.88082,-103.37
    31156 
    31157 > view matrix models
    31158 > #5,-0.8011,-0.41235,0.43383,356.23,0.35913,-0.911,-0.20275,323.13,0.47883,-0.0066236,0.87788,-111.14
    31159 
    31160 > view matrix models
    31161 > #5,-0.84269,-0.41546,0.34245,385.79,0.3308,-0.90136,-0.2795,344.54,0.4248,-0.12225,0.897,-84.819
    31162 
    31163 > view matrix models
    31164 > #5,-0.79168,-0.41509,0.44827,351.66,0.24249,-0.88697,-0.39305,384.25,0.56075,-0.20247,0.80285,-71.174
    31165 
    31166 > view matrix models
    31167 > #5,-0.80765,-0.39545,0.43739,353.39,0.27696,-0.90927,-0.31067,362.79,0.52056,-0.12977,0.8439,-87.449
    31168 
    31169 > view matrix models
    31170 > #5,-0.80048,-0.3248,0.50372,323.24,0.18817,-0.93413,-0.3033,381.1,0.56905,-0.148,0.80887,-84.163
    31171 
    31172 > view matrix models
    31173 > #5,-0.83802,-0.27227,0.47285,327.36,0.14615,-0.94695,-0.28624,386.73,0.5257,-0.17076,0.83336,-78.221
    31174 
    31175 > view matrix models
    31176 > #5,-0.82968,-0.2976,0.47229,330.75,0.18414,-0.9446,-0.27172,376.23,0.52699,-0.13847,0.83852,-85.669
    31177 
    31178 > volume #8 level 0.07251
    31179 
    31180 > select subtract #5
    31181 
    31182 Nothing selected 
    31183 
    31184 > ui tool show Rotamers
    31185 
    31186 > select #3/B:1
    31187 
    31188 8 atoms, 7 bonds, 1 residue, 1 model selected 
    31189 
    31190 > select #3/B:1-2
    31191 
    31192 14 atoms, 13 bonds, 2 residues, 1 model selected 
    31193 
    31194 > select #5/L:1-2
    31195 
    31196 14 atoms, 13 bonds, 2 residues, 1 model selected 
    31197 
    31198 > select #5/L:1-3
    31199 
    31200 22 atoms, 21 bonds, 3 residues, 1 model selected 
    31201 
    31202 > ui tool show "Show Sequence Viewer"
    31203 
    31204 > sequence chain #5/H
    31205 
    31206 Alignment identifier is 5/H 
    31207 
    31208 > select #5/H:1-2
    31209 
    31210 13 atoms, 12 bonds, 2 residues, 1 model selected 
    31211 
    31212 > select #5/H:1-3
    31213 
    31214 22 atoms, 21 bonds, 3 residues, 1 model selected 
    31215 
    31216 > ui tool show "Model Loops"
    31217 
    31218 > modeller refine 5/H:1:all-missing numModels 5 fast false adjacentFlexible 1
    31219 > protocol standard
    31220 
    31221 Webservices job id: VWCNQFID77H03PPS 
    31222 Modeller job (ID VWCNQFID77H03PPS) finished 
    31223 Modeller failure; standard error: 
    31224 Traceback (most recent call last): 
    31225 File "ModellerModelling.py", line 93, in <module> 
    31226 a.make() 
    31227 File "/usr/lib64/python3.6/site-packages/modeller/automodel/loopmodel.py",
    31228 line 42, in make 
    31229 AutoModel.make(self, exit_stage) 
    31230 File "/usr/lib64/python3.6/site-packages/modeller/automodel/automodel.py",
    31231 line 151, in make 
    31232 atmsel = self._check_select_atoms() 
    31233 File "/usr/lib64/python3.6/site-packages/modeller/automodel/automodel.py",
    31234 line 701, in _check_select_atoms 
    31235 raise ModellerError("no atoms selected for optimization") 
    31236 _modeller.ModellerError: no atoms selected for optimization 
    31237  
    31238 
    31239 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    31240 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
    31241 > includeMaps true
    31242 
    31243 > ui tool show "Side View"
    31244 
    31245 > show #9 models
    31246 
    31247 > hide #9 models
    31248 
    31249 > show #9 models
    31250 
    31251 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    31252 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
    31253 > includeMaps true
    31254 
    31255 > select #5/H:89
    31256 
    31257 7 atoms, 6 bonds, 1 residue, 1 model selected 
    31258 
    31259 > select #5/H:89-116
    31260 
    31261 230 atoms, 242 bonds, 28 residues, 1 model selected 
    31262 
    31263 > select #5/H:28
    31264 
    31265 4 atoms, 3 bonds, 1 residue, 1 model selected 
    31266 
    31267 > select #5/H:28-36
    31268 
    31269 71 atoms, 73 bonds, 9 residues, 1 model selected 
    31270 
    31271 > select #5/H:28
    31272 
    31273 4 atoms, 3 bonds, 1 residue, 1 model selected 
    31274 
    31275 > select #5/H:28-35
    31276 
    31277 59 atoms, 60 bonds, 8 residues, 1 model selected 
    31278 
    31279 > select #5/H:29
    31280 
    31281 12 atoms, 12 bonds, 1 residue, 1 model selected 
    31282 
    31283 > select #5/H:29-34
    31284 
    31285 43 atoms, 43 bonds, 6 residues, 1 model selected 
    31286 
    31287 > select #5/H:29
    31288 
    31289 12 atoms, 12 bonds, 1 residue, 1 model selected 
    31290 
    31291 > select #5/H:29-35
    31292 
    31293 55 atoms, 56 bonds, 7 residues, 1 model selected 
    31294 
    31295 > select #5/H:36
    31296 
    31297 12 atoms, 12 bonds, 1 residue, 1 model selected 
    31298 
    31299 > select #5/H:36
    31300 
    31301 12 atoms, 12 bonds, 1 residue, 1 model selected 
    31302 
    31303 > select add #5
    31304 
    31305 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    31306 
    31307 > select subtract #5
    31308 
    31309 Nothing selected 
    31310 
    31311 > select add #5
    31312 
    31313 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    31314 
    31315 > view matrix models
    31316 > #5,-0.78057,-0.25347,0.57136,290.43,0.14361,-0.96236,-0.23074,376.82,0.60834,-0.098055,0.78759,-95.206
    31317 
    31318 > view matrix models
    31319 > #5,-0.70706,-0.3336,0.62352,280.11,0.24945,-0.94271,-0.22152,352.57,0.6617,-0.0010907,0.74977,-113.49
    31320 
    31321 > view matrix models
    31322 > #5,-0.69694,-0.29889,0.65187,265.15,0.22036,-0.95428,-0.20196,355.12,0.68243,0.0028993,0.73094,-113.36
    31323 
    31324 > view matrix models
    31325 > #5,-0.71926,-0.31911,0.61712,281.06,0.26188,-0.94728,-0.18461,342.47,0.6435,0.028824,0.7649,-119.48
    31326 
    31327 > view matrix models
    31328 > #5,-0.73098,-0.35003,0.58579,296.3,0.27751,-0.93672,-0.21342,344.64,0.62342,0.0065603,0.78186,-115.89
    31329 
    31330 > view matrix models
    31331 > #5,-0.744,-0.38717,0.54457,315.27,0.29793,-0.92173,-0.24828,346.61,0.59808,-0.022477,0.80112,-110.67
    31332 
    31333 > view matrix models
    31334 > #5,-0.64878,-0.44583,0.6167,292.42,0.35923,-0.89386,-0.26827,335.52,0.67084,0.047487,0.74008,-121.79
    31335 
    31336 > view matrix models
    31337 > #5,-0.62439,-0.46334,0.62884,288.54,0.36562,-0.88479,-0.2889,337.64,0.69026,0.049536,0.72187,-121.21
    31338 
    31339 > view matrix models
    31340 > #5,-0.63478,-0.46697,0.61562,294.17,0.35225,-0.88401,-0.30733,344.2,0.68773,0.021768,0.72564,-116.52
    31341 
    31342 > view matrix models
    31343 > #5,-0.61524,-0.38128,0.69001,257.16,0.33568,-0.91865,-0.20832,329.96,0.71331,0.10345,0.69318,-128.41
    31344 
    31345 > view matrix models
    31346 > #5,-0.76581,-0.22867,0.60103,276.2,0.13893,-0.9714,-0.19256,370.23,0.62788,-0.063967,0.77568,-102.1
    31347 
    31348 > view matrix models
    31349 > #5,-0.78982,-0.28243,0.54445,303.82,0.18289,-0.95574,-0.23046,368.69,0.58544,-0.082452,0.80651,-98.621
    31350 
    31351 > view matrix models
    31352 > #5,-0.79292,-0.27196,0.54527,302.22,0.18011,-0.95949,-0.21664,366.58,0.5821,-0.073569,0.80978,-100.47
    31353 
    31354 > view matrix models
    31355 > #5,-0.79401,-0.27238,0.54346,302.92,0.18004,-0.95926,-0.21773,366.81,0.58063,-0.075037,0.8107,-100.16
    31356 
    31357 > view matrix models
    31358 > #5,-0.80028,-0.30121,0.51848,315.31,0.14171,-0.93519,-0.32456,394.44,0.58264,-0.18627,0.7911,-75.192
    31359 
    31360 > view matrix models
    31361 > #5,-0.78732,-0.26873,0.55489,298.36,0.10956,-0.94667,-0.303,397.03,0.60673,-0.17777,0.77478,-77.078
    31362 
    31363 > view matrix models
    31364 > #5,-0.77396,-0.26304,0.57601,289.95,0.10485,-0.95032,-0.29309,396.17,0.62449,-0.16645,0.76309,-79.488
    31365 
    31366 > ui mousemode right "move picked models"
    31367 
    31368 > ui mousemode right "translate selected models"
    31369 
    31370 > view matrix models
    31371 > #5,-0.77396,-0.26304,0.57601,289.63,0.10485,-0.95032,-0.29309,395.77,0.62449,-0.16645,0.76309,-79.465
    31372 
    31373 > select subtract #5
    31374 
    31375 Nothing selected 
    31376 
    31377 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    31378 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
    31379 > includeMaps true
    31380 
    31381 > select #5/H:29
    31382 
    31383 12 atoms, 12 bonds, 1 residue, 1 model selected 
    31384 
    31385 > select #5/H:29-35
    31386 
    31387 55 atoms, 56 bonds, 7 residues, 1 model selected 
    31388 
    31389 > ui tool show "Model Loops"
    31390 
    31391 [Repeated 2 time(s)]
    31392 
    31393 > ui tool show "Modeller Comparative"
    31394 
    31395 > select #5/H:56
    31396 
    31397 12 atoms, 12 bonds, 1 residue, 1 model selected 
    31398 
    31399 > select #5/H:56-62
    31400 
    31401 58 atoms, 59 bonds, 7 residues, 1 model selected 
    31402 
    31403 > select #5/H:55
    31404 
    31405 11 atoms, 10 bonds, 1 residue, 1 model selected 
    31406 
    31407 > select #5/H:55-62
    31408 
    31409 69 atoms, 70 bonds, 8 residues, 1 model selected 
    31410 
    31411 > select #5/H:55
    31412 
    31413 11 atoms, 10 bonds, 1 residue, 1 model selected 
    31414 
    31415 > select #5/H:55-58
    31416 
    31417 35 atoms, 35 bonds, 4 residues, 1 model selected 
    31418 
    31419 > select #5/H:54-55
    31420 
    31421 19 atoms, 18 bonds, 2 residues, 1 model selected 
    31422 
    31423 > select #5/H:54-59
    31424 
    31425 49 atoms, 49 bonds, 6 residues, 1 model selected 
    31426 
    31427 > select #5/H:55-56
    31428 
    31429 23 atoms, 23 bonds, 2 residues, 1 model selected 
    31430 
    31431 > select #5/H:55-59
    31432 
    31433 41 atoms, 41 bonds, 5 residues, 1 model selected 
    31434 
    31435 > select #5/H:60
    31436 
    31437 8 atoms, 7 bonds, 1 residue, 1 model selected 
    31438 
    31439 > select #5/H:60
    31440 
    31441 8 atoms, 7 bonds, 1 residue, 1 model selected 
    31442 
    31443 > select #5/H:59
    31444 
    31445 6 atoms, 5 bonds, 1 residue, 1 model selected 
    31446 
    31447 > select #5/H:55-59
    31448 
    31449 41 atoms, 41 bonds, 5 residues, 1 model selected 
    31450 
    31451 > select #5/H:100-144
    31452 
    31453 341 atoms, 356 bonds, 45 residues, 1 model selected 
    31454 
    31455 > select #5/H:100-112
    31456 
    31457 113 atoms, 120 bonds, 13 residues, 1 model selected 
    31458 
    31459 > select #5/H:174
    31460 
    31461 7 atoms, 6 bonds, 1 residue, 1 model selected 
    31462 
    31463 > select #5/H:174-185
    31464 
    31465 87 atoms, 89 bonds, 12 residues, 1 model selected 
    31466 
    31467 > select #5/H:102
    31468 
    31469 12 atoms, 12 bonds, 1 residue, 1 model selected 
    31470 
    31471 > select #5/H:102-107
    31472 
    31473 54 atoms, 56 bonds, 6 residues, 1 model selected 
    31474 
    31475 > select #3/B:290-291
    31476 
    31477 14 atoms, 13 bonds, 2 residues, 1 model selected 
    31478 
    31479 > select #3/B:290-310
    31480 
    31481 150 atoms, 150 bonds, 21 residues, 1 model selected 
    31482 
    31483 > select #3/B:290-315
    31484 
    31485 193 atoms, 195 bonds, 26 residues, 1 model selected 
    31486 
    31487 > hide #3 models
    31488 
    31489 > show #3 models
    31490 
    31491 > hide #3 models
    31492 
    31493 > show #3 models
    31494 
    31495 > select #3/B:352
    31496 
    31497 5 atoms, 4 bonds, 1 residue, 1 model selected 
    31498 
    31499 > select #3/B:341-352
    31500 
    31501 91 atoms, 90 bonds, 12 residues, 1 model selected 
    31502 
    31503 > select
    31504 > #5/H:5-9,20-27,36-42,48-54,60-62,70-75,80-85,94-101,118-120,131-135,146-156,161-165,174-176,187-196,205-211,216-222
    31505 
    31506 837 atoms, 847 bonds, 101 residues, 1 model selected 
    31507 
    31508 > select #5/H:127
    31509 
    31510 7 atoms, 6 bonds, 1 residue, 1 model selected 
    31511 
    31512 > select #5/H:127-130
    31513 
    31514 27 atoms, 27 bonds, 4 residues, 1 model selected 
    31515 
    31516 > view matrix models
    31517 > #5,-0.77396,-0.26304,0.57601,280.18,0.10485,-0.95032,-0.29309,395.64,0.62449,-0.16645,0.76309,-74.626
    31518 
    31519 > hide #!8 models
    31520 
    31521 > show #!2 models
    31522 
    31523 > hide #!2 models
    31524 
    31525 > select #5/L:22
    31526 
    31527 8 atoms, 7 bonds, 1 residue, 1 model selected 
    31528 
    31529 > select #5/L:22-28
    31530 
    31531 47 atoms, 46 bonds, 7 residues, 1 model selected 
    31532 
    31533 > select #5/L:29
    31534 
    31535 6 atoms, 5 bonds, 1 residue, 1 model selected 
    31536 
    31537 > select #5/L:29-34
