| 946 | | > lighting full |
| 947 | | |
| 948 | | > volume #0-9 step 1 level 0.12 |
| 949 | | |
| 950 | | > hide #!5 models |
| 951 | | |
| 952 | | > show #!5 models |
| 953 | | |
| 954 | | > hide #!5 models |
| 955 | | |
| 956 | | > show #!5 models |
| 957 | | |
| 958 | | > hide #!5 models |
| 959 | | |
| 960 | | > show #!5 models |
| 961 | | |
| 962 | | > volume #0-9 step 1 level 0.2 |
| 963 | | |
| 964 | | > hide #!4 models |
| 965 | | |
| 966 | | > show #!3 models |
| 967 | | |
| 968 | | > fitmap #3 inMap #5 |
| 969 | | |
| 970 | | Fit map polish-stat3-cs_P24_J259_sharp.mrc in map polish- |
| 971 | | stat5-cs_P24_J261_sharp.mrc using 215387 points |
| 972 | | correlation = 0.9024, correlation about mean = 0.744, overlap = 4.798e+04 |
| 973 | | steps = 40, shift = 0.0344, angle = 0.0106 degrees |
| 974 | | |
| 975 | | Position of polish-stat3-cs_P24_J259_sharp.mrc (#3) relative to polish- |
| 976 | | stat5-cs_P24_J261_sharp.mrc (#5) coordinates: |
| 977 | | Matrix rotation and translation |
| 978 | | 0.98257846 0.13415442 0.12861633 -42.92728786 |
| 979 | | -0.13432869 0.99090951 -0.00735837 24.94050738 |
| 980 | | -0.12843430 -0.01004669 0.99166713 27.21963240 |
| 981 | | Axis -0.00723238 0.69154264 -0.72229943 |
| 982 | | Axis point 173.30825708 342.60365247 0.00000000 |
| 983 | | Rotation angle (degrees) 10.71087133 |
| 984 | | Shift along axis -2.10283387 |
| 985 | | |
| 986 | | |
| 987 | | > show #!4 models |
| 988 | | |
| 989 | | > hide #!5 models |
| 990 | | |
| 991 | | > volume #3-4 step 1 level 0.12 |
| 992 | | |
| 993 | | > hide #!3 models |
| 994 | | |
| 995 | | > show #!3 models |
| 996 | | |
| 997 | | > hide #!3 models |
| 998 | | |
| 999 | | > show #!3 models |
| 1000 | | |
| 1001 | | > hide #!3 models |
| 1002 | | |
| 1003 | | > show #!3 models |
| 1004 | | |
| 1005 | | > volume #3-4 step 1 level 0.15 |
| 1006 | | |
| 1007 | | > hide #!3 models |
| 1008 | | |
| 1009 | | > show #!3 models |
| 1010 | | |
| 1011 | | > hide #!3 models |
| 1012 | | |
| 1013 | | > show #!3 models |
| 1014 | | |
| 1015 | | > hide #!3 models |
| 1016 | | |
| 1017 | | > show #!3 models |
| 1018 | | |
| 1019 | | > volume #3-4 step 1 level 0.2 |
| 1020 | | |
| 1021 | | > fitmap #3 inMap #4 |
| 1022 | | |
| 1023 | | Fit map polish-stat3-cs_P24_J259_sharp.mrc in map polish- |
| 1024 | | stat4-cs_P24_J260_sharp.mrc using 215387 points |
| 1025 | | correlation = 0.9632, correlation about mean = 0.8769, overlap = 4.762e+04 |
| 1026 | | steps = 40, shift = 0.00656, angle = 0.00479 degrees |
| 1027 | | |
| 1028 | | Position of polish-stat3-cs_P24_J259_sharp.mrc (#3) relative to polish- |
| 1029 | | stat4-cs_P24_J260_sharp.mrc (#4) coordinates: |
| 1030 | | Matrix rotation and translation |
| 1031 | | 0.99892561 -0.00922543 0.04541498 -6.06312038 |
| 1032 | | 0.00784074 0.99950175 0.03057400 -8.01852571 |
| 1033 | | -0.04567441 -0.03018506 0.99850023 15.07939955 |
| 1034 | | Axis -0.54828753 0.82198746 0.15400451 |
| 1035 | | Axis point 328.32122008 0.00000000 152.67478308 |
| 1036 | | Rotation angle (degrees) 3.17627246 |
| 1037 | | Shift along axis -0.94449873 |
| 1038 | | |
| 1039 | | |
| 1040 | | > volume #3-4 step 1 level 0.12 |
| 1041 | | |
| 1042 | | > volume #0-9 step 1 level 0.2 |
| 1043 | | |
| 1044 | | > lighting full |
| 1045 | | |
| 1046 | | > lighting soft |
| 1047 | | |
| 1048 | | > graphics silhouettes true |
| 1049 | | |
| 1050 | | > hide #!3 models |
| 1051 | | |
| 1052 | | > graphics silhouettes false |
| 1053 | | |
| 1054 | | > graphics silhouettes true |
| 1055 | | |
| 1056 | | > lighting shadows true intensity 0.5 |
| 1057 | | |
| 1058 | | > lighting shadows false |
| 1059 | | |
| 1060 | | > lighting shadows true |
| 1061 | | |
| 1062 | | > lighting shadows false |
| 1063 | | |
| 1064 | | > lighting shadows true |
| 1065 | | |
| 1066 | | > lighting shadows false |
| 1067 | | |
| 1068 | | > lighting shadows true |
| 1069 | | |
| 1070 | | > lighting shadows false |
| 1071 | | |
| 1072 | | > lighting shadows true |
| 1073 | | |
| 1074 | | > lighting flat |
| 1075 | | |
| 1076 | | > graphics silhouettes false |
| 1077 | | |
| 1078 | | > graphics silhouettes true |
| 1079 | | |
| 1080 | | > lighting full |
| 1081 | | |
| 1082 | | > lighting shadows false |
| 1083 | | |
| 1084 | | > lighting shadows true |
| 1085 | | |
| 1086 | | > lighting full |
| 1087 | | |
| 1088 | | > lighting shadows false |
| 1089 | | |
| 1090 | | > lighting shadows true |
| 1091 | | |
| 1092 | | > lighting shadows false |
| 1093 | | |
| 1094 | | > lighting shadows true |
| 1095 | | |
| 1096 | | > graphics silhouettes false |
| 1097 | | |
| 1098 | | > graphics silhouettes true |
| 1099 | | |
| 1100 | | > lighting soft |
| 1101 | | |
| 1102 | | > show #!3 models |
| 1103 | | |
| 1104 | | > hide #!3 models |
| 1105 | | |
| 1106 | | > hide #!4 models |
| 1107 | | |
| 1108 | | > show #!2 models |
| 1109 | | |
| 1110 | | > show #!5 models |
| 1111 | | |
| 1112 | | > fitmap #2 inMap #5 |
| 1113 | | |
| 1114 | | Fit map polish-stat2-cs_P24_J258_sharp.mrc in map polish- |
| 1115 | | stat5-cs_P24_J261_sharp.mrc using 138689 points |
| 1116 | | correlation = 0.9114, correlation about mean = 0.6937, overlap = 2.679e+04 |
| 1117 | | steps = 36, shift = 0.0149, angle = 0.0131 degrees |
| 1118 | | |
| 1119 | | Position of polish-stat2-cs_P24_J258_sharp.mrc (#2) relative to polish- |
| 1120 | | stat5-cs_P24_J261_sharp.mrc (#5) coordinates: |
| 1121 | | Matrix rotation and translation |
| 1122 | | 0.98284064 0.09437251 0.15848691 -43.40986848 |
| 1123 | | -0.09430693 0.99551141 -0.00795160 18.30443788 |
| 1124 | | -0.15852594 -0.00713126 0.98732906 34.84365477 |
| 1125 | | Axis 0.00222367 0.85931303 -0.51144518 |
| 1126 | | Axis point 189.21117102 0.00000000 294.35708437 |
| 1127 | | Rotation angle (degrees) 10.62948441 |
| 1128 | | Shift along axis -2.18790652 |
| 1129 | | |
| 1130 | | |
| 1131 | | > hide #!5 models |
| 1132 | | |
| 1133 | | > show #!5 models |
| 1134 | | |
| 1135 | | > hide #!5 models |
| 1136 | | |
| 1137 | | > show #!5 models |
| 1138 | | |
| 1139 | | > volume #2 step 1 level 0.12 |
| 1140 | | |
| 1141 | | > volume #2 step 1 level 0.1 |
| 1142 | | |
| 1143 | | > hide #!5 models |
| 1144 | | |
| 1145 | | > show #!3 models |
| 1146 | | |
| 1147 | | > hide #!3 models |
| 1148 | | |
| 1149 | | > volume #2 step 1 level 0.08 |
| 1150 | | |
| 1151 | | > show #!3 models |
| 1152 | | |
| 1153 | | > hide #!3 models |
| 1154 | | |
| 1155 | | > show #!3 models |
| 1156 | | |
| 1157 | | > hide #!3 models |
| 1158 | | |
| 1159 | | > show #!3 models |
| 1160 | | |
| 1161 | | > hide #!3 models |
| 1162 | | |
| 1163 | | > show #!3 models |
| 1164 | | |
| 1165 | | > hide #!3 models |
| 1166 | | |
| 1167 | | > show #!3 models |
| 1168 | | |
| 1169 | | > hide #!3 models |
| 1170 | | |
| 1171 | | > show #!3 models |
| 1172 | | |
| 1173 | | > volume #2 step 2 level 0.07 |
| 1174 | | |
| 1175 | | > hide #!3 models |
| 1176 | | |
| 1177 | | > show #!3 models |
| 1178 | | |
| 1179 | | > hide #!3 models |
| 1180 | | |
| 1181 | | > show #!3 models |
| 1182 | | |
| 1183 | | > hide #!2 models |
| 1184 | | |
| 1185 | | > hide #!3 models |
| 1186 | | |
| 1187 | | > show #!2 models |
| 1188 | | |
| 1189 | | > volume #2 step 1 level 0.12 |
| 1190 | | |
| 1191 | | > show #!5 models |
| 1192 | | |
| 1193 | | > hide #!5 models |
| 1194 | | |
| 1195 | | > show #!5 models |
| 1196 | | |
| 1197 | | > show #!1 models |
| 1198 | | |
| 1199 | | > hide #!5 models |
| 1200 | | |
| 1201 | | > volume #1-2 step 2 level 0.07 |