    31538 
    31539 43 atoms, 43 bonds, 6 residues, 1 model selected 
    31540 
    31541 > select #5/L:29
    31542 
    31543 6 atoms, 5 bonds, 1 residue, 1 model selected 
    31544 
    31545 > select #5/L:29-35
    31546 
    31547 51 atoms, 51 bonds, 7 residues, 1 model selected 
    31548 
    31549 > select #5/L:22
    31550 
    31551 8 atoms, 7 bonds, 1 residue, 1 model selected 
    31552 
    31553 > select #5/L:22-26
    31554 
    31555 36 atoms, 35 bonds, 5 residues, 1 model selected 
    31556 
    31557 > select #5/L:29
    31558 
    31559 6 atoms, 5 bonds, 1 residue, 1 model selected 
    31560 
    31561 > select #5/L:29-34
    31562 
    31563 43 atoms, 43 bonds, 6 residues, 1 model selected 
    31564 
    31565 > select #5/L:50
    31566 
    31567 8 atoms, 7 bonds, 1 residue, 1 model selected 
    31568 
    31569 > select #5/L:50-54
    31570 
    31571 39 atoms, 39 bonds, 5 residues, 1 model selected 
    31572 
    31573 > select #5/L:51
    31574 
    31575 12 atoms, 12 bonds, 1 residue, 1 model selected 
    31576 
    31577 > select #5/L:51-55
    31578 
    31579 39 atoms, 39 bonds, 5 residues, 1 model selected 
    31580 
    31581 > select #5/L:51
    31582 
    31583 12 atoms, 12 bonds, 1 residue, 1 model selected 
    31584 
    31585 > select #5/L:51-56
    31586 
    31587 47 atoms, 47 bonds, 6 residues, 1 model selected 
    31588 
    31589 > select #5/L:51
    31590 
    31591 12 atoms, 12 bonds, 1 residue, 1 model selected 
    31592 
    31593 > select #5/L:51-62
    31594 
    31595 82 atoms, 83 bonds, 12 residues, 1 model selected 
    31596 
    31597 > select add #8
    31598 
    31599 82 atoms, 83 bonds, 12 residues, 3 models selected 
    31600 
    31601 > select subtract #8
    31602 
    31603 82 atoms, 83 bonds, 12 residues, 1 model selected 
    31604 
    31605 > select add #8
    31606 
    31607 82 atoms, 83 bonds, 12 residues, 3 models selected 
    31608 
    31609 > select subtract #8
    31610 
    31611 82 atoms, 83 bonds, 12 residues, 1 model selected 
    31612 
    31613 > select add #8
    31614 
    31615 82 atoms, 83 bonds, 12 residues, 3 models selected 
    31616 
    31617 > show #!8 models
    31618 
    31619 > select subtract #8
    31620 
    31621 82 atoms, 83 bonds, 12 residues, 1 model selected 
    31622 
    31623 > select add #8
    31624 
    31625 82 atoms, 83 bonds, 12 residues, 3 models selected 
    31626 
    31627 > select subtract #8
    31628 
    31629 82 atoms, 83 bonds, 12 residues, 1 model selected 
    31630 
    31631 > hide #!8 models
    31632 
    31633 > hide #8.1 models
    31634 
    31635 > select add #9
    31636 
    31637 3416 atoms, 3463 bonds, 426 residues, 2 models selected 
    31638 
    31639 > select subtract #9
    31640 
    31641 82 atoms, 83 bonds, 12 residues, 1 model selected 
    31642 
    31643 > select add #5
    31644 
    31645 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    31646 
    31647 > select subtract #5
    31648 
    31649 Nothing selected 
    31650 
    31651 > select add #5
    31652 
    31653 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    31654 
    31655 > view matrix models
    31656 > #5,-0.77396,-0.26304,0.57601,281.01,0.10485,-0.95032,-0.29309,395.7,0.62449,-0.16645,0.76309,-74.661
    31657 
    31658 > view matrix models
    31659 > #5,-0.77396,-0.26304,0.57601,281.22,0.10485,-0.95032,-0.29309,395.6,0.62449,-0.16645,0.76309,-74.86
    31660 
    31661 > view matrix models
    31662 > #5,-0.77396,-0.26304,0.57601,282.28,0.10485,-0.95032,-0.29309,396.27,0.62449,-0.16645,0.76309,-74.987
    31663 
    31664 > view matrix models
    31665 > #5,-0.77396,-0.26304,0.57601,283.04,0.10485,-0.95032,-0.29309,396.66,0.62449,-0.16645,0.76309,-75.111
    31666 
    31667 > view matrix models
    31668 > #5,-0.77396,-0.26304,0.57601,282.9,0.10485,-0.95032,-0.29309,397.32,0.62449,-0.16645,0.76309,-75.13
    31669 
    31670 > view matrix models
    31671 > #5,-0.77396,-0.26304,0.57601,283.39,0.10485,-0.95032,-0.29309,397.2,0.62449,-0.16645,0.76309,-75.14
    31672 
    31673 > view matrix models
    31674 > #5,-0.77396,-0.26304,0.57601,285.17,0.10485,-0.95032,-0.29309,397.62,0.62449,-0.16645,0.76309,-75.184
    31675 
    31676 > view matrix models
    31677 > #5,-0.77396,-0.26304,0.57601,285.99,0.10485,-0.95032,-0.29309,397.56,0.62449,-0.16645,0.76309,-75.367
    31678 
    31679 > view matrix models
    31680 > #5,-0.77396,-0.26304,0.57601,286.16,0.10485,-0.95032,-0.29309,397.36,0.62449,-0.16645,0.76309,-75.361
    31681 
    31682 > select add #8.1
    31683 
    31684 3401 atoms, 3493 bonds, 442 residues, 2 models selected 
    31685 
    31686 > show #8.1 models
    31687 
    31688 > select subtract #5
    31689 
    31690 1 model selected 
    31691 
    31692 > select add #8
    31693 
    31694 2 models selected 
    31695 
    31696 > select subtract #8
    31697 
    31698 Nothing selected 
    31699 
    31700 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    31701 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms_10min_recolored.cxs"
    31702 > includeMaps true
    31703 
    31704 > select #5/L:50
    31705 
    31706 8 atoms, 7 bonds, 1 residue, 1 model selected 
    31707 
    31708 > select #5/L:50
    31709 
    31710 8 atoms, 7 bonds, 1 residue, 1 model selected 
    31711 
    31712 > select #5/L:66
    31713 
    31714 4 atoms, 3 bonds, 1 residue, 1 model selected 
    31715 
    31716 > select #5/L:66-68
    31717 
    31718 14 atoms, 13 bonds, 3 residues, 1 model selected 
    31719 
    31720 > select #5/L:115
    31721 
    31722 7 atoms, 6 bonds, 1 residue, 1 model selected 
    31723 
    31724 > select #5/L:115-121
    31725 
    31726 57 atoms, 60 bonds, 7 residues, 1 model selected 
    31727 
    31728 > select #5/L:102
    31729 
    31730 7 atoms, 6 bonds, 1 residue, 1 model selected 
    31731 
    31732 > select #5/L:102-106
    31733 
    31734 41 atoms, 40 bonds, 5 residues, 1 model selected 
    31735 
    31736 > select #5/L:96
    31737 
    31738 14 atoms, 15 bonds, 1 residue, 1 model selected 
    31739 
    31740 > select #5/L:94-96
    31741 
    31742 26 atoms, 27 bonds, 3 residues, 1 model selected 
    31743 
    31744 > select #5/L:75
    31745 
    31746 8 atoms, 7 bonds, 1 residue, 1 model selected 
    31747 
    31748 > select #5/L:75-77
    31749 
    31750 23 atoms, 22 bonds, 3 residues, 1 model selected 
    31751 
    31752 > select #5/L:80
    31753 
    31754 7 atoms, 6 bonds, 1 residue, 1 model selected 
    31755 
    31756 > select #5/L:80-81
    31757 
    31758 16 atoms, 15 bonds, 2 residues, 1 model selected 
    31759 
    31760 > select #5/L:98
    31761 
    31762 11 atoms, 11 bonds, 1 residue, 1 model selected 
    31763 
    31764 > select #5/L:98-99
    31765 
    31766 15 atoms, 15 bonds, 2 residues, 1 model selected 
    31767 
    31768 > select #5/L:94
    31769 
    31770 6 atoms, 5 bonds, 1 residue, 1 model selected 
    31771 
    31772 > select #5/L:93-94
    31773 
    31774 20 atoms, 21 bonds, 2 residues, 1 model selected 
    31775 
    31776 > select #5/L:91
    31777 
    31778 10 atoms, 10 bonds, 1 residue, 1 model selected 
    31779 
    31780 > select #5/L:91
    31781 
    31782 10 atoms, 10 bonds, 1 residue, 1 model selected 
    31783 
    31784 > select #5/L:92
    31785 
    31786 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31787 
    31788 > select #5/L:92-93
    31789 
    31790 23 atoms, 24 bonds, 2 residues, 1 model selected 
    31791 
    31792 > select #5/L:92-93
    31793 
    31794 23 atoms, 24 bonds, 2 residues, 1 model selected 
    31795 
    31796 > select #5/L:92-97
    31797 
    31798 56 atoms, 59 bonds, 6 residues, 1 model selected 
    31799 
    31800 > select #5/L:1
    31801 
    31802 5 atoms, 4 bonds, 1 residue, 1 model selected 
    31803 
    31804 > select #5/L:1-100
    31805 
    31806 750 atoms, 769 bonds, 100 residues, 1 model selected 
    31807 
    31808 > select #5/L:1
    31809 
    31810 5 atoms, 4 bonds, 1 residue, 1 model selected 
    31811 
    31812 > select #5/L:1-111
    31813 
    31814 834 atoms, 853 bonds, 111 residues, 1 model selected 
    31815 
    31816 > select #5/L:108
    31817 
    31818 11 atoms, 10 bonds, 1 residue, 1 model selected 
    31819 
    31820 > select #5/L:1-108
    31821 
    31822 815 atoms, 834 bonds, 108 residues, 1 model selected 
    31823 
    31824 > select #5/L:95
    31825 
    31826 6 atoms, 5 bonds, 1 residue, 1 model selected 
    31827 
    31828 > select #5/L:95-96
    31829 
    31830 20 atoms, 21 bonds, 2 residues, 1 model selected 
    31831 
    31832 > select #5/L:95
    31833 
    31834 6 atoms, 5 bonds, 1 residue, 1 model selected 
    31835 
    31836 > select #5/L:95-105
    31837 
    31838 83 atoms, 85 bonds, 11 residues, 1 model selected 
    31839 
    31840 > select #5/L:95
    31841 
    31842 6 atoms, 5 bonds, 1 residue, 1 model selected 
    31843 
    31844 > select #5/L:95-102
    31845 
    31846 57 atoms, 59 bonds, 8 residues, 1 model selected 
    31847 
    31848 > select #5/L:93
    31849 
    31850 14 atoms, 15 bonds, 1 residue, 1 model selected 
    31851 
    31852 > select #5/L:93-101
    31853 
    31854 70 atoms, 74 bonds, 9 residues, 1 model selected 
    31855 
    31856 > ui tool show "Show Sequence Viewer"
    31857 
    31858 > sequence chain #9/B #9/C
    31859 
    31860 Alignment identifier is 1 
    31861 
    31862 > ui mousemode right select
    31863 
    31864 > select clear
    31865 
    31866 > toolshed show
    31867 
    31868 Downloading bundle ChimeraX_XMAS-1.1.2-py3-none-any.whl 
    31869 
    31870 Errors may have occurred when running pip: 
    31871 
    31872 pip standard error: 
    31873 \--- 
    31874  
    31875 [notice] A new release of pip available: 22.2.2 -> 23.0.1 
    31876 [notice] To update, run:
    31877 /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX -m pip install
    31878 --upgrade pip 
    31879 \--- 
    31880 
    31881 pip standard output: 
    31882 \--- 
    31883 Looking in indexes: https://pypi.org/simple,
    31884 https://cxtoolshed.rbvi.ucsf.edu/pypi/ 
    31885 Processing /Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl 
    31886 Requirement already satisfied: ChimeraX-UI~=1.3 in
    31887 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31888 packages (from ChimeraX-XMAS==1.1.2) (1.24.3) 
    31889 Requirement already satisfied: ChimeraX-Core~=1.3 in
    31890 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31891 packages (from ChimeraX-XMAS==1.1.2) (1.5) 
    31892 Collecting openpyxl 
    31893 Downloading openpyxl-3.1.2-py2.py3-none-any.whl (249 kB) 
    31894 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.0/250.0 kB 8.0 MB/s eta 0:00:00 
    31895 Collecting seaborn 
    31896 Downloading seaborn-0.12.2-py3-none-any.whl (293 kB) 
    31897 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 293.3/293.3 kB 18.8 MB/s eta 0:00:00 
    31898 Collecting pandas 
    31899 Downloading pandas-1.5.3-cp39-cp39-macosx_10_9_x86_64.whl (12.0 MB) 
    31900 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.0/12.0 MB 8.1 MB/s eta 0:00:00 
    31901 Collecting qtrangeslider 
    31902 Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB) 
    31903 Requirement already satisfied: ChimeraX-Graphics~=1.0 in
    31904 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31905 packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1) 
    31906 Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
    31907 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31908 packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1.1) 
    31909 Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
    31910 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31911 packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.0) 
    31912 Collecting et-xmlfile 
    31913 Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB) 
    31914 Requirement already satisfied: python-dateutil>=2.8.1 in
    31915 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31916 packages (from pandas->ChimeraX-XMAS==1.1.2) (2.8.2) 
    31917 Requirement already satisfied: numpy>=1.20.3 in
    31918 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31919 packages (from pandas->ChimeraX-XMAS==1.1.2) (1.23.1) 
    31920 Requirement already satisfied: pytz>=2020.1 in
    31921 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31922 packages (from pandas->ChimeraX-XMAS==1.1.2) (2022.6) 
    31923 Requirement already satisfied: matplotlib!=3.6.1,>=3.1 in
    31924 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31925 packages (from seaborn->ChimeraX-XMAS==1.1.2) (3.5.2) 
    31926 Requirement already satisfied: ChimeraX-Geometry~=1.0 in
    31927 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31928 packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
    31929 (1.2) 
    31930 Requirement already satisfied: ChimeraX-Arrays~=1.0 in
    31931 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31932 packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
    31933 (1.0) 
    31934 Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
    31935 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31936 packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX-
    31937 XMAS==1.1.2) (1.0.1) 
    31938 Requirement already satisfied: pyparsing>=2.2.1 in
    31939 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31940 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (3.0.9) 
    31941 Requirement already satisfied: fonttools>=4.22.0 in
    31942 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31943 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
    31944 (4.38.0) 
    31945 Requirement already satisfied: packaging>=20.0 in
    31946 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31947 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (21.3) 
    31948 Requirement already satisfied: kiwisolver>=1.0.1 in
    31949 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31950 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (1.4.4) 
    31951 Requirement already satisfied: cycler>=0.10 in
    31952 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31953 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
    31954 (0.11.0) 
    31955 Requirement already satisfied: pillow>=6.2.0 in
    31956 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31957 packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (9.2.0) 
    31958 Requirement already satisfied: six>=1.5 in
    31959 /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
    31960 packages (from python-dateutil>=2.8.1->pandas->ChimeraX-XMAS==1.1.2) (1.16.0) 
    31961 Installing collected packages: qtrangeslider, et-xmlfile, pandas, openpyxl,
    31962 seaborn, ChimeraX-XMAS 
    31963 Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2
    31964 pandas-1.5.3 qtrangeslider-0.1.5 seaborn-0.12.2 
    31965 \--- 
    31966 
    31967 Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2
    31968 pandas-1.5.3 qtrangeslider-0.1.5 seaborn-0.12.2 
    31969 Installed ChimeraX-XMAS (1.1.2) 
    31970 
    31971 > toolshed install Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl
    31972 
    31973 Missing or invalid "bundleNames" argument: Expected a bundle name or a wheel
    31974 file name 
    31975 
    31976 > toolshed install /Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-
    31977 > any.whl
    31978 
    31979 bundle '/Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl'
    31980 already installed 
    31981 
    31982 > save "/Users/alvinchew/OneDrive - Nanyang Technological
    31983 > University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms_10min_recolored.cxs"
    31984 > includeMaps true
    31985 
    31986 ——— End of log from Thu Mar 30 23:52:24 2023 ———
    31987 
    31988 opened ChimeraX session 
    31989 
    31990 > select down
    31991 
    31992 Nothing selected 
    31993 
    31994 > select down
    31995 
    31996 Nothing selected 
    31997 
    31998 > ui tool show "Show Sequence Viewer"
    31999 
    32000 > ui tool show "Change Chain IDs"
    32001 
    32002 > select add #3
    32003 
    32004 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    32005 
    32006 > select subtract #3
    32007 
    32008 Nothing selected 
    32009 
    32010 > select #3/B:1
    32011 
    32012 8 atoms, 7 bonds, 1 residue, 1 model selected 
    32013 
    32014 > select #3/B:1-20
    32015 
    32016 149 atoms, 151 bonds, 20 residues, 1 model selected 
    32017 
    32018 > select #3/B:1-20
    32019 
    32020 149 atoms, 151 bonds, 20 residues, 1 model selected 
    32021 
    32022 > select #3/B:1-20,136-352
    32023 
    32024 1872 atoms, 1920 bonds, 237 residues, 1 model selected 
    32025 
    32026 > select #3/B:1-20,136-352
    32027 
    32028 1872 atoms, 1920 bonds, 237 residues, 1 model selected 
    32029 
    32030 > select #3/B:1
    32031 
    32032 8 atoms, 7 bonds, 1 residue, 1 model selected 
    32033 
    32034 > select #3/B:1-180
    32035 
    32036 1439 atoms, 1472 bonds, 180 residues, 1 model selected 
    32037 
    32038 > select #3/A
    32039 
    32040 2801 atoms, 2872 bonds, 352 residues, 1 model selected 
    32041 
    32042 > save /Users/alvinchew/Downloads/NS1chainA.pdb selectedOnly true relModel
    32043 > #8.1
    32044 
    32045 > open /Users/alvinchew/Downloads/NS1chainA.pdb
    32046 
    32047 Summary of feedback from opening /Users/alvinchew/Downloads/NS1chainA.pdb 
    32048 --- 
    32049 warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
    32050 GLU B 51 1 13 
    32051 Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
    32052 11 
    32053 Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
    32054 9 
    32055 Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
    32056 1 7 
    32057 Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
    32058 1 3 
    32059 26 messages similar to the above omitted 
    32060  
    32061 Chain information for NS1chainA.pdb #6 
    32062 --- 
    32063 Chain | Description 
    32064 A | No description available 
    32065  
    32066 
    32067 > undo
    32068 
    32069 > close #6
    32070 
    32071 > select add #3
    32072 
    32073 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    32074 
    32075 > select subtract #3
    32076 
    32077 Nothing selected 
    32078 
    32079 > toolshed show
    32080 
    32081 > xmas
    32082 
    32083 Unknown command: xmas 
    32084 
    32085 > runscript xmas
    32086 
    32087 Missing or invalid "scriptFile" argument: File 'xmas' does not exist 
    32088 
    32089 > select #3/B:1
    32090 
    32091 8 atoms, 7 bonds, 1 residue, 1 model selected 
    32092 
    32093 > select #3/B:1-120
    32094 
    32095 956 atoms, 977 bonds, 120 residues, 1 model selected 
    32096 
    32097 > select #3/A
    32098 
    32099 2801 atoms, 2872 bonds, 352 residues, 1 model selected 
    32100 
    32101 > save /Users/alvinchew/Downloads/NS1chainA.pdb models #3 selectedOnly true
    32102 > relModel #3
    32103 
    32104 > open /Users/alvinchew/Downloads/NS1chainA.pdb
    32105 
    32106 Summary of feedback from opening /Users/alvinchew/Downloads/NS1chainA.pdb 
    32107 --- 
    32108 warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
    32109 GLU B 51 1 13 
    32110 Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
    32111 11 
    32112 Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
    32113 9 
    32114 Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
    32115 1 7 
    32116 Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
    32117 1 3 
    32118 26 messages similar to the above omitted 
    32119  
    32120 Chain information for NS1chainA.pdb #6 
    32121 --- 
    32122 Chain | Description 
    32123 A | No description available 
    32124  
    32125 
    32126 > close #6
    32127 
    32128 > hide #3 models
    32129 
    32130 > show #3 models
    32131 
    32132 > save /Users/alvinchew/Downloads/D2NS1_A #3/A relModel #3/B
    32133 
    32134 Cannot determine format for '/Users/alvinchew/Downloads/D2NS1_A' 
    32135 
    32136 > save /Users/alvinchew/Downloads/D2NS1_A.pdb #3/A relModel #3/B
    32137 
    32138 > open /Users/alvinchew/Downloads/D2NS1_A.pdb
    32139 
    32140 Chain information for D2NS1_A.pdb #6 
    32141 --- 
    32142 Chain | Description 
    32143 A B | No description available 
    32144  
    32145 
    32146 > hide #3 models
    32147 
    32148 > show #3 models
    32149 
    32150 > hide #6 models
    32151 
    32152 > show #6 models
    32153 
    32154 > hide #6 models
    32155 
    32156 > show #6 models
    32157 
    32158 > close #6
    32159 
    32160 > save /Users/alvinchew/Downloads/D2NS1_A.pdb #3/A selectedOnly true relModel
    32161 > #3/B
    32162 
    32163 > open /Users/alvinchew/Downloads/D2NS1_A.pdb
    32164 
    32165 Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_A.pdb 
    32166 --- 
    32167 warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
    32168 GLU B 51 1 13 
    32169 Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
    32170 11 
    32171 Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
    32172 9 
    32173 Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
    32174 1 7 
    32175 Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
    32176 1 3 
    32177 26 messages similar to the above omitted 
    32178  
    32179 Chain information for D2NS1_A.pdb #6 
    32180 --- 
    32181 Chain | Description 
    32182 A | No description available 
    32183  
    32184 
    32185 > hide #3 models
    32186 
    32187 > select #3/B:1-2
    32188 
    32189 14 atoms, 13 bonds, 2 residues, 1 model selected 
    32190 
    32191 > select #3/B:1-14
    32192 
    32193 110 atoms, 111 bonds, 14 residues, 1 model selected 
    32194 
    32195 > show #3 models
    32196 
    32197 > select add #8
    32198 
    32199 110 atoms, 111 bonds, 14 residues, 5 models selected 
    32200 
    32201 > select subtract #8
    32202 
    32203 110 atoms, 111 bonds, 14 residues, 1 model selected 
    32204 
    32205 > hide #!8 models
    32206 
    32207 > hide #3 models
    32208 
    32209 > show #3 models
    32210 
    32211 > mmaker #6 to #3/A
    32212 
    32213 Parameters 
    32214 --- 
    32215 Chain pairing | bb 
    32216 Alignment algorithm | Needleman-Wunsch 
    32217 Similarity matrix | BLOSUM-62 
    32218 SS fraction | 0.3 
    32219 Gap open (HH/SS/other) | 18/18/6 
    32220 Gap extend | 1 
    32221 SS matrix |  |  | H | S | O 
    32222 ---|---|---|--- 
    32223 H | 6 | -9 | -6 
    32224 S |  | 6 | -6 
    32225 O |  |  | 4 
    32226 Iteration cutoff | 2 
    32227  
    32228 Matchmaker eden2ns1.pdb, chain A (#3) with D2NS1_A.pdb, chain A (#6), sequence
    32229 alignment score = 1853.9 
    32230 RMSD between 352 pruned atom pairs is 0.000 angstroms; (across all 352 pairs:
    32231 0.000) 
    32232  
    32233 
    32234 > hide #3 models
    32235 
    32236 > show #3 models
    32237 
    32238 > hide #3 models
    32239 
    32240 > show #3 models
    32241 
    32242 > hide #3 models
    32243 
    32244 > show #3 models
    32245 
    32246 > hide #6 models
    32247 
    32248 > show #6 models
    32249 
    32250 > hide #6 models
    32251 
    32252 > show #6 models
    32253 
    32254 > select add #3
    32255 
    32256 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    32257 
    32258 > select subtract #3
    32259 
    32260 Nothing selected 
    32261 
    32262 > hide #3 models
    32263 
    32264 > show #3 models
    32265 
    32266 > hide #3 models
    32267 
    32268 > show #3 models
    32269 
    32270 > hide #3 models
    32271 
    32272 > show #3 models
    32273 
    32274 > hide #3 models
    32275 
    32276 > show #3 models
    32277 
    32278 > save /Users/alvinchew/Downloads/D2NS1_A.pdb #6
    32279 
    32280 > open /Users/alvinchew/Downloads/D2NS1_A.pdb
    32281 
    32282 Chain information for D2NS1_A.pdb #7 
    32283 --- 
    32284 Chain | Description 
    32285 A | No description available 
    32286  
    32287 
    32288 > select #3/B:1
    32289 
    32290 8 atoms, 7 bonds, 1 residue, 1 model selected 
    32291 
    32292 > select #3/B
    32293 
    32294 2801 atoms, 2872 bonds, 352 residues, 1 model selected 
    32295 
    32296 > save /Users/alvinchew/Downloads/D2NS1_B.pdb #3/B selectedOnly true relModel
    32297 > #3/A
    32298 
    32299 > open /Users/alvinchew/Downloads/D2NS1_B.pdb
    32300 
    32301 Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb 
    32302 --- 
    32303 warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
    32304 39 GLU A 51 1 13 
    32305 Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
    32306 1 11 
    32307 Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
    32308 1 9 
    32309 Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
    32310 121 1 7 
    32311 Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
    32312 147 1 3 
    32313 26 messages similar to the above omitted 
    32314  
    32315 Chain information for D2NS1_B.pdb #10 
    32316 --- 
    32317 Chain | Description 
    32318 B | No description available 
    32319  
    32320 
    32321 > close #10
    32322 
    32323 > save /Users/alvinchew/Downloads/D2NS1_B.pdb #3/B selectedOnly true
    32324 
    32325 > open /Users/alvinchew/Downloads/D2NS1_B.pdb
    32326 