| 1202 | | |
| 1203 | | > hide #!2 models |
| 1204 | | |
| 1205 | | > show #!2 models |
| 1206 | | |
| 1207 | | > hide #!2 models |
| 1208 | | |
| 1209 | | > show #!2 models |
| 1210 | | |
| 1211 | | > volume #1-2 step 2 level 0.08 |
| 1212 | | |
| 1213 | | > volume #0-9 step 1 level 0.2 |
| 1214 | | |
| 1215 | | > hide #!2 models |
| 1216 | | |
| 1217 | | > show #!2 models |
| 1218 | | |
| 1219 | | > hide #!2 models |
| 1220 | | |
| 1221 | | > show #!2 models |
| 1222 | | |
| 1223 | | > hide #!1 models |
| 1224 | | |
| 1225 | | > show #!1 models |
| 1226 | | |
| 1227 | | > hide #!2 models |
| 1228 | | |
| 1229 | | > hide #!1 models |
| 1230 | | |
| 1231 | | > show #!3 models |
| 1232 | | |
| 1233 | | > show #!4 models |
| 1234 | | |
| 1235 | | > hide #!3 models |
| 1236 | | |
| 1237 | | > show #!3 models |
| 1238 | | |
| 1239 | | > hide #!4 models |
| 1240 | | |
| 1241 | | > show #!4 models |
| 1242 | | |
| 1243 | | > hide #!4 models |
| 1244 | | |
| 1245 | | > show #!5 models |
| 1246 | | |
| 1247 | | > hide #!5 models |
| 1248 | | |
| 1249 | | > hide #!3 models |
| 1250 | | |
| 1251 | | > show #!3 models |
| 1252 | | |
| 1253 | | > hide #!3 models |
| 1254 | | |
| 1255 | | > show #!5 models |
| 1256 | | |
| 1257 | | > show #!3 models |
| 1258 | | |
| 1259 | | > hide #!5 models |
| 1260 | | |
| 1261 | | > show #!5 models |
| 1262 | | |
| 1263 | | > hide #!3 models |
| 1264 | | |
| 1265 | | > show #!3 models |
| 1266 | | |
| 1267 | | > hide #!3 models |
| 1268 | | |
| 1269 | | > show #!3 models |
| 1270 | | |
| 1271 | | > hide #!3 models |
| 1272 | | |
| 1273 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1274 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v2.cxs" |
| 1275 | | |
| 1276 | | ——— End of log from Thu May 19 10:48:15 2022 ——— |
| 1277 | | |
| 1278 | | opened ChimeraX session |
| 1279 | | |
| 1280 | | > show #!3 models |
| 1281 | | |
| 1282 | | > hide #!5 models |
| 1283 | | |
| 1284 | | > show #!5 models |
| 1285 | | |
| 1286 | | > hide #!5 models |
| 1287 | | |
| 1288 | | > show #!5 models |
| 1289 | | |
| 1290 | | > hide #!5 models |
| 1291 | | |
| 1292 | | > show #!5 models |
| 1293 | | |
| 1294 | | > hide #!3 models |
| 1295 | | |
| 1296 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1297 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v2.cxs" |
| 1298 | | |
| 1299 | | > show #!3 models |
| 1300 | | |
| 1301 | | > hide #!5 models |
| 1302 | | |
| 1303 | | > hide #!3 models |
| 1304 | | |
| 1305 | | > show #!5 models |
| 1306 | | |
| 1307 | | > hide #!5 models |
| 1308 | | |
| 1309 | | > show #!4 models |
| 1310 | | |
| 1311 | | > hide #!4 models |
| 1312 | | |
| 1313 | | > show #!3 models |
| 1314 | | |
| 1315 | | > hide #!3 models |
| 1316 | | |
| 1317 | | > show #!2 models |
| 1318 | | |
| 1319 | | > hide #!2 models |
| 1320 | | |
| 1321 | | > show #!1 models |
| 1322 | | |
| 1323 | | > graphics silhouettes false |
| 1324 | | |
| 1325 | | > graphics silhouettes true |
| 1326 | | |
| 1327 | | > graphics silhouettes false |
| 1328 | | |
| 1329 | | > lighting full |
| 1330 | | |
| 1331 | | > lighting soft |
| 1332 | | |
| 1333 | | > lighting simple |
| 1334 | | |
| 1335 | | [Repeated 1 time(s)] |
| 1336 | | |
| 1337 | | > graphics silhouettes true |
| 1338 | | |
| 1339 | | > lighting soft |
| 1340 | | |
| 1341 | | > show #!5 models |
| 1342 | | |
| 1343 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1344 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v1.cxs" |
| 1345 | | |
| 1346 | | > hide #!1 models |
| 1347 | | |
| 1348 | | > show #!1 models |
| 1349 | | |
| 1350 | | > hide #!5 models |
| 1351 | | |
| 1352 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1353 | | > Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat1-Rsr115-Ct4.pdb" |
| 1354 | | |
| 1355 | | Chain information for Stat1-Rsr115-Ct4.pdb #6 |
| 1356 | | --- |
| 1357 | | Chain | Description |
| 1358 | | A | No description available |
| 1359 | | B | No description available |
| 1360 | | C | No description available |
| 1361 | | D | No description available |
| 1362 | | E | No description available |
| 1363 | | F | No description available |
| 1364 | | G | No description available |
| 1365 | | H | No description available |
| 1366 | | I | No description available |
| 1367 | | K | No description available |
| 1368 | | |
| 1369 | | |
| 1370 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1371 | | > Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat2-Rsr101-Ct1.pdb" |
| 1372 | | |
| 1373 | | Summary of feedback from opening /Users/fengwei.zheng/OneDrive - Van Andel |
| 1374 | | Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat2-Rsr101-Ct1.pdb |
| 1375 | | --- |
| 1376 | | warning | End residue of secondary structure not found: HELIX 96 96 HIS F 74 |
| 1377 | | VAL F 76 1 3 |
| 1378 | | |
| 1379 | | Chain information for Stat2-Rsr101-Ct1.pdb #7 |
| 1380 | | --- |
| 1381 | | Chain | Description |
| 1382 | | A | No description available |
| 1383 | | B | No description available |
| 1384 | | C | No description available |
| 1385 | | D | No description available |
| 1386 | | E | No description available |
| 1387 | | F | No description available |
| 1388 | | G | No description available |
| 1389 | | H | No description available |
| 1390 | | I | No description available |
| 1391 | | J | No description available |
| 1392 | | K | No description available |
| 1393 | | |
| 1394 | | |
| 1395 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1396 | | > Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat3-Ref88-Ct3.pdb" |
| 1397 | | |
| 1398 | | Chain information for Stat3-Ref88-Ct3.pdb #8 |
| 1399 | | --- |
| 1400 | | Chain | Description |
| 1401 | | A | No description available |
| 1402 | | B | No description available |
| 1403 | | C | No description available |
| 1404 | | D | No description available |
| 1405 | | E | No description available |
| 1406 | | F | No description available |
| 1407 | | G | No description available |
| 1408 | | H | No description available |
| 1409 | | I | No description available |
| 1410 | | J | No description available |
| 1411 | | K | No description available |
| 1412 | | |
| 1413 | | |
| 1414 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1415 | | > Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat4-Ref80-Ct6.pdb" |
| 1416 | | |
| 1417 | | Chain information for Stat4-Ref80-Ct6.pdb #9 |
| 1418 | | --- |
| 1419 | | Chain | Description |
| 1420 | | A | No description available |
| 1421 | | B | No description available |
| 1422 | | C | No description available |
| 1423 | | D | No description available |
| 1424 | | E | No description available |
| 1425 | | F | No description available |
| 1426 | | G | No description available |
| 1427 | | H | No description available |
| 1428 | | I | No description available |
| 1429 | | J | No description available |
| 1430 | | K | No description available |
| 1431 | | |
| 1432 | | |
| 1433 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1434 | | > Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat5-ref59-v3.pdb" |
| 1435 | | |
| 1436 | | Chain information for Stat5-ref59-v3.pdb #10 |
| 1437 | | --- |
| 1438 | | Chain | Description |
| 1439 | | A | No description available |
| 1440 | | B | No description available |
| 1441 | | C | No description available |
| 1442 | | D | No description available |
| 1443 | | E | No description available |
| 1444 | | F | No description available |
| 1445 | | G | No description available |