    32327 Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb 
    32328 --- 
    32329 warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
    32330 39 GLU A 51 1 13 
    32331 Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
    32332 1 11 
    32333 Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
    32334 1 9 
    32335 Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
    32336 121 1 7 
    32337 Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
    32338 147 1 3 
    32339 26 messages similar to the above omitted 
    32340  
    32341 Chain information for D2NS1_B.pdb #10 
    32342 --- 
    32343 Chain | Description 
    32344 B | No description available 
    32345  
    32346 
    32347 > close #6
    32348 
    32349 > hide #9 models
    32350 
    32351 > show #9 models
    32352 
    32353 > hide #9 models
    32354 
    32355 > show #9 models
    32356 
    32357 > select #9/B-C:1
    32358 
    32359 12 atoms, 10 bonds, 2 residues, 1 model selected 
    32360 
    32361 > select #9/B-C:1-8
    32362 
    32363 114 atoms, 112 bonds, 16 residues, 1 model selected 
    32364 
    32365 > ui tool show "Show Sequence Viewer"
    32366 
    32367 > sequence chain #9/B
    32368 
    32369 Alignment identifier is 9/B 
    32370 
    32371 > sequence chain #9/C
    32372 
    32373 Alignment identifier is 9/C 
    32374 
    32375 > select #9/C:2-149,151-206
    32376 
    32377 1648 atoms, 1670 bonds, 204 residues, 1 model selected 
    32378 
    32379 > select #9/C:1
    32380 
    32381 6 atoms, 5 bonds, 1 residue, 1 model selected 
    32382 
    32383 > select #9/C
    32384 
    32385 1667 atoms, 1690 bonds, 207 residues, 1 model selected 
    32386 
    32387 > save /Users/alvinchew/Downloads/ApoA1_Y.pdb #9/C selectedOnly true
    32388 
    32389 > open /Users/alvinchew/Downloads/ApoA1_Y.pdb
    32390 
    32391 Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_Y.pdb 
    32392 --- 
    32393 warnings | Start residue of secondary structure not found: HELIX 1 1 ALA B 2
    32394 ALA B 129 1 128 
    32395 Start residue of secondary structure not found: HELIX 2 2 PRO B 130 GLY B 149
    32396 1 20 
    32397 Start residue of secondary structure not found: HELIX 3 3 GLY B 151 ALA B 206
    32398 1 56 
    32399  
    32400 Chain information for ApoA1_Y.pdb #6 
    32401 --- 
    32402 Chain | Description 
    32403 C | No description available 
    32404  
    32405 
    32406 > select #9/B:1
    32407 
    32408 6 atoms, 5 bonds, 1 residue, 1 model selected 
    32409 
    32410 > select #9/B
    32411 
    32412 1667 atoms, 1690 bonds, 207 residues, 1 model selected 
    32413 
    32414 > save /Users/alvinchew/Downloads/ApoA1_X.pdb #9/B selectedOnly true
    32415 
    32416 > open /Users/alvinchew/Downloads/ApoA1_X.pdb
    32417 
    32418 Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_X.pdb 
    32419 --- 
    32420 warnings | Start residue of secondary structure not found: HELIX 4 4 ALA C 2
    32421 ALA C 129 1 128 
    32422 Start residue of secondary structure not found: HELIX 5 5 PRO C 130 GLY C 149
    32423 1 20 
    32424 Start residue of secondary structure not found: HELIX 6 6 GLY C 151 ALA C 206
    32425 1 56 
    32426  
    32427 Chain information for ApoA1_X.pdb #11 
    32428 --- 
    32429 Chain | Description 
    32430 B | No description available 
    32431  
    32432 
    32433 > hide #11 models
    32434 
    32435 > show #11 models
    32436 
    32437 > hide #11 models
    32438 
    32439 > show #11 models
    32440 
    32441 > hide #9 models
    32442 
    32443 > hide #8.1 models
    32444 
    32445 > hide #10 models
    32446 
    32447 > hide #11 models
    32448 
    32449 > select add #9
    32450 
    32451 3334 atoms, 3380 bonds, 414 residues, 1 model selected 
    32452 
    32453 > select subtract #9
    32454 
    32455 Nothing selected 
    32456 
    32457 > hide #5 models
    32458 
    32459 > show #5 models
    32460 
    32461 > hide #5 models
    32462 
    32463 > show #5 models
    32464 
    32465 > hide #3 models
    32466 
    32467 > show #3 models
    32468 
    32469 > hide #7 models
    32470 
    32471 > hide #6 models
    32472 
    32473 > show #!8 models
    32474 
    32475 > hide #!8 models
    32476 
    32477 > show #8.1 models
    32478 
    32479 > hide #8.1 models
    32480 
    32481 > show #7 models
    32482 
    32483 > hide #7 models
    32484 
    32485 > show #6 models
    32486 
    32487 > hide #6 models
    32488 
    32489 > show #6 models
    32490 
    32491 > hide #6 models
    32492 
    32493 > hide #!8 models
    32494 
    32495 > show #!8 models
    32496 
    32497 > hide #!8 models
    32498 
    32499 > show #!8 models
    32500 
    32501 > hide #!8 models
    32502 
    32503 > hide #5 models
    32504 
    32505 > show #5 models
    32506 
    32507 > hide #5 models
    32508 
    32509 > show #5 models
    32510 
    32511 > hide #5 models
    32512 
    32513 > show #5 models
    32514 
    32515 > hide #5 models
    32516 
    32517 > show #5 models
    32518 
    32519 > hide #5 models
    32520 
    32521 > show #5 models
    32522 
    32523 [Repeated 1 time(s)]
    32524 
    32525 > save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min.defattr attrName
    32526 > Fab_rDeutdelta_10min models #5
    32527 
    32528 No known/registered attribute Fab_rDeutdelta_10min 
    32529 
    32530 > setattr #5 residues Fab_rDeutdelta_10min_color models create true type color
    32531 
    32532 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    32533 Invalid color name or specifier 
    32534 
    32535 > setattr #5 residues Fab_rDeutdelta_10min_color create true type color
    32536 
    32537 Expected a keyword 
    32538 
    32539 > setattr #5 residues Fab_rDeutdelta_10min_color value create true type color
    32540 
    32541 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    32542 Invalid color name or specifier 
    32543 
    32544 > save /Users/alvinchew/Downloads/ Fab_rDeutdelta_10min_color.defattr attrName
    32545 > Fab_rDeutdelta_10min_color models #5
    32546 
    32547 Cannot determine format for '/Users/alvinchew/Downloads/' 
    32548 
    32549 > save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
    32550 > Fab_rDeutdelta_10min_color models #5
    32551 
    32552 No known/registered attribute Fab_rDeutdelta_10min_color 
    32553 
    32554 > save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
    32555 > Fab_rDeutdelta_10min_color models #5
    32556 
    32557 No known/registered attribute Fab_rDeutdelta_10min_color 
    32558 
    32559 > setattr #5 residues Fab_rDeutdelta_10min_color value create true type color
    32560 
    32561 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    32562 Invalid color name or specifier 
    32563 
    32564 > setattr #5 residues Fab_rDeutdelta_10min_color value create true type float
    32565 
    32566 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    32567 Expected a number 
    32568 
    32569 > setattr #5 residues Fab_rDeutdelta_10min_color value create true
    32570 
    32571 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    32572 Invalid color name or specifier 
    32573 
    32574 > setattr #5 residues Fab_rDeutdelta_10min_color value create true type string
    32575 
    32576 Assigning Fab_rDeutdelta_10min_color attribute to 442 items 
    32577 
    32578 > save /Users/alvinchew/Downloads/ Fab_rDeutdelta_10min_color.defattr attrName
    32579 > Fab_rDeutdelta_10min_color models #5
    32580 
    32581 Cannot determine format for '/Users/alvinchew/Downloads/' 
    32582 
    32583 > save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
    32584 > Fab_rDeutdelta_10min_color models #5
    32585 
    32586 Saved attribute 'Fab_rDeutdelta_10min_color' of 442 residues using match mode:
    32587 1-to-1 to /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr 
    32588 
    32589 > ui tool show "Color Actions"
    32590 
    32591 > close session
    32592 
    32593 > open /Users/alvinchew/Downloads/ApoA1_X.pdb
    32594 
    32595 Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_X.pdb 
    32596 --- 
    32597 warnings | Start residue of secondary structure not found: HELIX 4 4 ALA C 2
    32598 ALA C 129 1 128 
    32599 Start residue of secondary structure not found: HELIX 5 5 PRO C 130 GLY C 149
    32600 1 20 
    32601 Start residue of secondary structure not found: HELIX 6 6 GLY C 151 ALA C 206
    32602 1 56 
    32603  
    32604 Chain information for ApoA1_X.pdb #1 
    32605 --- 
    32606 Chain | Description 
    32607 B | No description available 
    32608  
    32609 
    32610 > open /Users/alvinchew/Downloads/ApoA1_Y.pdb
    32611 
    32612 Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_Y.pdb 
    32613 --- 
    32614 warnings | Start residue of secondary structure not found: HELIX 1 1 ALA B 2
    32615 ALA B 129 1 128 
    32616 Start residue of secondary structure not found: HELIX 2 2 PRO B 130 GLY B 149
    32617 1 20 
    32618 Start residue of secondary structure not found: HELIX 3 3 GLY B 151 ALA B 206
    32619 1 56 
    32620  
    32621 Chain information for ApoA1_Y.pdb #2 
    32622 --- 
    32623 Chain | Description 
    32624 C | No description available 
    32625  
    32626 
    32627 > open /Users/alvinchew/Downloads/D2NS1_B.pdb
    32628 
    32629 Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb 
    32630 --- 
    32631 warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
    32632 39 GLU A 51 1 13 
    32633 Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
    32634 1 11 
    32635 Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
    32636 1 9 
    32637 Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
    32638 121 1 7 
    32639 Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
    32640 147 1 3 
    32641 26 messages similar to the above omitted 
    32642  
    32643 Chain information for D2NS1_B.pdb #3 
    32644 --- 
    32645 Chain | Description 
    32646 B | No description available 
    32647  
    32648 
    32649 > open /Users/alvinchew/Downloads/D2NS1_A.pdb
    32650 
    32651 Chain information for D2NS1_A.pdb #4 
    32652 --- 
    32653 Chain | Description 
    32654 A | No description available 
    32655  
    32656 
    32657 > color #2 #e0e6ecff
    32658 
    32659 > color #2 #b1b6bbff
    32660 
    32661 > color #1 #d7d0cbff
    32662 
    32663 > color #3 #93a3e1ff
    32664 
    32665 > color #3 #8a9ae1ff
    32666 
    32667 > color #3 #969ae1ff
    32668 
    32669 > color #3 #8496e1ff
    32670 
    32671 > color #4 #b7d7ecff
    32672 
    32673 > save /Users/alvinchew/Downloads/NS1-apoAI_monomers-forwint.cxs includeMaps
    32674 > true
    32675 
    32676 ——— End of log from Sat Apr 1 16:55:32 2023 ———
    32677 
    32678 opened ChimeraX session 
    32679 
    32680 > ui tool show XMAS
    32681 
    32682  
    32683 Peptide pair mapping of XlinkX evidence file:
    32684 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy.txt 
    32685 428 Peptide pairs are disregarded due to lacking/decoy sequence 
    32686 Unique peptide pairs: 28 out of 33 
    32687 Unique peptide pairs with pseudobonds: 28 
    32688 Pseudobonds are stored in
    32689 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy_1,2,3,4.pb 
    32690 Mapping information is stored in
    32691 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy_1,2,3,4.tsv 
    32692 Please select pseudobonds 
    32693 Please select pseudobonds 
    32694 Please select pseudobonds 
    32695 
    32696 > select subtract #5
    32697 
    32698 Nothing selected 
    32699 
    32700 > save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    32701 
    32702 ——— End of log from Mon Apr 3 15:19:20 2023 ———
    32703 
    32704 opened ChimeraX session 
    32705  
    32706 Peptide pair mapping of XlinkX evidence file:
    32707 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS.txt 
    32708 432 Peptide pairs are disregarded due to lacking/decoy sequence 
    32709 Unique peptide pairs: 29 out of 29 
    32710 Unique peptide pairs with pseudobonds: 26 
    32711 Pseudobonds are stored in
    32712 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2.pb 
    32713 Mapping information is stored in
    32714 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2.tsv 
    32715 
    32716 > save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    32717 
    32718 Please select pseudobonds 
    32719 /Users/wintwintphoo/Library/Application Support/ChimeraX/1.5/site-
    32720 packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette
    32721 using color= is deprecated and will be removed in version 0.13. Set
    32722 `palette='dark:gray'` for same effect. 
    32723 warnings.warn(msg, FutureWarning) 
    32724 
    32725 > color #1 #684bdfff
    32726 
    32727 > undo
    32728 
    32729 > select subtract #6
    32730 
    32731 Nothing selected 
    32732 
    32733 > select add #5
    32734 
    32735 102 pseudobonds, 1 model selected 
    32736 
    32737 > select subtract #5
    32738 
    32739 Nothing selected 
    32740 
    32741 > save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    32742 
    32743  
    32744 Peptide pair mapping of XlinkX evidence file:
    32745 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS.txt 
    32746 432 Peptide pairs are disregarded due to lacking/decoy sequence 
    32747 Unique peptide pairs: 29 out of 29 
    32748 Unique peptide pairs with pseudobonds: 26 
    32749 Pseudobonds are stored in
    32750 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2,3,4.pb 
    32751 Mapping information is stored in
    32752 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2,3,4.tsv 
    32753  
    32754 Peptide pair mapping of XlinkX evidence file:
    32755 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS.txt 
    32756 436 Peptide pairs are disregarded due to lacking/decoy sequence 
    32757 Unique peptide pairs: 25 out of 25 
    32758 Unique peptide pairs with pseudobonds: 20 
    32759 Pseudobonds are stored in
    32760 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS_1,2,3,4.pb 
    32761 Mapping information is stored in
    32762 /Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS_1,2,3,4.tsv 
    32763 
    32764 > select subtract #7
    32765 
    32766 Nothing selected 
    32767 
    32768 > close #7
    32769 
    32770 > save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    32771 
    32772 [Repeated 1 time(s)]Pseudobonds are stored in
    32773 /Users/wintwintphoo/Downloads/20220215_denv_ns1_apoA1_xmas_xlinks_list.pb 
    32774 
    32775 > select subtract #8
    32776 
    32777 195 pseudobonds, 2 models selected 
    32778 
    32779 > select add #8
    32780 
    32781 275 pseudobonds, 3 models selected 
    32782 
    32783 > hide #8 models
    32784 
    32785 > show #8 models
    32786 
    32787 > hide #7 models
    32788 
    32789 > save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
    32790 
    32791 ——— End of log from Mon Apr 3 16:43:31 2023 ———
    32792 
    32793 opened ChimeraX session 
    32794 
    32795 > show #7 models
    32796 
    32797 > hide #7 models
    32798 
    32799 > show #7 models
    32800 
    32801 > hide #7 models
    32802 
    32803 > select subtract #7
    32804 
    32805 275 pseudobonds, 3 models selected 
    32806 
    32807 > hide #5 models
    32808 
    32809 > show #5 models
    32810 
    32811 > hide #6 models
    32812 
    32813 > show #6 models
    32814 
    32815 > hide #6 models
    32816 
    32817 > show #6 models
    32818 
    32819 > hide #6 models
    32820 
    32821 > show #6 models
    32822 
    32823 > hide #8 models
    32824 
    32825 > show #8 models
    32826 
    32827 > hide #8 models
    32828 
    32829 > show #8 models
    32830 
    32831 > hide #6 models
    32832 
    32833 > show #6 models
    32834 
    32835 > hide #6 models
    32836 
    32837 > show #6 models
    32838 
    32839 > hide #6 models
    32840 
    32841 > show #6 models
    32842 
    32843 > hide #6 models
    32844 
    32845 > show #6 models
    32846 
    32847 > hide #5 models
    32848 
    32849 > show #5 models
    32850 
    32851 > hide #5 models
    32852 
    32853 > show #5 models
    32854 
    32855 > hide #5 models
    32856 
    32857 > show #5 models
    32858 
    32859 > open "/Users/alvinchew/Library/CloudStorage/OneDrive-
    32860 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM
    32861 > Maps_docked structures/EDEN2 sNS1wt-Fab562/sNS1wt-Fab562.mrc"
    32862 
    32863 Opened sNS1wt-Fab562.mrc as #9, grid size 416,416,416, pixel 0.85, shown at
    32864 level 0.0324, step 2, values float32 
    32865 
    32866 > volume #9 step 1
    32867 
    32868 > volume #9 color #b2b2b25f
    32869 
    32870 > volume #9 color #b2b2b24d
    32871 
    32872 > volume #9 color #aebfbb4d
    32873 
    32874 > volume #9 color #96bdbf4d
    32875 
    32876 > volume #9 color #b4e3e64d
    32877 
    32878 > select subtract #5
    32879 
    32880 173 pseudobonds, 2 models selected 
    32881 
    32882 > select subtract #6
    32883 
    32884 80 pseudobonds, 1 model selected 
    32885 
    32886 > select subtract #8
    32887 
    32888 Nothing selected 
    32889 
    32890 > select add #9
    32891 
    32892 2 models selected 
    32893 
    32894 > ui mousemode right "rotate selected models"
    32895 
    32896 > view matrix models
    32897 > #9,-0.87886,-0.26868,-0.39424,454.61,-2.4853e-05,0.82637,-0.56313,136.08,0.47709,-0.4949,-0.72627,325.9
    32898 
    32899 > view matrix models
    32900 > #9,-0.58078,0.6843,0.44094,79.244,0.37206,0.7049,-0.6039,98.706,-0.72406,-0.18668,-0.66399,474.16
    32901 
    32902 > volume #9 level 0.08346
    32903 
    32904 > view matrix models
    32905 > #9,-0.62302,0.6249,0.47048,91.383,0.37769,0.76704,-0.51866,70.685,-0.68498,-0.14544,-0.71389,469.61
    32906 
    32907 > view matrix models
    32908 > #9,-0.59735,0.62471,0.5029,80.705,0.44544,0.7799,-0.43971,41.448,-0.6669,-0.038648,-0.74414,453.65
    32909 
    32910 > view matrix models
    32911 > #9,-0.73179,-0.006901,0.6815,180.03,-0.57374,0.54594,-0.61055,294.56,-0.36785,-0.83779,-0.40347,474.63
    32912 
    32913 > view matrix models
    32914 > #9,-0.79319,-0.093028,0.60182,221,-0.596,0.32149,-0.73582,361.32,-0.12503,-0.94233,-0.31045,432.17
    32915 
    32916 > view matrix models
    32917 > #9,-0.58382,-0.31126,0.74985,193.7,-0.73407,0.59693,-0.32375,259.38,-0.34683,-0.73946,-0.57698,486.91
    32918 
    32919 > view matrix models
    32920 > #9,-0.34202,-0.16644,0.92484,92.532,-0.84723,0.48035,-0.22687,281.13,-0.40649,-0.86114,-0.3053,466.79
    32921 
    32922 > view matrix models
    32923 > #9,-0.55882,0.49146,0.66797,65.577,-0.45981,0.4867,-0.74277,309.92,-0.69014,-0.72222,-0.045999,443.36
    32924 
    32925 > view matrix models
    32926 > #9,-0.54201,-0.3239,0.77544,183.64,-0.79241,0.50424,-0.34326,289.48,-0.27982,-0.80052,-0.52997,476.72
    32927 
    32928 > view matrix models
    32929 > #9,-0.58956,-0.063726,0.80521,141.21,-0.57182,0.737,-0.36035,213.39,-0.57047,-0.67289,-0.47094,494.64
    32930 
    32931 > view matrix models
    32932 > #9,-0.39155,-0.00207,0.92016,73.642,-0.67059,0.68539,-0.28381,225.21,-0.63008,-0.72818,-0.26975,476.42
    32933 
    32934 > view matrix models
    32935 > #9,-0.28776,-0.19817,0.93698,86.145,-0.87695,0.44774,-0.17463,282.08,-0.38491,-0.87193,-0.30263,464.35
    32936 
    32937 > view matrix models
    32938 > #9,-0.25456,-0.094965,0.96238,57.53,-0.75216,0.64493,-0.13531,218.34,-0.60782,-0.75832,-0.2356,471.22
    32939 
    32940 > view matrix models
    32941 > #9,0.08179,0.053136,0.99523,-33.823,-0.83033,0.55594,0.038556,214.45,-0.55124,-0.82952,0.089591,411.62
    32942 
    32943 > view matrix models
    32944 > #9,-0.066864,0.18014,0.98137,-26.974,-0.92402,0.35991,-0.12902,296.95,-0.37644,-0.91543,0.14239,385.61
    32945 
    32946 > view matrix models
    32947 > #9,-0.1796,0.42981,0.88488,-32.014,-0.68511,0.59085,-0.42605,271.28,-0.70595,-0.68276,0.18835,394.65
    32948 
    32949 > view matrix models
    32950 > #9,-0.38938,-0.35219,0.85108,147.19,-0.71886,0.6939,-0.041736,186.13,-0.57587,-0.62806,-0.52337,497.8
    32951 
    32952 > ui mousemode right "translate selected models"
    32953 
    32954 > view matrix models
    32955 > #9,-0.38938,-0.35219,0.85108,163.76,-0.71886,0.6939,-0.041736,188.56,-0.57587,-0.62806,-0.52337,496.31
    32956 
    32957 > view matrix models
    32958 > #9,-0.38938,-0.35219,0.85108,168.86,-0.71886,0.6939,-0.041736,197.29,-0.57587,-0.62806,-0.52337,495.68
    32959 
    32960 > view matrix models
    32961 > #9,-0.38938,-0.35219,0.85108,169.85,-0.71886,0.6939,-0.041736,197.13,-0.57587,-0.62806,-0.52337,494.81
    32962 
    32963 > volume #9 level 0.09622
    32964 
    32965 > volume #9 level 0.1218
    32966 
    32967 > volume #9 level 0.1102
    32968 
    32969 > ui mousemode right "rotate selected models"
    32970 
    32971 > view matrix models
    32972 > #9,-0.37051,-0.036777,0.9281,96.88,-0.68448,0.68625,-0.24606,231.42,-0.62786,-0.72644,-0.27943,474.52
    32973 
    32974 > view matrix models
    32975 > #9,-0.31168,-0.049862,0.94888,84.726,-0.69125,0.69707,-0.19043,220.1,-0.65194,-0.71527,-0.25173,471.56
    32976 
    32977 > view matrix models
    32978 > #9,-0.1857,-0.07265,0.97992,60.36,-0.66701,0.74162,-0.07142,185.28,-0.72154,-0.66687,-0.18618,462.98
    32979 
    32980 > view matrix models
    32981 > #9,-0.23942,-0.0021906,0.97091,59.372,-0.51422,0.84851,-0.12489,149.75,-0.82356,-0.52917,-0.20428,460.62
    32982 
    32983 > view matrix models
    32984 > #9,-0.22507,0.022971,0.97407,51.838,-0.51742,0.84429,-0.13947,153.84,-0.8256,-0.5354,-0.17814,457.06
    32985 
    32986 > view matrix models
    32987 > #9,-0.22651,0.020133,0.9738,52.639,-0.51714,0.84474,-0.13775,153.38,-0.82538,-0.5348,-0.18093,457.45
    32988 
    32989 > view matrix models
    32990 > #9,-0.21551,0.029869,0.97604,48.561,-0.50806,0.85017,-0.1382,150.91,-0.83393,-0.52567,-0.16805,454.92
    32991 
    32992 > view matrix models
    32993 > #9,-0.26159,0.28099,0.92337,23.126,-0.7227,0.57709,-0.38035,282.89,-0.63974,-0.76682,0.052114,420.27
    32994 
    32995 > view matrix models
    32996 > #9,-0.41669,0.2104,0.88436,70.441,-0.68255,0.57014,-0.45725,291.66,-0.60041,-0.79415,-0.093959,445.96
    32997 
    32998 > view matrix models
    32999 > #9,-0.43816,0.2546,0.86209,70.827,-0.46829,0.75397,-0.46068,222.24,-0.76728,-0.60556,-0.21113,465.21
    33000 
    33001 > view matrix models
    33002 > #9,-0.40829,0.25984,0.87509,62.119,-0.47771,0.75607,-0.44739,221.01,-0.77788,-0.6007,-0.18457,461.17
    33003 
    33004 > view matrix models
    33005 > #9,-0.44661,0.14869,0.88229,86.897,-0.5092,0.76859,-0.38728,212.93,-0.7357,-0.62223,-0.26755,473.29
    33006 
    33007 > view matrix models
    33008 > #9,-0.44407,0.15675,0.88217,85.065,-0.50686,0.76795,-0.3916,213.45,-0.73884,-0.62104,-0.26158,472.5
    33009 
    33010 > ui mousemode right "move picked models"
    33011 
    33012 > ui mousemode right "rotate selected models"
    33013 
    33014 > ui mousemode right "translate selected models"
    33015 
    33016 > view matrix models
    33017 > #9,-0.44407,0.15675,0.88217,83.534,-0.50686,0.76795,-0.3916,214.96,-0.73884,-0.62104,-0.26158,474.33
    33018 
    33019 > ui mousemode right "rotate selected models"
    33020 
    33021 > view matrix models
    33022 > #9,-0.47173,0.10261,0.87575,99.098,-0.49372,0.79217,-0.35876,202.13,-0.73056,-0.60161,-0.32303,481.23
    33023 
    33024 > view matrix models
    33025 > #9,-0.46188,0.17351,0.86981,86.145,-0.45527,0.79525,-0.40039,202.72,-0.76118,-0.58093,-0.28831,476.44
    33026 
    33027 > view matrix models
    33028 > #9,-0.17678,0.17743,0.96813,15.981,-0.55919,0.79135,-0.24714,192.57,-0.80997,-0.58505,-0.040674,438.48
    33029 
    33030 > view matrix models
    33031 > #9,-0.20822,0.22068,0.95286,16.964,-0.47946,0.8261,-0.2961,181.71,-0.8525,-0.51851,-0.066201,439.34
    33032 
    33033 > view matrix models
    33034 > #9,-0.23313,0.22067,0.94708,22.5,-0.51218,0.80002,-0.31248,195.19,-0.82664,-0.55792,-0.073484,442.99
    33035 
    33036 > view matrix models
    33037 > #9,-0.272,0.31817,0.90818,19.883,-0.43497,0.80119,-0.41096,200.1,-0.85838,-0.50681,-0.07953,440.9
    33038 
    33039 > ui mousemode right "translate selected models"
    33040 
    33041 > view matrix models
    33042 > #9,-0.272,0.31817,0.90818,20.776,-0.43497,0.80119,-0.41096,197.63,-0.85838,-0.50681,-0.07953,443.72