| 1446 | | H | No description available |
| 1447 | | I | No description available |
| 1448 | | J | No description available |
| 1449 | | K | No description available |
| 1450 | | |
| 1451 | | |
| 1452 | | > hide #6-10 |
| 1453 | | |
| 1454 | | > show cartoons |
| 1455 | | |
| 1456 | | > hide #!1 models |
| 1457 | | |
| 1458 | | > hide #!7 models |
| 1459 | | |
| 1460 | | > hide #!8 models |
| 1461 | | |
| 1462 | | > hide #!9 models |
| 1463 | | |
| 1464 | | > hide #!10 models |
| 1465 | | |
| 1466 | | > show #!7 models |
| 1467 | | |
| 1468 | | > show #!8 models |
| 1469 | | |
| 1470 | | > show #!9 models |
| 1471 | | |
| 1472 | | > show #!10 models |
| 1473 | | |
| 1474 | | > dssp |
| 1475 | | |
| 1476 | | > undo |
| 1477 | | |
| 1478 | | > dssp |
| 1479 | | |
| 1480 | | > undo |
| 1481 | | |
| 1482 | | > hide #!7 models |
| 1483 | | |
| 1484 | | > hide #!8 models |
| 1485 | | |
| 1486 | | > hide #!9 models |
| 1487 | | |
| 1488 | | > hide #!10 models |
| 1489 | | |
| 1490 | | > show #!7 models |
| 1491 | | |
| 1492 | | > dssp #6 |
| 1493 | | |
| 1494 | | > undo |
| 1495 | | |
| 1496 | | > hide #!7 models |
| 1497 | | |
| 1498 | | > dssp #6 |
| 1499 | | |
| 1500 | | > undo |
| 1501 | | |
| 1502 | | > dssp #6 |
| 1503 | | |
| 1504 | | > undo |
| 1505 | | |
| 1506 | | > show #!7 models |
| 1507 | | |
| 1508 | | > hide #!6 models |
| 1509 | | |
| 1510 | | > show #!6 models |
| 1511 | | |
| 1512 | | > hide #!7 models |
| 1513 | | |
| 1514 | | > show #!7 models |
| 1515 | | |
| 1516 | | > hide #!6 models |
| 1517 | | |
| 1518 | | > hide #!7 models |
| 1519 | | |
| 1520 | | > show #!8 models |
| 1521 | | |
| 1522 | | > hide #!8 models |
| 1523 | | |
| 1524 | | > show #!9 models |
| 1525 | | |
| 1526 | | > hide #!9 models |
| 1527 | | |
| 1528 | | > show #!10 models |
| 1529 | | |
| 1530 | | > hide #!10 models |
| 1531 | | |
| 1532 | | > show #!8 models |
| 1533 | | |
| 1534 | | > hide #!8 models |
| 1535 | | |
| 1536 | | > show #!6 models |
| 1537 | | |
| 1538 | | > hide #!6 models |
| 1539 | | |
| 1540 | | > show #!7 models |
| 1541 | | |
| 1542 | | > hide #!7 models |
| 1543 | | |
| 1544 | | > show #!8 models |
| 1545 | | |
| 1546 | | > hide #!8 models |
| 1547 | | |
| 1548 | | > show #!9 models |
| 1549 | | |
| 1550 | | > hide #!9 models |
| 1551 | | |
| 1552 | | > show #!10 models |
| 1553 | | |
| 1554 | | > show #!5 models |
| 1555 | | |
| 1556 | | > fitmap #10 inMap #5 |
| 1557 | | |
| 1558 | | Fit molecule Stat5-ref59-v3.pdb (#10) to map polish- |
| 1559 | | stat5-cs_P24_J261_sharp.mrc (#5) using 22190 atoms |
| 1560 | | average map value = 0.4749, steps = 40 |
| 1561 | | shifted from previous position = 0.0118 |
| 1562 | | rotated from previous position = 0.0154 degrees |
| 1563 | | atoms outside contour = 4549, contour level = 0.2 |
| 1564 | | |
| 1565 | | Position of Stat5-ref59-v3.pdb (#10) relative to polish- |
| 1566 | | stat5-cs_P24_J261_sharp.mrc (#5) coordinates: |
| 1567 | | Matrix rotation and translation |
| 1568 | | 0.99999996 -0.00023189 -0.00013098 0.07248581 |
| 1569 | | 0.00023189 0.99999997 0.00003749 -0.03958209 |
| 1570 | | 0.00013098 -0.00003752 0.99999999 -0.01549584 |
| 1571 | | Axis -0.13944471 -0.48700260 0.86219699 |
| 1572 | | Axis point 179.53137965 310.04211664 0.00000000 |
| 1573 | | Rotation angle (degrees) 0.01540985 |
| 1574 | | Shift along axis -0.00419165 |
| 1575 | | |
| 1576 | | |
| 1577 | | > hide #!10 models |
| 1578 | | |
| 1579 | | > hide #!5 models |
| 1580 | | |
| 1581 | | > show #!4 models |
| 1582 | | |
| 1583 | | > show #!9 models |
| 1584 | | |
| 1585 | | > fitmap #9 inMap #4 |
| 1586 | | |
| 1587 | | Fit molecule Stat4-Ref80-Ct6.pdb (#9) to map polish- |
| 1588 | | stat4-cs_P24_J260_sharp.mrc (#4) using 22260 atoms |
| 1589 | | average map value = 0.394, steps = 116 |
| 1590 | | shifted from previous position = 0.393 |
| 1591 | | rotated from previous position = 9.66 degrees |
| 1592 | | atoms outside contour = 7049, contour level = 0.2 |
| 1593 | | |
| 1594 | | Position of Stat4-Ref80-Ct6.pdb (#9) relative to polish- |
| 1595 | | stat4-cs_P24_J260_sharp.mrc (#4) coordinates: |
| 1596 | | Matrix rotation and translation |
| 1597 | | 0.99999996 -0.00020731 0.00019735 -0.00273479 |
| 1598 | | 0.00020730 0.99999998 0.00005282 -0.02601563 |
| 1599 | | -0.00019736 -0.00005277 0.99999998 0.03690394 |
| 1600 | | Axis -0.18139255 0.67806855 0.71226384 |
| 1601 | | Axis point 155.39639231 -5.22421209 0.00000000 |
| 1602 | | Rotation angle (degrees) 0.01667605 |
| 1603 | | Shift along axis 0.00914104 |
| 1604 | | |
| 1605 | | |
| 1606 | | > fitmap #9 inMap #4 |
| 1607 | | |
| 1608 | | Fit molecule Stat4-Ref80-Ct6.pdb (#9) to map polish- |
| 1609 | | stat4-cs_P24_J260_sharp.mrc (#4) using 22260 atoms |
| 1610 | | average map value = 0.394, steps = 28 |
| 1611 | | shifted from previous position = 0.0124 |
| 1612 | | rotated from previous position = 0.00991 degrees |
| 1613 | | atoms outside contour = 7040, contour level = 0.2 |
| 1614 | | |
| 1615 | | Position of Stat4-Ref80-Ct6.pdb (#9) relative to polish- |
| 1616 | | stat4-cs_P24_J260_sharp.mrc (#4) coordinates: |
| 1617 | | Matrix rotation and translation |
| 1618 | | 0.99999998 -0.00007086 0.00020828 -0.02653646 |
| 1619 | | 0.00007083 0.99999998 0.00015866 -0.03295482 |
| 1620 | | -0.00020829 -0.00015864 0.99999997 0.05873668 |
| 1621 | | Axis -0.58489918 0.76790127 0.26119070 |
| 1622 | | Axis point 275.00727809 -0.00000000 111.83556729 |
| 1623 | | Rotation angle (degrees) 0.01554089 |
| 1624 | | Shift along axis 0.00555658 |
| 1625 | | |
| 1626 | | |
| 1627 | | > hide #!9 models |
| 1628 | | |
| 1629 | | > show #!8 models |
| 1630 | | |
| 1631 | | > hide #!4 models |
| 1632 | | |
| 1633 | | > show #!3 models |
| 1634 | | |
| 1635 | | > fitmap #8 inMap #3 |
| 1636 | | |
| 1637 | | Fit molecule Stat3-Ref88-Ct3.pdb (#8) to map polish- |
| 1638 | | stat3-cs_P24_J259_sharp.mrc (#3) using 22206 atoms |
| 1639 | | average map value = 0.5003, steps = 112 |
| 1640 | | shifted from previous position = 2.15 |
| 1641 | | rotated from previous position = 10.7 degrees |
| 1642 | | atoms outside contour = 4839, contour level = 0.2 |
| 1643 | | |
| 1644 | | Position of Stat3-Ref88-Ct3.pdb (#8) relative to polish- |
| 1645 | | stat3-cs_P24_J259_sharp.mrc (#3) coordinates: |
| 1646 | | Matrix rotation and translation |
| 1647 | | 0.99999998 -0.00003724 0.00017100 -0.02704958 |
| 1648 | | 0.00003728 0.99999998 -0.00021766 0.04254268 |
| 1649 | | -0.00017099 0.00021767 0.99999996 -0.00638064 |
| 1650 | | Axis 0.77933426 0.61224054 0.13341527 |
| 1651 | | Axis point 0.00000000 31.86795610 183.87738750 |
| 1652 | | Rotation angle (degrees) 0.01600241 |
| 1653 | | Shift along axis 0.00411441 |
| 1654 | | |
| 1655 | | |
| 1656 | | > fitmap #8 inMap #3 |
| 1657 | | |
| 1658 | | Fit molecule Stat3-Ref88-Ct3.pdb (#8) to map polish- |
| 1659 | | stat3-cs_P24_J259_sharp.mrc (#3) using 22206 atoms |
| 1660 | | average map value = 0.5003, steps = 40 |
| 1661 | | shifted from previous position = 0.00299 |
| 1662 | | rotated from previous position = 0.00503 degrees |
| 1663 | | atoms outside contour = 4833, contour level = 0.2 |
| 1664 | | |
| 1665 | | Position of Stat3-Ref88-Ct3.pdb (#8) relative to polish- |
| 1666 | | stat3-cs_P24_J259_sharp.mrc (#3) coordinates: |
| 1667 | | Matrix rotation and translation |
| 1668 | | 0.99999998 -0.00001612 0.00021454 -0.03743634 |
| 1669 | | 0.00001616 0.99999999 -0.00014440 0.03068096 |
| 1670 | | -0.00021453 0.00014440 0.99999997 0.01462916 |
| 1671 | | Axis 0.55729248 0.82797633 0.06229190 |
| 1672 | | Axis point 66.57801523 0.00000000 188.66655366 |
| 1673 | | Rotation angle (degrees) 0.01484581 |
| 1674 | | Shift along axis 0.00545140 |
| 1675 | | |
| 1676 | | |
| 1677 | | > hide #!3 models |
| 1678 | | |
| 1679 | | > show #!2 models |
| 1680 | | |
| 1681 | | > hide #!8 models |
| 1682 | | |
| 1683 | | > show #!7 models |
| 1684 | | |
| 1685 | | > fitmap #7 inMap #2 |
| 1686 | | |
| 1687 | | Fit molecule Stat2-Rsr101-Ct1.pdb (#7) to map polish- |
| 1688 | | stat2-cs_P24_J258_sharp.mrc (#2) using 21450 atoms |
| 1689 | | average map value = 0.2812, steps = 124 |
| 1690 | | shifted from previous position = 4.43 |
| 1691 | | rotated from previous position = 10.7 degrees |
| 1692 | | atoms outside contour = 9695, contour level = 0.2 |
| 1693 | | |
| 1694 | | Position of Stat2-Rsr101-Ct1.pdb (#7) relative to polish- |
| 1695 | | stat2-cs_P24_J258_sharp.mrc (#2) coordinates: |
| 1696 | | Matrix rotation and translation |
| 1697 | | 0.99999971 -0.00033689 0.00068872 -0.06283759 |
| 1698 | | 0.00033697 0.99999994 -0.00011560 -0.04225239 |
| 1699 | | -0.00068868 0.00011583 0.99999976 0.05695438 |
| 1700 | | Axis 0.14923236 0.88820430 0.43453748 |
| 1701 | | Axis point 96.65069623 0.00000000 86.47841398 |
| 1702 | | Rotation angle (degrees) 0.04442630 |
| 1703 | | Shift along axis -0.02215735 |
| 1704 | | |
| 1705 | | |
| 1706 | | > fitmap #7 inMap #2 |
| 1707 | | |
| 1708 | | Fit molecule Stat2-Rsr101-Ct1.pdb (#7) to map polish- |
| 1709 | | stat2-cs_P24_J258_sharp.mrc (#2) using 21450 atoms |
| 1710 | | average map value = 0.2812, steps = 28 |
| 1711 | | shifted from previous position = 0.00926 |
| 1712 | | rotated from previous position = 0.00543 degrees |
| 1713 | | atoms outside contour = 9694, contour level = 0.2 |
| 1714 | | |
| 1715 | | Position of Stat2-Rsr101-Ct1.pdb (#7) relative to polish- |
| 1716 | | stat2-cs_P24_J258_sharp.mrc (#2) coordinates: |
| 1717 | | Matrix rotation and translation |
| 1718 | | 0.99999976 -0.00035258 0.00059576 -0.03904426 |
| 1719 | | 0.00035265 0.99999993 -0.00012583 -0.04023357 |
| 1720 | | -0.00059572 0.00012604 0.99999981 0.04605711 |
| 1721 | | Axis 0.17897638 0.84666029 0.50113252 |
| 1722 | | Axis point 92.41276833 0.00000000 60.17480644 |
| 1723 | | Rotation angle (degrees) 0.04031540 |
| 1724 | | Shift along axis -0.01797145 |
| 1725 | | |
| 1726 | | |
| 1727 | | > hide #!7 models |
| 1728 | | |
| 1729 | | > show #!6 models |
| 1730 | | |
| 1731 | | > hide #!2 models |
| 1732 | | |
| 1733 | | > show #!1 models |
| 1734 | | |
| 1735 | | > fitmap #6 inMap #1 |
| 1736 | | |
| 1737 | | Fit molecule Stat1-Rsr115-Ct4.pdb (#6) to map polish- |
| 1738 | | stat1-cs_P24_J252_sharp.mrc (#1) using 21221 atoms |
| 1739 | | average map value = 0.3671, steps = 64 |
| 1740 | | shifted from previous position = 1.96 |
| 1741 | | rotated from previous position = 3.15 degrees |
| 1742 | | atoms outside contour = 7031, contour level = 0.2 |
| 1743 | | |
| 1744 | | Position of Stat1-Rsr115-Ct4.pdb (#6) relative to polish- |
| 1745 | | stat1-cs_P24_J252_sharp.mrc (#1) coordinates: |
| 1746 | | Matrix rotation and translation |
| 1747 | | 0.99999989 -0.00039481 0.00023409 0.03368282 |
| 1748 | | 0.00039486 0.99999990 -0.00019020 -0.02899819 |
| 1749 | | -0.00023401 0.00019029 0.99999995 -0.00137993 |
| 1750 | | Axis 0.38290067 0.47106031 0.79466299 |
| 1751 | | Axis point 71.24272862 87.09758706 0.00000000 |
| 1752 | | Rotation angle (degrees) 0.02846790 |
| 1753 | | Shift along axis -0.00185931 |
| 1754 | | |
| 1755 | | |
| 1756 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1757 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-maps-models-v3.cxs" |
| 1758 | | |
| 1759 | | > hide #!1 models |
| 1760 | | |
| 1761 | | > show #!1 models |
| 1762 | | |
| 1763 | | > hide #!1 models |
| 1764 | | |
| 1765 | | > show #!7 models |
| 1766 | | |
| 1767 | | > hide #!6 models |
| 1768 | | |
| 1769 | | > show #!8 models |
| 1770 | | |
| 1771 | | > hide #!7 models |
| 1772 | | |
| 1773 | | > hide #!8 models |
| 1774 | | |
| 1775 | | > show #!9 models |
| 1776 | | |
| 1777 | | > hide #!9 models |
| 1778 | | |
| 1779 | | > show #!10 models |
| 1780 | | |
| 1781 | | > show #!5 models |
| 1782 | | |
| 1783 | | > hide #!5 models |
| 1784 | | |
| 1785 | | > show #!6 models |
| 1786 | | |
| 1787 | | > hide #!10 models |
| 1788 | | |
| 1789 | | > show #!7 models |
| 1790 | | |
| 1791 | | > hide #!6 models |
| 1792 | | |
| 1793 | | > show #!6 models |
| 1794 | | |
| 1795 | | > hide #!7 models |
| 1796 | | |
| 1797 | | > hide #!6 models |
| 1798 | | |
| 1799 | | > show #!7 models |
| 1800 | | |
| 1801 | | > hide #!7 models |
| 1802 | | |
| 1803 | | > show #!8 models |
| 1804 | | |
| 1805 | | > hide #!8 models |
| 1806 | | |
| 1807 | | > show #!8 models |
| 1808 | | |
| 1809 | | > hide #!8 models |
| 1810 | | |
| 1811 | | > show #!9 models |
| 1812 | | |
| 1813 | | > hide #!9 models |
| 1814 | | |
| 1815 | | > show #!10 models |
| 1816 | | |
| 1817 | | > hide #!10 models |
| 1818 | | |
| 1819 | | > show #!9 models |
| 1820 | | |
| 1821 | | > hide #!9 models |
| 1822 | | |
| 1823 | | > show #!8 models |
| 1824 | | |
| 1825 | | > show #!10 models |
| 1826 | | |
| 1827 | | > hide #!8 models |
| 1828 | | |
| 1829 | | > show #!8 models |
| 1830 | | |
| 1831 | | > hide #!10 models |
| 1832 | | |
| 1833 | | > hide #!8 models |
| 1834 | | |
| 1835 | | > show #!3 models |
| 1836 | | |
| 1837 | | > hide #!3 models |
| 1838 | | |
| 1839 | | > show #!5 models |
| 1840 | | |
| 1841 | | > hide #!5 models |
| 1842 | | |
| 1843 | | > show #!5 models |
| 1844 | | |
| 1845 | | > show #!10 models |
| 1846 | | |
| 1847 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1848 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v3-maps-models.cxs" |
| 1849 | | |
| 1850 | | ——— End of log from Thu May 19 12:06:54 2022 ——— |
| 1851 | | |
| 1852 | | opened ChimeraX session |
| 1853 | | |
| 1854 | | > rename #1-5 maps id #1 |
| 1855 | | |
| 1856 | | > rename #6-10 models id #2 |
| 1857 | | |
| 1858 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1859 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v4-maps-models.cxs" |
| 1860 | | |
| 1861 | | ——— End of log from Thu May 19 16:17:48 2022 ——— |
| 1862 | | |
| 1863 | | opened ChimeraX session |
| 1864 | | |
| 1865 | | > hide #!1 models |
| 1866 | | |
| 1867 | | > cartoon style nucleic xsection oval width 2.5 thickness 2.5 |
| 1868 | | |
| 1869 | | > cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true |
| 1870 | | > xsection oval width 2.75 thickness 1 arrowScale 1.5 |
| 1871 | | |
| 1872 | | > select /I-K |
| 1873 | | |
| 1874 | | 5046 atoms, 5628 bonds, 5 pseudobonds, 251 residues, 10 models selected |
| 1875 | | |
| 1876 | | > show sel & #!2.5 atoms |
| 1877 | | |
| 1878 | | > nucleotides sel & #!2.5 stubs |
| 1879 | | |
| 1880 | | > select clear |
| 1881 | | |
| 1882 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 1883 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v5-maps-models.cxs" |
| 1884 | | |
| 1885 | | > hide #!2 models |
| 1886 | | |
| 1887 | | > show #!2.1 models |
| 1888 | | |
| 1889 | | > hide #!2.5 models |
| 1890 | | |
| 1891 | | > hide #!2.1 models |
| 1892 | | |
| 1893 | | > show #!2.3 models |
| 1894 | | |
| 1895 | | > show #!2.5 models |
| 1896 | | |
| 1897 | | > hide #!2.3 models |
| 1898 | | |
| 1899 | | > hide #!2.5 models |
| 1900 | | |
| 1901 | | > show #!2.1 models |
| 1902 | | |