    33043 
    33044 > view matrix models
    33045 > #9,-0.272,0.31817,0.90818,21.653,-0.43497,0.80119,-0.41096,197.64,-0.85838,-0.50681,-0.07953,444.39
    33046 
    33047 > view matrix models
    33048 > #9,-0.272,0.31817,0.90818,21.578,-0.43497,0.80119,-0.41096,197.39,-0.85838,-0.50681,-0.07953,444.75
    33049 
    33050 > ui mousemode right "rotate selected models"
    33051 
    33052 > view matrix models
    33053 > #9,-0.34138,0.16793,0.9248,56.875,-0.43348,0.8449,-0.31343,170.87,-0.834,-0.50788,-0.21564,466.63
    33054 
    33055 > hide #1 models
    33056 
    33057 > show #1 models
    33058 
    33059 > hide #2 models
    33060 
    33061 > show #2 models
    33062 
    33063 > hide #3 models
    33064 
    33065 > show #3 models
    33066 
    33067 > hide #4 models
    33068 
    33069 > show #4 models
    33070 
    33071 > combine #1-4
    33072 
    33073 Remapping chain ID 'B' in D2NS1_B.pdb #3 to 'D' 
    33074 
    33075 > hide #10 models
    33076 
    33077 > show #10 models
    33078 
    33079 > hide #1 models
    33080 
    33081 > hide #2 models
    33082 
    33083 > hide #3 models
    33084 
    33085 > hide #4 models
    33086 
    33087 > hide #10 models
    33088 
    33089 > show #10 models
    33090 
    33091 > hide #5 models
    33092 
    33093 > show #5 models
    33094 
    33095 > show #1 models
    33096 
    33097 > hide #1 models
    33098 
    33099 > show #1 models
    33100 
    33101 > hide #1 models
    33102 
    33103 > show #2 models
    33104 
    33105 > show #3 models
    33106 
    33107 > show #4 models
    33108 
    33109 > view matrix models
    33110 > #9,0.52951,-0.025333,0.84793,-49.614,-0.39781,0.87542,0.27457,46.784,-0.74925,-0.4827,0.45346,319.24
    33111 
    33112 > undo
    33113 
    33114 > select subtract #9
    33115 
    33116 Nothing selected 
    33117 
    33118 > ui mousemode right zoom
    33119 
    33120 > molmap #1-4 onGrid #9 sigmaFactor 6
    33121 
    33122 Missing or invalid "resolution" argument: Expected a number 
    33123 
    33124 > molmap #1-4 resolution 8 onGrid #9
    33125 
    33126 Missing or invalid "resolution" argument: Expected a number 
    33127 
    33128 > molmap #1-4 8 onGrid #9
    33129 
    33130 Opened map 8 as #11, grid size 416,416,416, pixel 0.85, shown at level 0.0635,
    33131 step 1, values float32 
    33132 
    33133 > volume #11 level 0.03753
    33134 
    33135 > mmaker #9 to #11
    33136 
    33137 No 'to' model specified 
    33138 
    33139 > fitmap #9 to #11
    33140 
    33141 Expected a keyword 
    33142 
    33143 > Fit #9 in map #11
    33144 
    33145 Unknown command: Fit #9 in map #11 
    33146 
    33147 > fitmap #9 inMap map #11
    33148 
    33149 Invalid "inMap" argument: invalid density map specifier 
    33150 
    33151 > fitmap #9 inMap #11
    33152 
    33153 Fit map sNS1wt-Fab562.mrc in map map 8 using 131473 points 
    33154 correlation = 0.6323, correlation about mean = 0.08876, overlap = 2834 
    33155 steps = 292, shift = 12.1, angle = 16.9 degrees 
    33156  
    33157 Position of sNS1wt-Fab562.mrc (#9) relative to map 8 (#11) coordinates: 
    33158 Matrix rotation and translation 
    33159 0.96199493 -0.17308261 0.21120645 -4.02299000 
    33160 0.19395657 0.97754937 -0.08232910 -24.62700524 
    33161 -0.19221500 0.12016506 0.97396805 10.65384009 
    33162 Axis 0.34805838 0.69342351 0.63088763 
    33163 Axis point 91.81802475 0.00000000 16.19663836 
    33164 Rotation angle (degrees) 16.91131195 
    33165 Shift along axis -11.75580388 
    33166  
    33167 
    33168 > save "/Users/alvinchew/OneDrive - Nanyang Technological University
    33169 > (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
    33170 > MS_recolored.cxs" includeMaps true
    33171 
    33172 ——— End of log from Wed Apr 19 14:11:57 2023 ———
    33173 
    33174 opened ChimeraX session 
    33175 
    33176 > open /Users/alvinchew/Library/CloudStorage/OneDrive-
    33177 > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/F562a.pdb
    33178 
    33179 Chain information for F562a.pdb #12 
    33180 --- 
    33181 Chain | Description 
    33182 C | No description available 
    33183 D | No description available 
    33184  
    33185 
    33186 > color #12 #8b92d7ff
    33187 
    33188 > color #12 #718dd7ff
    33189 
    33190 > color #12 #7693d7ff
    33191 
    33192 > color #12 #849ed7ff
    33193 
    33194 > select add #12
    33195 
    33196 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    33197 
    33198 > ui mousemode right zoom
    33199 
    33200 > ui mousemode right "translate selected models"
    33201 
    33202 > ui mousemode right "rotate selected models"
    33203 
    33204 > view matrix models
    33205 > #12,0.59826,0.23414,-0.76633,188.86,-0.29309,-0.82615,-0.48122,476.1,-0.74578,0.5125,-0.42563,337.4
    33206 
    33207 > view matrix models
    33208 > #12,0.8198,-0.22926,-0.52475,175.64,-0.56234,-0.49535,-0.66212,513.22,-0.10814,0.8379,-0.53501,149.05
    33209 
    33210 > view matrix models
    33211 > #12,0.70505,-0.47588,-0.52578,246.35,-0.42704,-0.87682,0.22096,392.51,-0.56617,0.068741,-0.82142,443.24
    33212 
    33213 > ui mousemode right "translate selected models"
    33214 
    33215 > view matrix models
    33216 > #12,0.70505,-0.47588,-0.52578,242.09,-0.42704,-0.87682,0.22096,378.11,-0.56617,0.068741,-0.82142,460.51
    33217 
    33218 > ui mousemode right zoom
    33219 
    33220 > ui mousemode right "rotate selected models"
    33221 
    33222 > view matrix models
    33223 > #12,0.89785,-0.43928,-0.030063,102.58,-0.37117,-0.71836,-0.58838,480.03,0.23687,0.53943,-0.80803,185.85
    33224 
    33225 > ui mousemode right "translate selected models"
    33226 
    33227 > view matrix models
    33228 > #12,0.89785,-0.43928,-0.030063,97.925,-0.37117,-0.71836,-0.58838,480.91,0.23687,0.53943,-0.80803,179.17
    33229 
    33230 > ui mousemode right "rotate selected models"
    33231 
    33232 > view matrix models
    33233 > #12,0.96357,-0.26121,-0.057389,55.865,-0.25517,-0.8337,-0.48973,456.47,0.080078,0.48653,-0.86998,236.41
    33234 
    33235 > view matrix models
    33236 > #12,0.90596,-0.39388,-0.15525,110.13,-0.42323,-0.85213,-0.30783,467.19,-0.011043,0.34459,-0.93869,295.05
    33237 
    33238 > view matrix models
    33239 > #12,0.89108,-0.41763,-0.17768,121.79,-0.45249,-0.84775,-0.2767,467.81,-0.035067,0.32696,-0.94439,304.83
    33240 
    33241 > ui mousemode right "translate selected models"
    33242 
    33243 > view matrix models
    33244 > #12,0.89108,-0.41763,-0.17768,121.19,-0.45249,-0.84775,-0.2767,465.74,-0.035067,0.32696,-0.94439,307.63
    33245 
    33246 > view matrix models
    33247 > #12,0.89108,-0.41763,-0.17768,120.89,-0.45249,-0.84775,-0.2767,466.02,-0.035067,0.32696,-0.94439,307.05
    33248 
    33249 > ui mousemode right "rotate selected models"
    33250 
    33251 > view matrix models
    33252 > #12,0.90549,-0.36137,-0.22248,115.49,-0.40743,-0.88694,-0.21757,451.86,-0.11871,0.28765,-0.95035,334.75
    33253 
    33254 Must specify one map, got 0 
    33255 
    33256 > fitmap #12 inMap #9
    33257 
    33258 Fit molecule F562a.pdb (#12) to map sNS1wt-Fab562.mrc (#9) using 3401 atoms 
    33259 average map value = 0.09851, steps = 92 
    33260 shifted from previous position = 4.5 
    33261 rotated from previous position = 18.4 degrees 
    33262 atoms outside contour = 1988, contour level = 0.11015 
    33263  
    33264 Position of F562a.pdb (#12) relative to sNS1wt-Fab562.mrc (#9) coordinates: 
    33265 Matrix rotation and translation 
    33266 -0.10510217 -0.15771336 0.98187577 53.64785327 
    33267 -0.09250566 -0.98151278 -0.16755707 397.45943422 
    33268 0.99014960 -0.10843968 0.08856975 -3.70781985 
    33269 Axis 0.66871425 -0.09359056 0.73760562 
    33270 Axis point 22.55285651 199.33929044 0.00000000 
    33271 Rotation angle (degrees) 177.46657060 
    33272 Shift along axis -4.05827537 
    33273  
    33274 
    33275 > select subtract #12
    33276 
    33277 Nothing selected 
    33278 
    33279 > ui tool show "Show Sequence Viewer"
    33280 
    33281 > sequence chain #12/C
    33282 
    33283 Alignment identifier is 12/C 
    33284 
    33285 > select #12/C:1-2
    33286 
    33287 13 atoms, 12 bonds, 2 residues, 1 model selected 
    33288 
    33289 > select #12/C:1-18
    33290 
    33291 131 atoms, 132 bonds, 18 residues, 1 model selected 
    33292 
    33293 > color #12 #d0d2dfff
    33294 
    33295 > select #12/C:5
    33296 
    33297 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33298 
    33299 > select #12/C:5-14
    33300 
    33301 71 atoms, 71 bonds, 10 residues, 1 model selected 
    33302 
    33303 > ui tool show "Color Actions"
    33304 
    33305 > color sel #cbd8ffff
    33306 
    33307 > color sel #9fbcffff
    33308 
    33309 > color sel #93abffff
    33310 
    33311 > color sel #88a4ffff
    33312 
    33313 > color sel #8484f7ff
    33314 
    33315 > select #12/C:15
    33316 
    33317 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33318 
    33319 > select #12/C:15-35
    33320 
    33321 163 atoms, 168 bonds, 21 residues, 1 model selected 
    33322 
    33323 > color sel #fdf2f2ff
    33324 
    33325 > select #12/C:21
    33326 
    33327 6 atoms, 5 bonds, 1 residue, 1 model selected 
    33328 
    33329 > select #12/C:21
    33330 
    33331 6 atoms, 5 bonds, 1 residue, 1 model selected 
    33332 
    33333 > color sel #fae0e0ff
    33334 
    33335 > select #12/C:22
    33336 
    33337 11 atoms, 11 bonds, 1 residue, 1 model selected 
    33338 
    33339 > select #12/C:22-35
    33340 
    33341 112 atoms, 116 bonds, 14 residues, 1 model selected 
    33342 
    33343 > color sel #fbe8e7ff
    33344 
    33345 > select #12/C:36-37
    33346 
    33347 26 atoms, 28 bonds, 2 residues, 1 model selected 
    33348 
    33349 > select #12/C:36-42
    33350 
    33351 77 atoms, 81 bonds, 7 residues, 1 model selected 
    33352 
    33353 > select #12/C:30
    33354 
    33355 6 atoms, 5 bonds, 1 residue, 1 model selected 
    33356 
    33357 > select #12/C:30-35
    33358 
    33359 43 atoms, 43 bonds, 6 residues, 1 model selected 
    33360 
    33361 > color sel #3535f5ff
    33362 
    33363 > select #12/C:36-37
    33364 
    33365 26 atoms, 28 bonds, 2 residues, 1 model selected 
    33366 
    33367 > select #12/C:36-47
    33368 
    33369 115 atoms, 120 bonds, 12 residues, 1 model selected 
    33370 
    33371 > color sel #fbe8e7ff
    33372 
    33373 > select #12/C:48-49
    33374 
    33375 17 atoms, 16 bonds, 2 residues, 1 model selected 
    33376 
    33377 > select #12/C:48-57
    33378 
    33379 94 atoms, 97 bonds, 10 residues, 1 model selected 
    33380 
    33381 > select #12/C:58-59
    33382 
    33383 10 atoms, 9 bonds, 2 residues, 1 model selected 
    33384 
    33385 > select #12/C:58-61
    33386 
    33387 26 atoms, 25 bonds, 4 residues, 1 model selected 
    33388 
    33389 > color sel #f1f1feff
    33390 
    33391 > select #12/C:62-63
    33392 
    33393 20 atoms, 20 bonds, 2 residues, 1 model selected 
    33394 
    33395 > select #12/C:62-73
    33396 
    33397 99 atoms, 100 bonds, 12 residues, 1 model selected 
    33398 
    33399 > color sel #fadfdfff
    33400 
    33401 > select #12/C:79
    33402 
    33403 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33404 
    33405 > select #12/C:79-94
    33406 
    33407 126 atoms, 128 bonds, 16 residues, 1 model selected 
    33408 
    33409 > color sel #efeffeff
    33410 
    33411 > select #12/C:95
    33412 
    33413 7 atoms, 6 bonds, 1 residue, 1 model selected 
    33414 
    33415 > select #12/C:95-103
    33416 
    33417 82 atoms, 85 bonds, 9 residues, 1 model selected 
    33418 
    33419 > color sel #ddddfcff
    33420 