| 1903 | | > select #2.1-5/I-K |
| 1904 | | |
| 1905 | | 5046 atoms, 5628 bonds, 5 pseudobonds, 251 residues, 10 models selected |
| 1906 | | |
| 1907 | | > show sel & #!2.1 atoms |
| 1908 | | |
| 1909 | | > nucleotides sel & #!2.1 stubs |
| 1910 | | |
| 1911 | | > select clear |
| 1912 | | |
| 1913 | | > show #!2.2 models |
| 1914 | | |
| 1915 | | > hide #!2.1 models |
| 1916 | | |
| 1917 | | > show #!2.1 models |
| 1918 | | |
| 1919 | | > show #!2.3 models |
| 1920 | | |
| 1921 | | > show #!2.4 models |
| 1922 | | |
| 1923 | | > show #!2.5 models |
| 1924 | | |
| 1925 | | > select #2.1-5/I-K |
| 1926 | | |
| 1927 | | 5046 atoms, 5628 bonds, 5 pseudobonds, 251 residues, 10 models selected |
| 1928 | | |
| 1929 | | > show sel atoms |
| 1930 | | |
| 1931 | | > nucleotides sel stubs |
| 1932 | | |
| 1933 | | > hide #!2.1 models |
| 1934 | | |
| 1935 | | > hide #!2.2 models |
| 1936 | | |
| 1937 | | > hide #!2.3 models |
| 1938 | | |
| 1939 | | > hide #!2.4 models |
| 1940 | | |
| 1941 | | > hide #!2.5 models |
| 1942 | | |
| 1943 | | > show #!2.1 models |
| 1944 | | |
| 1945 | | > show #!2.5 models |
| 1946 | | |
| 1947 | | > select clear |
| 1948 | | |
| 1949 | | > hide #!2.1 models |
| 1950 | | |
| 1951 | | > show #!2.1 models |
| 1952 | | |
| 1953 | | > hide #!2.5 models |
| 1954 | | |
| 1955 | | > view name v1 |
| 1956 | | |
| 1957 | | > color /F plum |
| 1958 | | |
| 1959 | | > show #!2.5 models |
| 1960 | | |
| 1961 | | > hide #!2.1 models |
| 1962 | | |
| 1963 | | > hide #!2.5 models |
| 1964 | | |
| 1965 | | > show #!2.1 models |
| 1966 | | |
| 1967 | | > hide #!2.1 models |
| 1968 | | |
| 1969 | | > show #!2.5 models |
| 1970 | | |
| 1971 | | > color /I #8E8CDF |
| 1972 | | |
| 1973 | | > show #!2.1 models |
| 1974 | | |
| 1975 | | > hide #!2.5 models |
| 1976 | | |
| 1977 | | > color /I magenta |
| 1978 | | |
| 1979 | | > show #!2.5 models |
| 1980 | | |
| 1981 | | > hide #!2.1 models |
| 1982 | | |
| 1983 | | > hide #!2.5 models |
| 1984 | | |
| 1985 | | > show #!2.1 models |
| 1986 | | |
| 1987 | | > show #!2.5 models |
| 1988 | | |
| 1989 | | > hide #!2.1 models |
| 1990 | | |
| 1991 | | > color /I dark magenta |
| 1992 | | |
| 1993 | | > show #!2.1 models |
| 1994 | | |
| 1995 | | > hide #!2.5 models |
| 1996 | | |
| 1997 | | > color /I purple |
| 1998 | | |
| 1999 | | [Repeated 1 time(s)] |
| 2000 | | |
| 2001 | | > show #!2.5 models |
| 2002 | | |
| 2003 | | > color /I medium orchid |
| 2004 | | |
| 2005 | | > hide #!2.1 models |
| 2006 | | |
| 2007 | | > show #!2.1 models |
| 2008 | | |
| 2009 | | > hide #!2.5 models |
| 2010 | | |
| 2011 | | > hide #!2.1 models |
| 2012 | | |
| 2013 | | > show #!2.5 models |
| 2014 | | |
| 2015 | | > color /J teel |
| 2016 | | |
| 2017 | | Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', |
| 2018 | | 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' |
| 2019 | | or a keyword |
| 2020 | | |
| 2021 | | > color /J teal |
| 2022 | | |
| 2023 | | > show #!2.3 models |
| 2024 | | |
| 2025 | | > hide #!2 models |
| 2026 | | |
| 2027 | | > hide #!2.3 models |
| 2028 | | |
| 2029 | | > show #!2.2 models |
| 2030 | | |
| 2031 | | > hide #!2.2 models |
| 2032 | | |
| 2033 | | > show #!2.3 models |
| 2034 | | |
| 2035 | | > hide #!2.3 models |
| 2036 | | |
| 2037 | | > color /J steel blue |
| 2038 | | |
| 2039 | | > color /J dark sea green |
| 2040 | | |
| 2041 | | > color /J sea green |
| 2042 | | |
| 2043 | | > color /J aquamarine |
| 2044 | | |
| 2045 | | > show #!2.1 models |
| 2046 | | |
| 2047 | | > hide #!2.5 models |
| 2048 | | |
| 2049 | | > show #!2.5 models |
| 2050 | | |
| 2051 | | > hide #!2.1 models |
| 2052 | | |
| 2053 | | > show #!2.1 models |
| 2054 | | |
| 2055 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 2056 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v6-maps-models.cxs" |
| 2057 | | |
| 2058 | | > hide #!2.1 models |
| 2059 | | |
| 2060 | | > show #!2.1 models |
| 2061 | | |
| 2062 | | > hide #!2.5 models |
| 2063 | | |
| 2064 | | > color /K dark slate grey |
| 2065 | | |
| 2066 | | > color /K light cyan |
| 2067 | | |
| 2068 | | > show #!2.5 models |
| 2069 | | |
| 2070 | | > color /K wheat |
| 2071 | | |
| 2072 | | > color /K gold |
| 2073 | | |
| 2074 | | > hide #!2.1 models |
| 2075 | | |
| 2076 | | > show #!2.1 models |
| 2077 | | |
| 2078 | | > hide #!2.5 models |
| 2079 | | |
| 2080 | | > color /K orange |
| 2081 | | |
| 2082 | | > show #!2.5 models |
| 2083 | | |
| 2084 | | > hide #!2.1 models |
| 2085 | | |
| 2086 | | > show #!2.1 models |
| 2087 | | |
| 2088 | | > hide #!2.5 models |
| 2089 | | |
| 2090 | | > color /K olive |
| 2091 | | |
| 2092 | | > color /K pale goldenrod |
| 2093 | | |
| 2094 | | > show #!2.5 models |
| 2095 | | |
| 2096 | | > hide #!2.1 models |
| 2097 | | |
| 2098 | | > show #!2.1 models |
| 2099 | | |
| 2100 | | > hide #!2.5 models |
| 2101 | | |
| 2102 | | > hide #!2.1 models |
| 2103 | | |
| 2104 | | > show #!2.2 models |
| 2105 | | |
| 2106 | | > show #!2.1 models |
| 2107 | | |
| 2108 | | > hide #!2.1 models |
| 2109 | | |
| 2110 | | > show #!2.1 models |
| 2111 | | |
| 2112 | | > hide #!2.1 models |
| 2113 | | |
| 2114 | | > show #!2.1 models |
| 2115 | | |
| 2116 | | > hide #!2.2 models |
| 2117 | | |
| 2118 | | > show #!2.2 models |
| 2119 | | |
| 2120 | | > hide #!2.1 models |
| 2121 | | |
| 2122 | | > show #!2.1 models |
| 2123 | | |
| 2124 | | > hide #!2.1 models |
| 2125 | | |
| 2126 | | > show #!2.1 models |
| 2127 | | |
| 2128 | | > hide #!2.2 models |
| 2129 | | |
| 2130 | | > show #!2.2 models |
| 2131 | | |
| 2132 | | > hide #!2.1 models |
| 2133 | | |
| 2134 | | > hide #!2.2 models |
| 2135 | | |
| 2136 | | > show #!2.5 models |
| 2137 | | |
| 2138 | | > color /J light cyan |
| 2139 | | |
| 2140 | | > color /J light blue |
| 2141 | | |
| 2142 | | > color /J powder blue |
| 2143 | | |
| 2144 | | > color /J sky blue |
| 2145 | | |
| 2146 | | > show #!2.3 models |
| 2147 | | |
| 2148 | | > hide #!2.5 models |
| 2149 | | |
| 2150 | | > hide #!2.3 models |
| 2151 | | |
| 2152 | | > show #!2.5 models |
| 2153 | | |
| 2154 | | > color /J light sky blue |
| 2155 | | |
| 2156 | | > show #!2.3 models |
| 2157 | | |
| 2158 | | > hide #!2.5 models |
| 2159 | | |
| 2160 | | > hide #!2.3 models |
| 2161 | | |
| 2162 | | > show #!2.1 models |
| 2163 | | |
| 2164 | | > color /I palegreen purple |
| 2165 | | |
| 2166 | | Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', |
| 2167 | | 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword |
| 2168 | | |
| 2169 | | > color /I #CAC6FD |
| 2170 | | |
| 2171 | | > undo |
| 2172 | | |
| 2173 | | > color /I violet |
| 2174 | | |
| 2175 | | > show #!2.5 models |
| 2176 | | |
| 2177 | | > hide #!2.1 models |
| 2178 | | |
| 2179 | | > show #!2.1 models |
| 2180 | | |
| 2181 | | > hide #!2.5 models |
| 2182 | | |
| 2183 | | > hide #!2.1 models |
| 2184 | | |
| 2185 | | > show #!2.2 models |
| 2186 | | |
| 2187 | | > show #!2.1 models |
| 2188 | | |
| 2189 | | > hide #!2.2 models |
| 2190 | | |
| 2191 | | > show #!2.2 models |
| 2192 | | |
| 2193 | | > hide #!2.2 models |
| 2194 | | |
| 2195 | | > hide #!2.1 models |
| 2196 | | |
| 2197 | | > show #!2.2 models |
| 2198 | | |
| 2199 | | > show #!2.1 models |
| 2200 | | |
| 2201 | | > hide #!2.2 models |
| 2202 | | |
| 2203 | | > show #!2.2 models |
| 2204 | | |
| 2205 | | > hide #!2.1 models |
| 2206 | | |
| 2207 | | > show #!2.1 models |
| 2208 | | |
| 2209 | | > hide #!2.1 models |
| 2210 | | |
| 2211 | | > show #!2.5 models |
| 2212 | | |
| 2213 | | > hide #!2.2 models |
| 2214 | | |
| 2215 | | > show #!2.1 models |
| 2216 | | |
| 2217 | | > hide #!2.5 models |
| 2218 | | |
| 2219 | | > hide #!2.1 models |
| 2220 | | |
| 2221 | | > show #!2.2 models |
| 2222 | | |
| 2223 | | > show #!2.1 models |
| 2224 | | |
| 2225 | | > hide #!2.2 models |
| 2226 | | |
| 2227 | | > show #!2.5 models |
| 2228 | | |
| 2229 | | > hide #!2.1 models |
| 2230 | | |
| 2231 | | > show #!2.1 models |
| 2232 | | |
| 2233 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 2234 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v7-maps-models.cxs" |
| 2235 | | |
| 2236 | | > view v1 |
| 2237 | | |
| 2238 | | > hide #!2.1 models |
| 2239 | | |
| 2240 | | > show #!2.1 models |
| 2241 | | |
| 2242 | | > hide #!2.5 models |
| 2243 | | |
| 2244 | | > undo |
| 2245 | | |
| 2246 | | [Repeated 1 time(s)] |
| 2247 | | |
| 2248 | | > hide #!2.5 models |
| 2249 | | |
| 2250 | | > show #!2.5 models |
| 2251 | | |
| 2252 | | > hide #!2.5 models |
| 2253 | | |
| 2254 | | > show #!2.1 models |
| 2255 | | |
| 2256 | | > show #!2.2 models |
| 2257 | | |
| 2258 | | > hide #!2.1 models |
| 2259 | | |
| 2260 | | > hide #!2.2 models |
| 2261 | | |
| 2262 | | > show #!2.4 models |
| 2263 | | |
| 2264 | | > show #!2.5 models |
| 2265 | | |
| 2266 | | > hide #!2.4 models |
| 2267 | | |
| 2268 | | > hide #!2.5 models |
| 2269 | | |
| 2270 | | > show #!2.4 models |
| 2271 | | |
| 2272 | | > hide #!2.4 models |
| 2273 | | |
| 2274 | | > show #!2.2 models |
| 2275 | | |
| 2276 | | > show #!2.1 models |
| 2277 | | |
| 2278 | | > hide #!2.2 models |
| 2279 | | |
| 2280 | | > hide #!2.1 models |
| 2281 | | |
| 2282 | | > show #!2.2 models |
| 2283 | | |
| 2284 | | > combine #2.2 modelId #3 |
| 2285 | | |
| 2286 | | > hide #!2.2 models |
| 2287 | | |
| 2288 | | > delete #3 & ~/B |
| 2289 | | |
| 2290 | | > hide #!3 models |
| 2291 | | |
| 2292 | | > show #!2.5 models |
| 2293 | | |
| 2294 | | > show #!2.1 models |
| 2295 | | |
| 2296 | | > hide #!2.5 models |
| 2297 | | |
| 2298 | | > color /H #E0F49C |
| 2299 | | |
| 2300 | | > close #3 |
| 2301 | | |
| 2302 | | > show #!2.2 models |
| 2303 | | |
| 2304 | | > hide #!2.1 models |
| 2305 | | |
| 2306 | | > combine #2.2 modelId #3 |
| 2307 | | |
| 2308 | | > hide #!2.2 models |
| 2309 | | |
| 2310 | | > delete #3 & ~/G |
| 2311 | | |
| 2312 | | > show #!2.5 models |
| 2313 | | |
| 2314 | | > hide #!3 models |
| 2315 | | |
| 2316 | | > show #!2.1 models |
| 2317 | | |
| 2318 | | > hide #!2.5 models |
| 2319 | | |
| 2320 | | > color /F #B48FE3 |
| 2321 | | |
| 2322 | | > undo |
| 2323 | | |
| 2324 | | > hide #!2.1 models |
| 2325 | | |
| 2326 | | > show #!2.2 models |
| 2327 | | |
| 2328 | | > show #!2.1 models |
| 2329 | | |
| 2330 | | > hide #!2.2 models |
| 2331 | | |
| 2332 | | > color /F #B48FE3 |
| 2333 | | |
| 2334 | | > undo |
| 2335 | | |
| 2336 | | > color /I #B48FE3 |
| 2337 | | |
| 2338 | | > show #!3 models |
| 2339 | | |
| 2340 | | > hide #!2.1 models |
| 2341 | | |
| 2342 | | > close #3 |
| 2343 | | |
| 2344 | | > show #!2.5 models |
| 2345 | | |
| 2346 | | > show #!2.3 models |
| 2347 | | |
| 2348 | | > hide #!2.5 models |
| 2349 | | |
| 2350 | | > hide #!2.3 models |
| 2351 | | |
| 2352 | | > show #!2.2 models |
| 2353 | | |
| 2354 | | > hide #!2.2 models |
| 2355 | | |
| 2356 | | > show #!2.1 models |
| 2357 | | |
| 2358 | | > undo |
| 2359 | | |
| 2360 | | [Repeated 1 time(s)] |
| 2361 | | |
| 2362 | | > hide #!2.2 models |
| 2363 | | |
| 2364 | | > show #!2.1 models |
| 2365 | | |
| 2366 | | > color /G #B48FE3 |
| 2367 | | |
| 2368 | | > color /I medium orchid |
| 2369 | | |
| 2370 | | > color /F plum |
| 2371 | | |
| 2372 | | > show #!2.3 models |
| 2373 | | |
| 2374 | | > hide #!2.1 models |
| 2375 | | |
| 2376 | | > show #!2.5 models |
| 2377 | | |
| 2378 | | > hide #!2.3 models |
| 2379 | | |
| 2380 | | > show #!2.3 models |
| 2381 | | |
| 2382 | | > hide #!2.3 models |
| 2383 | | |
| 2384 | | > show #!2.3 models |
| 2385 | | |
| 2386 | | > hide #!2.5 models |
| 2387 | | |
| 2388 | | > show #!2.1 models |
| 2389 | | |
| 2390 | | > hide #!2.3 models |
| 2391 | | |
| 2392 | | > show #!2.3 models |
| 2393 | | |
| 2394 | | > hide #!2.1 models |
| 2395 | | |
| 2396 | | > color /I violet |
| 2397 | | |
| 2398 | | > undo |
| 2399 | | |
| 2400 | | > color /I #CAC6FD |
| 2401 | | |
| 2402 | | > undo |
| 2403 | | |
| 2404 | | > show #!2.1 models |
| 2405 | | |
| 2406 | | > hide #!2.3 models |
| 2407 | | |
| 2408 | | > color /K #CAC6FD |
| 2409 | | |
| 2410 | | > undo |
| 2411 | | |
| 2412 | | > color /G #CAC6FD |
| 2413 | | |
| 2414 | | > undo |
| 2415 | | |
| 2416 | | > color /C #CAC6FD |
| 2417 | | |
| 2418 | | > hide #!2.1 models |
| 2419 | | |
| 2420 | | > show #!2.3 models |
| 2421 | | |
| 2422 | | > hide #!2 models |
| 2423 | | |
| 2424 | | > show #!2.1 models |
| 2425 | | |
| 2426 | | > hide #!2.3 models |
| 2427 | | |
| 2428 | | > show #!2.2 models |
| 2429 | | |
| 2430 | | > hide #!2.1 models |
| 2431 | | |
| 2432 | | > hide #!2.2 models |
| 2433 | | |
| 2434 | | > show #!2.3 models |
| 2435 | | |
| 2436 | | > hide #!2.3 models |
| 2437 | | |
| 2438 | | > show #!2.4 models |
| 2439 | | |
| 2440 | | > show #!2.1 models |
| 2441 | | |
| 2442 | | > hide #!2.4 models |
| 2443 | | |
| 2444 | | > show #!2.4 models |
| 2445 | | |
| 2446 | | > hide #!2.1 models |
| 2447 | | |
| 2448 | | > show #!2.5 models |
| 2449 | | |
| 2450 | | > hide #!2.4 models |
| 2451 | | |
| 2452 | | > show #!2.4 models |
| 2453 | | |
| 2454 | | > hide #!2.4 models |
| 2455 | | |
| 2456 | | > show #!2.4 models |
| 2457 | | |
| 2458 | | > hide #!2.4 models |
| 2459 | | |
| 2460 | | > show #!2.4 models |
| 2461 | | |
| 2462 | | > hide #!2.5 models |
| 2463 | | |
| 2464 | | > show #!2.5 models |
| 2465 | | |
| 2466 | | > hide #!2.4 models |
| 2467 | | |
| 2468 | | > hide #!2.5 models |
| 2469 | | |
| 2470 | | > show #!2.1 models |
| 2471 | | |
| 2472 | | > show #!2.3 models |
| 2473 | | |
| 2474 | | > hide #!2.1 models |
| 2475 | | |
| 2476 | | > hide #!2.3 models |
| 2477 | | |
| 2478 | | > show #!2.1 models |
| 2479 | | |
| 2480 | | > color /H yellow green |
| 2481 | | |
| 2482 | | > color /H light green |
| 2483 | | |
| 2484 | | > color /H pale green |
| 2485 | | |
| 2486 | | > show #!2.3 models |
| 2487 | | |
| 2488 | | > hide #!2.1 models |
| 2489 | | |
| 2490 | | > hide #!2.3 models |
| 2491 | | |
| 2492 | | > show #!2.5 models |
| 2493 | | |
| 2494 | | > show #!2.1 models |
| 2495 | | |
| 2496 | | > hide #!2.5 models |
| 2497 | | |
| 2498 | | > graphics silhouettes false |
| 2499 | | |
| 2500 | | > graphics silhouettes true |
| 2501 | | |
| 2502 | | > lighting soft |
| 2503 | | |
| 2504 | | > lighting full |
| 2505 | | |
| 2506 | | > lighting simple |
| 2507 | | |
| 2508 | | > graphics silhouettes false |
| 2509 | | |
| 2510 | | > lighting shadows true |
| 2511 | | |
| 2512 | | > lighting shadows false |
| 2513 | | |
| 2514 | | > graphics silhouettes true |
| 2515 | | |
| 2516 | | > lighting soft |
| 2517 | | |
| 2518 | | > hide #!2.1 models |
| 2519 | | |
| 2520 | | > show #!2.2 models |
| 2521 | | |
| 2522 | | > show #!2.3 models |
| 2523 | | |
| 2524 | | > hide #!2.2 models |
| 2525 | | |
| 2526 | | > hide #!2.3 models |
| 2527 | | |
| 2528 | | > show #!2.4 models |
| 2529 | | |
| 2530 | | > show #!2.5 models |
| 2531 | | |
| 2532 | | > hide #!2.4 models |
| 2533 | | |
| 2534 | | > show #!2.1 models |
| 2535 | | |
| 2536 | | > hide #!2.5 models |
| 2537 | | |
| 2538 | | > color /K #E7F981 |