    33421 > select #12/C:102
    33422 
    33423 12 atoms, 12 bonds, 1 residue, 1 model selected 
    33424 
    33425 > select #12/C:102-103
    33426 
    33427 24 atoms, 25 bonds, 2 residues, 1 model selected 
    33428 
    33429 > color sel #c9d0ffff
    33430 
    33431 > hide #!9 models
    33432 
    33433 > select #12/C:104
    33434 
    33435 12 atoms, 12 bonds, 1 residue, 1 model selected 
    33436 
    33437 > select #12/C:104-105
    33438 
    33439 18 atoms, 18 bonds, 2 residues, 1 model selected 
    33440 
    33441 > set bgColor white
    33442 
    33443 > select #12/C:104
    33444 
    33445 12 atoms, 12 bonds, 1 residue, 1 model selected 
    33446 
    33447 > select #12/C:104-112
    33448 
    33449 73 atoms, 78 bonds, 9 residues, 1 model selected 
    33450 
    33451 > color sel #d3d3fbff
    33452 
    33453 > color sel #bec7feff
    33454 
    33455 > select #12/C:113
    33456 
    33457 12 atoms, 12 bonds, 1 residue, 1 model selected 
    33458 
    33459 > select #12/C:113-120
    33460 
    33461 65 atoms, 67 bonds, 8 residues, 1 model selected 
    33462 
    33463 > color sel #d3d9feff
    33464 
    33465 > select #12/C:123
    33466 
    33467 11 atoms, 11 bonds, 1 residue, 1 model selected 
    33468 
    33469 > select #12/C:123-145
    33470 
    33471 153 atoms, 157 bonds, 23 residues, 1 model selected 
    33472 
    33473 > color sel #f6f6feff
    33474 
    33475 > color sel #e7e8ffff
    33476 
    33477 > color sel #edf0ffff
    33478 
    33479 > select #12/C:146
    33480 
    33481 7 atoms, 6 bonds, 1 residue, 1 model selected 
    33482 
    33483 > select #12/C:146-156
    33484 
    33485 79 atoms, 79 bonds, 11 residues, 1 model selected 
    33486 
    33487 > color sel #fdf1f1ff
    33488 
    33489 > select #12/C:157
    33490 
    33491 11 atoms, 11 bonds, 1 residue, 1 model selected 
    33492 
    33493 > select #12/C:157-168
    33494 
    33495 93 atoms, 97 bonds, 12 residues, 1 model selected 
    33496 
    33497 > color sel #fbeae9ff
    33498 
    33499 > select #12/C:169
    33500 
    33501 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33502 
    33503 > select #12/C:169-176
    33504 
    33505 54 atoms, 54 bonds, 8 residues, 1 model selected 
    33506 
    33507 > color sel #f0f0feff
    33508 
    33509 > select #12/C:177-178
    33510 
    33511 18 atoms, 19 bonds, 2 residues, 1 model selected 
    33512 
    33513 > select #12/C:177-179
    33514 
    33515 23 atoms, 24 bonds, 3 residues, 1 model selected 
    33516 
    33517 > select #12/C:177
    33518 
    33519 11 atoms, 11 bonds, 1 residue, 1 model selected 
    33520 
    33521 > select #12/C:177-178
    33522 
    33523 18 atoms, 19 bonds, 2 residues, 1 model selected 
    33524 
    33525 > color sel #ffe7efff
    33526 
    33527 > color sel #fdf6ffff
    33528 
    33529 > color sel #fff0ffff
    33530 
    33531 > color sel #ffeffdff
    33532 
    33533 > color sel #ffedfaff
    33534 
    33535 > color sel #ffecf9ff
    33536 
    33537 > color sel #ffecfaff
    33538 
    33539 > color sel #ffebf9ff
    33540 
    33541 > color sel #ffecfaff
    33542 
    33543 [Repeated 1 time(s)]
    33544 
    33545 > color sel #ffecfbff
    33546 
    33547 > color sel #ffecfcff
    33548 
    33549 [Repeated 1 time(s)]
    33550 
    33551 > color sel #ffedfdff
    33552 
    33553 > color sel #ffecfdff
    33554 
    33555 > color sel #ffedfdff
    33556 
    33557 > color sel #ffeaffff
    33558 
    33559 > color sel #ffeafeff
    33560 
    33561 [Repeated 1 time(s)]
    33562 
    33563 > color sel #ffe9feff
    33564 
    33565 [Repeated 1 time(s)]
    33566 
    33567 > color sel #ffe8feff
    33568 
    33569 > color sel #ffe8fdff
    33570 
    33571 [Repeated 1 time(s)]
    33572 
    33573 > color sel #ffe8fcff
    33574 
    33575 [Repeated 1 time(s)]
    33576 
    33577 > color sel #ffe8fbff
    33578 
    33579 [Repeated 2 time(s)]
    33580 
    33581 > color sel #ffe8faff
    33582 
    33583 > color sel #ffe8f8ff
    33584 
    33585 [Repeated 1 time(s)]
    33586 
    33587 > color sel #ffe8f7ff
    33588 
    33589 [Repeated 1 time(s)]
    33590 
    33591 > color sel #ffe9f7ff
    33592 
    33593 > color sel #ffe8f6ff
    33594 
    33595 > color sel #ffe9f6ff
    33596 
    33597 [Repeated 1 time(s)]
    33598 
    33599 > color sel #ffe9f5ff
    33600 
    33601 > color sel #ffeaf5ff
    33602 
    33603 [Repeated 1 time(s)]
    33604 
    33605 > color sel #ffeaf4ff
    33606 
    33607 [Repeated 1 time(s)]
    33608 
    33609 > color sel #ffebf4ff
    33610 
    33611 > color sel #ffebf3ff
    33612 
    33613 [Repeated 2 time(s)]
    33614 
    33615 > color sel #ffecf2ff
    33616 
    33617 [Repeated 1 time(s)]
    33618 
    33619 > color sel #ffecf1ff
    33620 
    33621 [Repeated 2 time(s)]
    33622 
    33623 > color sel #ffecf0ff
    33624 
    33625 [Repeated 1 time(s)]
    33626 
    33627 > color sel #ffebefff
    33628 
    33629 > color sel #ffebeeff
    33630 
    33631 > color sel #ffeaedff
    33632 
    33633 [Repeated 1 time(s)]
    33634 
    33635 > color sel #ffe9ecff
    33636 
    33637 [Repeated 1 time(s)]
    33638 
    33639 > color sel #ffe8ebff
    33640 
    33641 > color sel #ffe7ebff
    33642 
    33643 [Repeated 1 time(s)]
    33644 
    33645 > color sel #ffe6eaff
    33646 
    33647 > color sel #ffe6e9ff
    33648 
    33649 [Repeated 1 time(s)]
    33650 
    33651 > select #12/C:181
    33652 
    33653 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33654 
    33655 > select #12/C:181-187
    33656 
    33657 53 atoms, 53 bonds, 7 residues, 1 model selected 
    33658 
    33659 > color sel #fff7fdff
    33660 
    33661 > color sel #f9f3ffff
    33662 
    33663 > select #12/C:188-189
    33664 
    33665 14 atoms, 13 bonds, 2 residues, 1 model selected 
    33666 
    33667 > select #12/C:188-198
    33668 
    33669 73 atoms, 73 bonds, 11 residues, 1 model selected 
    33670 
    33671 > color sel #f4efffff
    33672 
    33673 > select #12/C:200
    33674 
    33675 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33676 
    33677 > select #12/C:200-208
    33678 
    33679 69 atoms, 70 bonds, 9 residues, 1 model selected 
    33680 
    33681 > color sel #cdd3ffff
    33682 
    33683 > color sel #8e8ef8ff
    33684 
    33685 > color sel #9da0ffff
    33686 
    33687 > color sel #9c9fffff
    33688 
    33689 > color sel #9c9effff
    33690 
    33691 > color sel #9b9effff
    33692 
    33693 > color sel #9b9dffff
    33694 
    33695 > color sel #9a9cffff
    33696 
    33697 > color sel #9696f8ff
    33698 
    33699 > select #12/C:209
    33700 
    33701 7 atoms, 6 bonds, 1 residue, 1 model selected 
    33702 
    33703 > select #12/C:209-213
    33704 
    33705 41 atoms, 42 bonds, 5 residues, 1 model selected 
    33706 
    33707 > color sel #f1f1feff
    33708 
    33709 > select #12/C:214-215
    33710 
    33711 14 atoms, 13 bonds, 2 residues, 1 model selected 
    33712 
    33713 > select #12/C:214-223
    33714 
    33715 79 atoms, 78 bonds, 10 residues, 1 model selected 
    33716 
    33717 > color sel #b8b8faff
    33718 
    33719 > select #12/C:224-225
    33720 
    33721 16 atoms, 16 bonds, 2 residues, 1 model selected 
    33722 
    33723 > select #12/C:224-228
    33724 
    33725 36 atoms, 36 bonds, 5 residues, 1 model selected 
    33726 
    33727 > color sel #f8f6ffff
    33728 
    33729 > color sel #dad8e0ff
    33730 
    33731 > color sel #c5c3caff
    33732 
    33733 > color sel #c4c3caff
    33734 
    33735 > color sel #b5b4baff
    33736 
    33737 > color sel #b4b3baff
    33738 
    33739 > color sel dim gray
    33740 
    33741 > select #12/C:1
    33742 
    33743 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33744 
    33745 > select #12/C:1-4
    33746 
    33747 29 atoms, 28 bonds, 4 residues, 1 model selected 
    33748 
    33749 > color sel dim gray
    33750 
    33751 > select #12/C:122
    33752 
    33753 7 atoms, 6 bonds, 1 residue, 1 model selected 
    33754 
    33755 > select #12/C:121-122
    33756 
    33757 14 atoms, 13 bonds, 2 residues, 1 model selected 
    33758 
    33759 > color sel dim gray
    33760 
    33761 > select #12/C:178-179
    33762 
    33763 12 atoms, 12 bonds, 2 residues, 1 model selected 
    33764 
    33765 > select #12/C:178-180
    33766 
    33767 19 atoms, 19 bonds, 3 residues, 1 model selected 
    33768 
    33769 > color sel dim gray
    33770 
    33771 > select #12/C:73-74
    33772 
    33773 19 atoms, 18 bonds, 2 residues, 1 model selected 
    33774 
    33775 > select #12/C:73-78
    33776 
    33777 54 atoms, 54 bonds, 6 residues, 1 model selected 
    33778 
    33779 > color sel dim gray
    33780 
    33781 > select add #12
    33782 
    33783 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    33784 
    33785 > select subtract #12
    33786 
    33787 Nothing selected 
    33788 
    33789 > ui tool show "Show Sequence Viewer"
    33790 
    33791 > sequence chain #12/D
    33792 
    33793 Alignment identifier is 12/D 
    33794 
    33795 > select #12/D:1
    33796 
    33797 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33798 
    33799 > select #12/D
    33800 
    33801 1632 atoms, 1668 bonds, 214 residues, 1 model selected 
    33802 
    33803 > color sel dim gray
    33804 
    33805 > view matrix models
    33806 > #12,0.71436,-0.39661,-0.57653,226.88,-0.66803,-0.63185,-0.39307,496.97,-0.20839,0.66593,-0.71632,245.16
    33807 
    33808 > undo
    33809 
    33810 > ui mousemode right select
    33811 
    33812 > select clear
    33813 
    33814 [Repeated 2 time(s)]
    33815 
    33816 > ui mousemode right zoom
    33817 
    33818 > select #12/D:7-8
    33819 
    33820 15 atoms, 14 bonds, 2 residues, 1 model selected 
    33821 
    33822 > select #12/D:7-14
    33823 
    33824 58 atoms, 58 bonds, 8 residues, 1 model selected 
    33825 
    33826 > color sel #e0e0fcff
    33827 
    33828 > select #12/D:15
    33829 
    33830 6 atoms, 5 bonds, 1 residue, 1 model selected 
    33831 
    33832 > select #12/D:15-21
    33833 
    33834 47 atoms, 46 bonds, 7 residues, 1 model selected 
    33835 
    33836 > color sel #fdf4f4ff
    33837 
    33838 > color sel #ffefedff
    33839 
    33840 > select #12/D:22
    33841 
    33842 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33843 
    33844 > select #12/D:22-26
    33845 
    33846 36 atoms, 35 bonds, 5 residues, 1 model selected 
    33847 
    33848 > color sel #fff1f0ff
    33849 
    33850 > color sel #fff2f0ff
    33851 
    33852 > select #12/D:27
    33853 
    33854 6 atoms, 5 bonds, 1 residue, 1 model selected 
    33855 
    33856 > select #12/D:27-28
    33857 
    33858 11 atoms, 10 bonds, 2 residues, 1 model selected 
    33859 
    33860 > color sel #e0e0fcff
    33861 
    33862 > select #12/D:29
    33863 
    33864 6 atoms, 5 bonds, 1 residue, 1 model selected 
    33865 
    33866 > select #12/D:29-36
    33867 
    33868 61 atoms, 62 bonds, 8 residues, 1 model selected 
    33869 
    33870 > color sel #f9f9ffff
    33871 
    33872 > select #12/D:37
    33873 
    33874 14 atoms, 15 bonds, 1 residue, 1 model selected 
    33875 
    33876 > select #12/D:37-38
    33877 
    33878 26 atoms, 28 bonds, 2 residues, 1 model selected 
    33879 
    33880 > color sel #ededfdff
    33881 
    33882 > select #12/D:39
    33883 
    33884 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33885 
    33886 > select #12/D:39-48
    33887 
    33888 74 atoms, 74 bonds, 10 residues, 1 model selected 
    33889 
    33890 > color sel #dcdcfcff
    33891 
    33892 > select
    33893 > #12/D:7-10,13-17,22-28,35-40,47-50,64-69,72-77,86-92,102-107,114-118,129-137,144-150,153-155,159-163,175-182,191-198,205-210
    33894 