| 2539 | | |
| 2540 | | > show #!2.3 models |
| 2541 | | |
| 2542 | | > hide #!2.1 models |
| 2543 | | |
| 2544 | | > show #!2.1 models |
| 2545 | | |
| 2546 | | > show #!2.4 models |
| 2547 | | |
| 2548 | | > hide #!2.3 models |
| 2549 | | |
| 2550 | | > hide #!2.1 models |
| 2551 | | |
| 2552 | | > show #!2.5 models |
| 2553 | | |
| 2554 | | > hide #!2.4 models |
| 2555 | | |
| 2556 | | > hide #!2.5 models |
| 2557 | | |
| 2558 | | > show #!2.1 models |
| 2559 | | |
| 2560 | | > color /H olive drab |
| 2561 | | |
| 2562 | | > color /H olive |
| 2563 | | |
| 2564 | | > color /H dark khaki |
| 2565 | | |
| 2566 | | > color /H light salmon |
| 2567 | | |
| 2568 | | > color /H light coral |
| 2569 | | |
| 2570 | | > show #!2.5 models |
| 2571 | | |
| 2572 | | > hide #!2.1 models |
| 2573 | | |
| 2574 | | > color /H hot pink |
| 2575 | | |
| 2576 | | > color /H indian red |
| 2577 | | |
| 2578 | | > show #!2.1 models |
| 2579 | | |
| 2580 | | > hide #!2.5 models |
| 2581 | | |
| 2582 | | > color /H misty rose |
| 2583 | | |
| 2584 | | > color /H moccasin |
| 2585 | | |
| 2586 | | > color /H navajo white |
| 2587 | | |
| 2588 | | > show #!2.5 models |
| 2589 | | |
| 2590 | | > hide #!2.1 models |
| 2591 | | |
| 2592 | | > show #!2.4 models |
| 2593 | | |
| 2594 | | > hide #!2.5 models |
| 2595 | | |
| 2596 | | > hide #!2.4 models |
| 2597 | | |
| 2598 | | > show #!2.3 models |
| 2599 | | |
| 2600 | | > hide #!2.3 models |
| 2601 | | |
| 2602 | | > show #!2.1 models |
| 2603 | | |
| 2604 | | > color /G #CAC6FD |
| 2605 | | |
| 2606 | | > color /C #B48FE3 |
| 2607 | | |
| 2608 | | > view v1 |
| 2609 | | |
| 2610 | | [Repeated 1 time(s)] |
| 2611 | | |
| 2612 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 2613 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v8-maps-models.cxs" |
| 2614 | | |
| 2615 | | > show #!2.4 models |
| 2616 | | |
| 2617 | | > hide #!2.1 models |
| 2618 | | |
| 2619 | | > show #!2.1 models |
| 2620 | | |
| 2621 | | > hide #!2.4 models |
| 2622 | | |
| 2623 | | > show #!2.4 models |
| 2624 | | |
| 2625 | | > hide #!2.1 models |
| 2626 | | |
| 2627 | | > show #!2.1 models |
| 2628 | | |
| 2629 | | > hide #!2.4 models |
| 2630 | | |
| 2631 | | > color /E #EB9BC1 |
| 2632 | | |
| 2633 | | > color /E salmon |
| 2634 | | |
| 2635 | | > color /E light salmon |
| 2636 | | |
| 2637 | | > color /E dark salmon |
| 2638 | | |
| 2639 | | > color /E salmon |
| 2640 | | |
| 2641 | | > color /E light coral |
| 2642 | | |
| 2643 | | > undo |
| 2644 | | |
| 2645 | | > color /B #EB9BC1 |
| 2646 | | |
| 2647 | | > undo |
| 2648 | | |
| 2649 | | > show #!2.2 models |
| 2650 | | |
| 2651 | | > hide #!2.1 models |
| 2652 | | |
| 2653 | | > show #!2.1 models |
| 2654 | | |
| 2655 | | > hide #!2.2 models |
| 2656 | | |
| 2657 | | > combine #2.1 modelId #3 |
| 2658 | | |
| 2659 | | > delete #3 & ~/B |
| 2660 | | |
| 2661 | | > close #3 |
| 2662 | | |
| 2663 | | > combine #2.1 modelId #3 |
| 2664 | | |
| 2665 | | > delete #3 & ~/D |
| 2666 | | |
| 2667 | | > close #3 |
| 2668 | | |
| 2669 | | > color /A #FFB381 |
| 2670 | | |
| 2671 | | > color /B #D7819F |
| 2672 | | |
| 2673 | | > color /C #B48FE3 |
| 2674 | | |
| 2675 | | > color /D #D7CD85 |
| 2676 | | |
| 2677 | | > color /E salmon |
| 2678 | | |
| 2679 | | > color /F plum |
| 2680 | | |
| 2681 | | > color /G #CAC6FD |
| 2682 | | |
| 2683 | | > color /H navajo white |
| 2684 | | |
| 2685 | | > color /I medium orchid |
| 2686 | | |
| 2687 | | > color /J light sky blue |
| 2688 | | |
| 2689 | | > color /K #E7F981 |
| 2690 | | |
| 2691 | | > show #!2.2 models |
| 2692 | | |
| 2693 | | > show #!2.3 models |
| 2694 | | |
| 2695 | | > show #!2.4 models |
| 2696 | | |
| 2697 | | > show #!2.5 models |
| 2698 | | |
| 2699 | | > tile #2.1-5 |
| 2700 | | |
| 2701 | | 5 models tiled |
| 2702 | | |
| 2703 | | > tile #2.1-5 columns 3 |
| 2704 | | |
| 2705 | | 5 models tiled |
| 2706 | | |
| 2707 | | > undo |
| 2708 | | |
| 2709 | | [Repeated 1 time(s)] |
| 2710 | | |
| 2711 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 2712 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v9-maps-models-color |
| 2713 | | > assigned.cxs" |
| 2714 | | |
| 2715 | | > hide #!2 models |
| 2716 | | |
| 2717 | | > show #!2 models |
| 2718 | | |
| 2719 | | > hide #!2 models |
| 2720 | | |
| 2721 | | > show #!2 models |
| 2722 | | |
| 2723 | | > hide #!2.1 models |
| 2724 | | |
| 2725 | | > hide #!2.2 models |
| 2726 | | |
| 2727 | | > hide #!2.3 models |
| 2728 | | |
| 2729 | | > hide #!2.5 models |
| 2730 | | |
| 2731 | | > hide #!2.4 models |
| 2732 | | |
| 2733 | | > show #!2.3 models |
| 2734 | | |
| 2735 | | > hide #!2.3 models |
| 2736 | | |
| 2737 | | > show #!2.5 models |
| 2738 | | |
| 2739 | | > color /F navajo white |
| 2740 | | |
| 2741 | | > color /I plum |
| 2742 | | |
| 2743 | | > undo |
| 2744 | | |
| 2745 | | > color /H plum |
| 2746 | | |
| 2747 | | > show #!2.1 models |
| 2748 | | |
| 2749 | | > hide #!2.5 models |
| 2750 | | |
| 2751 | | > view v1 |
| 2752 | | |
| 2753 | | > hide #!2.1 models |
| 2754 | | |
| 2755 | | > show #!2.3 models |
| 2756 | | |
| 2757 | | > hide #!2.3 models |
| 2758 | | |
| 2759 | | > show #!2.2 models |
| 2760 | | |
| 2761 | | > hide #!2.2 models |
| 2762 | | |
| 2763 | | > show #!2.3 models |
| 2764 | | |
| 2765 | | > hide #!2.3 models |
| 2766 | | |
| 2767 | | > show #!2.2 models |
| 2768 | | |
| 2769 | | > hide #!2.2 models |
| 2770 | | |
| 2771 | | > show #!2.1 models |
| 2772 | | |
| 2773 | | > hide #!2.1 models |
| 2774 | | |
| 2775 | | > show #!2.2 models |
| 2776 | | |
| 2777 | | > hide #!2.2 models |
| 2778 | | |
| 2779 | | > show #!2.3 models |
| 2780 | | |
| 2781 | | > hide #!2.3 models |
| 2782 | | |
| 2783 | | > show #!2.4 models |
| 2784 | | |
| 2785 | | > hide #!2.4 models |
| 2786 | | |
| 2787 | | > show #!2.5 models |
| 2788 | | |
| 2789 | | > hide #!2.5 models |
| 2790 | | |
| 2791 | | > show #!2.4 models |
| 2792 | | |
| 2793 | | > hide #!2.4 models |
| 2794 | | |
| 2795 | | > show #!2.3 models |
| 2796 | | |
| 2797 | | > hide #!2.3 models |
| 2798 | | |
| 2799 | | > show #!2.2 models |
| 2800 | | |
| 2801 | | > hide #!2.2 models |
| 2802 | | |
| 2803 | | > show #!2.1 models |
| 2804 | | |
| 2805 | | > view v1 |
| 2806 | | |
| 2807 | | > turn y 1 90 |
| 2808 | | |
| 2809 | | [Repeated 1 time(s)] |
| 2810 | | |
| 2811 | | > turn y 1 180 |
| 2812 | | |
| 2813 | | > hide #!2.1 models |
| 2814 | | |
| 2815 | | > show #!2.3 models |
| 2816 | | |
| 2817 | | > hide #!2.3 models |
| 2818 | | |
| 2819 | | > show #!2.5 models |
| 2820 | | |
| 2821 | | > turn y 1 180 |
| 2822 | | |
| 2823 | | > hide #!2.5 models |
| 2824 | | |
| 2825 | | > show #!2.1 models |
| 2826 | | |
| 2827 | | > turn y 1 180 |
| 2828 | | |
| 2829 | | [Repeated 2 time(s)] |
| 2830 | | |
| 2831 | | > hide #!2.1 models |
| 2832 | | |
| 2833 | | > show #!2.2 models |
| 2834 | | |
| 2835 | | > hide #!2.2 models |
| 2836 | | |
| 2837 | | > show #!2.3 models |
| 2838 | | |
| 2839 | | > show #!2.4 models |
| 2840 | | |
| 2841 | | > hide #!2.3 models |
| 2842 | | |
| 2843 | | > hide #!2.4 models |
| 2844 | | |
| 2845 | | > show #!2.5 models |
| 2846 | | |
| 2847 | | > turn y 1 180 |
| 2848 | | |
| 2849 | | [Repeated 1 time(s)] |
| 2850 | | |
| 2851 | | > hide #!2.5 models |
| 2852 | | |
| 2853 | | > show #!2.4 models |
| 2854 | | |
| 2855 | | > hide #!2.4 models |
| 2856 | | |
| 2857 | | > show #!2.3 models |
| 2858 | | |
| 2859 | | > hide #!2.3 models |
| 2860 | | |