    33895 797 atoms, 797 bonds, 102 residues, 1 model selected 
    33896 
    33897 > select #12/D:49
    33898 
    33899 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33900 
    33901 > select #12/D:49
    33902 
    33903 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33904 
    33905 > color sel #e4e4fdff
    33906 
    33907 > select #12/D:50
    33908 
    33909 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33910 
    33911 > select #12/D:50-56
    33912 
    33913 55 atoms, 55 bonds, 7 residues, 1 model selected 
    33914 
    33915 > color sel #5c5cf6ff
    33916 
    33917 > select #12/D:57
    33918 
    33919 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33920 
    33921 > select #12/D:57-58
    33922 
    33923 11 atoms, 10 bonds, 2 residues, 1 model selected 
    33924 
    33925 > select #12/D:57-58
    33926 
    33927 11 atoms, 10 bonds, 2 residues, 1 model selected 
    33928 
    33929 > select #12/D:57
    33930 
    33931 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33932 
    33933 > color sel #fdf6f6ff
    33934 
    33935 > select #12/D:58
    33936 
    33937 6 atoms, 5 bonds, 1 residue, 1 model selected 
    33938 
    33939 > select #12/D:58-67
    33940 
    33941 68 atoms, 69 bonds, 10 residues, 1 model selected 
    33942 
    33943 > color sel #efeffeff
    33944 
    33945 > select #12/D:58-67
    33946 
    33947 68 atoms, 69 bonds, 10 residues, 1 model selected 
    33948 
    33949 > select #12/D:58
    33950 
    33951 6 atoms, 5 bonds, 1 residue, 1 model selected 
    33952 
    33953 > select #12/D:58-69
    33954 
    33955 78 atoms, 79 bonds, 12 residues, 1 model selected 
    33956 
    33957 > color sel #e8e8fdff
    33958 
    33959 > select #12/D:70
    33960 
    33961 4 atoms, 3 bonds, 1 residue, 1 model selected 
    33962 
    33963 > select #12/D:70-73
    33964 
    33965 34 atoms, 35 bonds, 4 residues, 1 model selected 
    33966 
    33967 > color sel #d8d8fcff
    33968 
    33969 > select #12/D:74-75
    33970 
    33971 14 atoms, 13 bonds, 2 residues, 1 model selected 
    33972 
    33973 > select #12/D:74-79
    33974 
    33975 41 atoms, 40 bonds, 6 residues, 1 model selected 
    33976 
    33977 > color sel #f4f4feff
    33978 
    33979 > select #12/D:80
    33980 
    33981 7 atoms, 6 bonds, 1 residue, 1 model selected 
    33982 
    33983 > select #12/D:80-81
    33984 
    33985 16 atoms, 15 bonds, 2 residues, 1 model selected 
    33986 
    33987 > color sel #fff6f4ff
    33988 
    33989 > select #12/D:82
    33990 
    33991 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33992 
    33993 > select #12/D:82-84
    33994 
    33995 22 atoms, 21 bonds, 3 residues, 1 model selected 
    33996 
    33997 > color sel #efeffeff
    33998 
    33999 > select #12/D:85
    34000 
    34001 5 atoms, 4 bonds, 1 residue, 1 model selected 
    34002 
    34003 > select #12/D:85-87
    34004 
    34005 18 atoms, 17 bonds, 3 residues, 1 model selected 
    34006 
    34007 > select #12/D:84-85
    34008 
    34009 13 atoms, 12 bonds, 2 residues, 1 model selected 
    34010 
    34011 > select #12/D:84-87
    34012 
    34013 26 atoms, 25 bonds, 4 residues, 1 model selected 
    34014 
    34015 > color sel #ffdedeff
    34016 
    34017 > color sel #ffe8e9ff
    34018 
    34019 > select #12/D:88
    34020 
    34021 12 atoms, 12 bonds, 1 residue, 1 model selected 
    34022 
    34023 > select #12/D:88-97
    34024 
    34025 96 atoms, 102 bonds, 10 residues, 1 model selected 
    34026 
    34027 > select #12/D:98
    34028 
    34029 11 atoms, 11 bonds, 1 residue, 1 model selected 
    34030 
    34031 > select #12/D:98-105
    34032 
    34033 56 atoms, 56 bonds, 8 residues, 1 model selected 
    34034 
    34035 > color sel #d0d0fbff
    34036 
    34037 > select #12/D:114
    34038 
    34039 6 atoms, 5 bonds, 1 residue, 1 model selected 
    34040 
    34041 > select #12/D:114-125
    34042 
    34043 97 atoms, 100 bonds, 12 residues, 1 model selected 
    34044 
    34045 > color sel #d6d6fcff
    34046 
    34047 > select #12/D:128-129
    34048 
    34049 11 atoms, 10 bonds, 2 residues, 1 model selected 
    34050 
    34051 > select #12/D:128-131
    34052 
    34053 22 atoms, 21 bonds, 4 residues, 1 model selected 
    34054 
    34055 > color sel #dfdffcff
    34056 
    34057 > select #12/D:132-133
    34058 
    34059 14 atoms, 13 bonds, 2 residues, 1 model selected 
    34060 
    34061 > select #12/D:132-137
    34062 
    34063 44 atoms, 43 bonds, 6 residues, 1 model selected 
    34064 
    34065 > color sel #fbeae9ff
    34066 
    34067 > color sel #ffeeeaff
    34068 
    34069 > select #12/D:138
    34070 
    34071 8 atoms, 7 bonds, 1 residue, 1 model selected 
    34072 
    34073 > select #12/D:138-146
    34074 
    34075 79 atoms, 81 bonds, 9 residues, 1 model selected 
    34076 
    34077 > color sel #c9c9fbff
    34078 
    34079 > select #12/D:147
    34080 
    34081 9 atoms, 8 bonds, 1 residue, 1 model selected 
    34082 
    34083 > select #12/D:147-158
    34084 
    34085 95 atoms, 96 bonds, 12 residues, 1 model selected 
    34086 
    34087 > color sel #f7cbcaff
    34088 
    34089 > select #12/D:161
    34090 
    34091 9 atoms, 8 bonds, 1 residue, 1 model selected 
    34092 
    34093 > select #12/D:161-179
    34094 
    34095 144 atoms, 144 bonds, 19 residues, 1 model selected 
    34096 
    34097 > color sel #c9c9fbff
    34098 
    34099 > select #12/D:183
    34100 
    34101 9 atoms, 8 bonds, 1 residue, 1 model selected 
    34102 
    34103 > select #12/D:183-204
    34104 
    34105 176 atoms, 180 bonds, 22 residues, 1 model selected 
    34106 
    34107 > color sel #bbbbfaff
    34108 
    34109 > select #12/D:205
    34110 
    34111 7 atoms, 6 bonds, 1 residue, 1 model selected 
    34112 
    34113 > select #12/D:205-213
    34114 
    34115 72 atoms, 72 bonds, 9 residues, 1 model selected 
    34116 
    34117 > color sel #fbebffff
    34118 
    34119 > color sel #f1eaffff
    34120 
    34121 > color sel #f6eeffff
    34122 
    34123 [Repeated 2 time(s)]
    34124 
    34125 > color sel #f7eeffff
    34126 
    34127 [Repeated 1 time(s)]
    34128 
    34129 > select add #12
    34130 
    34131 3401 atoms, 3493 bonds, 442 residues, 1 model selected 
    34132 
    34133 > select subtract #12
    34134 
    34135 Nothing selected 
    34136 
    34137 > ui tool show "Show Sequence Viewer"
    34138 
    34139 > sequence chain #3/B #4/A #10/D #10/A
    34140 
    34141 Alignment identifier is 1 
    34142 
    34143 > show #!9 models
    34144 
    34145 > hide #8 models
    34146 
    34147 > show #8 models
    34148 
    34149 > hide #8 models
    34150 
    34151 > show #8 models
    34152 
    34153 > hide #8 models
    34154 
    34155 > show #8 models
    34156 
    34157 > hide #8 models
    34158 
    34159 > show #8 models
    34160 
    34161 > show #7 models
    34162 
    34163 > hide #7 models
    34164 
    34165 > show #7 models
    34166 
    34167 > hide #7 models
    34168 
    34169 > show #7 models
    34170 
    34171 > hide #7 models
    34172 
    34173 > select #3/B:1-81 #4/A:1-81 #10/D,A:1-81
    34174 
    34175 2576 atoms, 2632 bonds, 14 pseudobonds, 324 residues, 5 models selected 
    34176 
    34177 > select #3/B:1-275 #4/A:1-275 #10/D,A:1-275
    34178 
    34179 8808 atoms, 9044 bonds, 154 pseudobonds, 1100 residues, 5 models selected 
    34180 
    34181 > select #3/B:276 #4/A:276 #10/D,A:276
    34182 
    34183 32 atoms, 28 bonds, 4 residues, 3 models selected 
    34184 
    34185 > select #3/B:276-352 #4/A:276-352 #10/D,A:276-352
    34186 
    34187 2396 atoms, 2440 bonds, 1 pseudobond, 308 residues, 4 models selected 
    34188 
    34189 > select #3/B:101-352 #4/A:101-352 #10/D,A:101-352
    34190 
    34191 8076 atoms, 8300 bonds, 31 pseudobonds, 1008 residues, 5 models selected 
    34192 
    34193 > select #3/B #4/A #10/D,A
    34194 
    34195 11204 atoms, 11488 bonds, 155 pseudobonds, 1408 residues, 5 models selected 
    34196 
    34197 > select subtract #5
    34198 
    34199 11204 atoms, 11488 bonds, 53 pseudobonds, 1408 residues, 4 models selected 
    34200 
    34201 > select subtract #4
    34202 
    34203 8403 atoms, 8616 bonds, 21 pseudobonds, 1056 residues, 3 models selected 
    34204 
    34205 > select subtract #3
    34206 
    34207 5602 atoms, 5744 bonds, 704 residues, 1 model selected 
    34208 
    34209 > select add #10
    34210 
    34211 8936 atoms, 9124 bonds, 1118 residues, 1 model selected 
    34212 
    34213 > select subtract #10
    34214 
    34215 Nothing selected 
    34216 
    34217 > select add #3
    34218 
    34219 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected 
    34220 
    34221 > select add #4
    34222 
    34223 5602 atoms, 5744 bonds, 90 pseudobonds, 704 residues, 4 models selected 
    34224 
    34225 > select add #5
    34226 
    34227 5602 atoms, 5744 bonds, 144 pseudobonds, 704 residues, 4 models selected 
    34228 
    34229 > select subtract #5
    34230 
    34231 5602 atoms, 5744 bonds, 42 pseudobonds, 704 residues, 3 models selected 
    34232 
    34233 > select add #7
    34234 
    34235 5602 atoms, 5744 bonds, 97 pseudobonds, 704 residues, 3 models selected 
    34236 
    34237 > select subtract #7
    34238 
    34239 5602 atoms, 5744 bonds, 704 residues, 2 models selected 
    34240 
    34241 > color sel dim gray
    34242 
    34243 > select subtract #3
    34244 
    34245 2801 atoms, 2872 bonds, 352 residues, 1 model selected 
    34246 
    34247 > select subtract #4
    34248 
    34249 Nothing selected 
    34250 
    34251 > select #3/B:175 #4/A:175 #10/D,A:175
    34252 
    34253 36 atoms, 32 bonds, 4 residues, 3 models selected 
    34254 
    34255 > select #3/B:175-178 #4/A:175-178 #10/D,A:175-178
    34256 
    34257 120 atoms, 116 bonds, 16 residues, 3 models selected 
    34258 
    34259 > ui tool show "Color Actions"
    34260 
    34261 > color sel #d8d8fcff
    34262 
    34263 > select #3/B:180 #4/A:180 #10/D,A:180
    34264 
    34265 32 atoms, 28 bonds, 4 residues, 3 models selected 
    34266 
    34267 > select #3/B:180-185 #4/A:180-185 #10/D,A:180-185
    34268 
    34269 180 atoms, 176 bonds, 24 residues, 3 models selected 
    34270 
    34271 > select #3/B:179 #4/A:179 #10/D,A:179
    34272 
    34273 24 atoms, 20 bonds, 4 residues, 3 models selected 
    34274 
    34275 > select #3/B:179-186 #4/A:179-186 #10/D,A:179-186
    34276 
    34277 224 atoms, 220 bonds, 32 residues, 3 models selected 
    34278 
    34279 > color sel #e5e3ffff
    34280 
    34281 > select #3/B:187-188 #4/A:187-188 #10/D,A:187-188
    34282 
    34283 52 atoms, 48 bonds, 8 residues, 3 models selected 
    34284 
    34285 > select #3/B:187-198 #4/A:187-198 #10/D,A:187-198
    34286 
    34287 368 atoms, 368 bonds, 48 residues, 3 models selected 
    34288 
    34289 > color sel #dbdcffff
    34290 
    34291 > select #3/B:199-200 #4/A:199-200 #10/D,A:199-200
    34292 
    34293 64 atoms, 64 bonds, 8 residues, 3 models selected 
    34294 
    34295 > select #3/B:199-200 #4/A:199-200 #10/D,A:199-200
    34296 
    34297 64 atoms, 64 bonds, 8 residues, 3 models selected 
    34298 
    34299 > color sel #d2d5ffff
    34300 
    34301 > select #3/B:201 #4/A:201 #10/D,A:201
    34302 
    34303 56 atoms, 60 bonds, 4 residues, 3 models selected 
    34304 
    34305 > select #3/B:201-211 #4/A:201-211 #10/D,A:201-211
    34306 
    34307 384 atoms, 396 bonds, 44 residues, 3 models selected 
    34308 
    34309 > color sel #d9dbffff
    34310 
    34311 > select #3/B:212 #4/A:212 #10/D,A:212
    34312 
    34313 32 atoms, 28 bonds, 4 residues, 3 models selected 
     909
     910[deleted to fit within ticket limits]
    34314911
    34315912> select #3/B:212-217 #4/A:212-217 #10/D,A:212-217