| 2861 | | > show #!2.2 models |
| 2862 | | |
| 2863 | | > hide #!2.2 models |
| 2864 | | |
| 2865 | | > show #!2.1 models |
| 2866 | | |
| 2867 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 2868 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v10-maps-models-color |
| 2869 | | > assigned.cxs" |
| 2870 | | |
| 2871 | | > hide #!2.1 models |
| 2872 | | |
| 2873 | | > show #!2.2 models |
| 2874 | | |
| 2875 | | > hide #!2.2 models |
| 2876 | | |
| 2877 | | > show #!2.3 models |
| 2878 | | |
| 2879 | | > hide #!2.3 models |
| 2880 | | |
| 2881 | | > show #!2.4 models |
| 2882 | | |
| 2883 | | > hide #!2.4 models |
| 2884 | | |
| 2885 | | > show #!2.5 models |
| 2886 | | |
| 2887 | | > hide #!2.5 models |
| 2888 | | |
| 2889 | | > show #!2.1 models |
| 2890 | | |
| 2891 | | > hide #!2.1 models |
| 2892 | | |
| 2893 | | > show #!2.5 models |
| 2894 | | |
| 2895 | | > select /F:119-124 |
| 2896 | | |
| 2897 | | 245 atoms, 240 bonds, 30 residues, 5 models selected |
| 2898 | | |
| 2899 | | > select /F:118-124 |
| 2900 | | |
| 2901 | | 285 atoms, 280 bonds, 35 residues, 5 models selected |
| 2902 | | |
| 2903 | | > select /F:1-7,118-124 |
| 2904 | | |
| 2905 | | 570 atoms, 560 bonds, 70 residues, 5 models selected |
| 2906 | | |
| 2907 | | > select /F:1-7,79-84,118-124 |
| 2908 | | |
| 2909 | | 810 atoms, 800 bonds, 100 residues, 5 models selected |
| 2910 | | |
| 2911 | | > select /F:2-7,79-84,118-124 |
| 2912 | | |
| 2913 | | 770 atoms, 760 bonds, 95 residues, 5 models selected |
| 2914 | | |
| 2915 | | > select /F:2-7,79-84,91-94,118-124 |
| 2916 | | |
| 2917 | | 930 atoms, 915 bonds, 115 residues, 5 models selected |
| 2918 | | |
| 2919 | | > select /F:2-7,68-72,79-84,91-94,118-124 |
| 2920 | | |
| 2921 | | 1145 atoms, 1135 bonds, 140 residues, 5 models selected |
| 2922 | | |
| 2923 | | > select /F:2-7,68-72,79-84,91-94,118-124,462-467 |
| 2924 | | |
| 2925 | | 1410 atoms, 1405 bonds, 170 residues, 5 models selected |
| 2926 | | |
| 2927 | | > select /F:2-7,68-72,79-84,91-94,118-124,407-410,462-467 |
| 2928 | | |
| 2929 | | 1570 atoms, 1560 bonds, 190 residues, 5 models selected |
| 2930 | | |
| 2931 | | > select /F:2-7,68-72,79-84,91-94,118-124,406-410,462-467 |
| 2932 | | |
| 2933 | | 1620 atoms, 1615 bonds, 195 residues, 5 models selected |
| 2934 | | |
| 2935 | | > select /F:2-7,68-72,79-84,91-94,118-124,262-266,406-410,462-467 |
| 2936 | | |
| 2937 | | 1810 atoms, 1805 bonds, 220 residues, 5 models selected |
| 2938 | | |
| 2939 | | > select /F:2-7,68-72,79-84,91-94,118-124,262-266,281-286,406-410,462-467 |
| 2940 | | |
| 2941 | | 2050 atoms, 2040 bonds, 250 residues, 5 models selected |
| 2942 | | |
| 2943 | | > setattr sel res ss_type 2 |
| 2944 | | |
| 2945 | | Assigning ss_type attribute to 250 items |
| 2946 | | |
| 2947 | | > setattr sel res ss_id 88 |
| 2948 | | |
| 2949 | | Assigning ss_id attribute to 250 items |
| 2950 | | |
| 2951 | | > select clear |
| 2952 | | |
| 2953 | | > select /H:320-325 |
| 2954 | | |
| 2955 | | 255 atoms, 255 bonds, 30 residues, 5 models selected |
| 2956 | | |
| 2957 | | > select /H:252,256,320-325 |
| 2958 | | |
| 2959 | | 330 atoms, 320 bonds, 40 residues, 5 models selected |
| 2960 | | |
| 2961 | | > select /H:252-256,320-325 |
| 2962 | | |
| 2963 | | 460 atoms, 455 bonds, 55 residues, 5 models selected |
| 2964 | | |
| 2965 | | > select /H:251-256,320-325 |
| 2966 | | |
| 2967 | | 505 atoms, 500 bonds, 60 residues, 5 models selected |
| 2968 | | |
| 2969 | | > select /H:251-256,262-266,320-325 |
| 2970 | | |
| 2971 | | 690 atoms, 685 bonds, 85 residues, 5 models selected |
| 2972 | | |
| 2973 | | > select /H:251-256,261-266,320-325 |
| 2974 | | |
| 2975 | | 730 atoms, 725 bonds, 90 residues, 5 models selected |
| 2976 | | |
| 2977 | | > select /H:251-256,261-266,283-288,320-325 |
| 2978 | | |
| 2979 | | 945 atoms, 935 bonds, 1 pseudobond, 120 residues, 6 models selected |
| 2980 | | |
| 2981 | | > setattr sel res ss_type 2 |
| 2982 | | |
| 2983 | | Assigning ss_type attribute to 120 items |
| 2984 | | |
| 2985 | | > setattr sel res ss_id 88 |
| 2986 | | |
| 2987 | | Assigning ss_id attribute to 120 items |
| 2988 | | |
| 2989 | | > select clear |
| 2990 | | |
| 2991 | | > hide #!2.5 models |
| 2992 | | |
| 2993 | | > show #!2.1 models |
| 2994 | | |
| 2995 | | > select /E:83-89 |
| 2996 | | |
| 2997 | | 265 atoms, 260 bonds, 35 residues, 5 models selected |
| 2998 | | |
| 2999 | | > select /E:83-89,69-75 |
| 3000 | | |
| 3001 | | 580 atoms, 575 bonds, 70 residues, 5 models selected |
| 3002 | | |
| 3003 | | > hide #!2.1 models |
| 3004 | | |
| 3005 | | > show #!2.2 models |
| 3006 | | |
| 3007 | | > hide #!2.2 models |
| 3008 | | |
| 3009 | | > show #!2.3 models |
| 3010 | | |
| 3011 | | > hide #!2.3 models |
| 3012 | | |
| 3013 | | > show #!2.4 models |
| 3014 | | |
| 3015 | | > hide #!2.4 models |
| 3016 | | |
| 3017 | | > show #!2.5 models |
| 3018 | | |
| 3019 | | > select /E:82-89,69-75 |
| 3020 | | |
| 3021 | | 625 atoms, 620 bonds, 75 residues, 5 models selected |
| 3022 | | |
| 3023 | | > select /E:82-89,69-76 |
| 3024 | | |
| 3025 | | 660 atoms, 655 bonds, 80 residues, 5 models selected |
| 3026 | | |
| 3027 | | > setattr sel res ss_type 2 |
| 3028 | | |
| 3029 | | Assigning ss_type attribute to 80 items |
| 3030 | | |
| 3031 | | > setattr sel res ss_id 88 |
| 3032 | | |
| 3033 | | Assigning ss_id attribute to 80 items |
| 3034 | | |
| 3035 | | > select clear |
| 3036 | | |
| 3037 | | > hide #!2.5 models |
| 3038 | | |
| 3039 | | > show #!2.4 models |
| 3040 | | |
| 3041 | | > hide #!2.4 models |
| 3042 | | |
| 3043 | | > show #!2.3 models |
| 3044 | | |
| 3045 | | > hide #!2.3 models |
| 3046 | | |
| 3047 | | > show #!2.2 models |
| 3048 | | |
| 3049 | | > hide #!2.2 models |
| 3050 | | |
| 3051 | | > show #!2.1 models |
| 3052 | | |
| 3053 | | > select /A:162-173 |
| 3054 | | |
| 3055 | | 466 atoms, 471 bonds, 59 residues, 5 models selected |
| 3056 | | |
| 3057 | | > hide #!2.1 models |
| 3058 | | |
| 3059 | | > show #!2.2 models |
| 3060 | | |
| 3061 | | > hide #!2.2 models |
| 3062 | | |
| 3063 | | > show #!2.3 models |
| 3064 | | |
| 3065 | | > hide #!2.3 models |
| 3066 | | |
| 3067 | | > show #!2.4 models |
| 3068 | | |
| 3069 | | > hide #!2.4 models |
| 3070 | | |
| 3071 | | > show #!2.5 models |
| 3072 | | |
| 3073 | | > hide #!2.5 models |
| 3074 | | |
| 3075 | | > show #!2.2 models |
| 3076 | | |
| 3077 | | > select /A:162-174 |
| 3078 | | |
| 3079 | | 521 atoms, 526 bonds, 64 residues, 5 models selected |
| 3080 | | |
| 3081 | | > hide #!2.2 models |
| 3082 | | |
| 3083 | | > show #!2.1 models |
| 3084 | | |
| 3085 | | > hide #!2.1 models |
| 3086 | | |
| 3087 | | > show #!2.2 models |
| 3088 | | |
| 3089 | | > hide #!2.2 models |
| 3090 | | |
| 3091 | | > show #!2.3 models |
| 3092 | | |
| 3093 | | > hide #!2.3 models |
| 3094 | | |
| 3095 | | > show #!2.4 models |
| 3096 | | |
| 3097 | | > hide #!2.4 models |
| 3098 | | |
| 3099 | | > show #!2.5 models |
| 3100 | | |
| 3101 | | > show #!2.4 models |
| 3102 | | |
| 3103 | | > hide #!2.4 models |
| 3104 | | |
| 3105 | | > show #!2.3 models |
| 3106 | | |
| 3107 | | > hide #!2.3 models |
| 3108 | | |
| 3109 | | > show #!2.2 models |
| 3110 | | |
| 3111 | | > hide #!2.2 models |
| 3112 | | |
| 3113 | | > show #!2.2 models |
| 3114 | | |
| 3115 | | > hide #!2.2 models |
| 3116 | | |
| 3117 | | > show #!2.2 models |
| 3118 | | |
| 3119 | | > hide #!2.2 models |
| 3120 | | |
| 3121 | | > show #!2.1 models |
| 3122 | | |
| 3123 | | > hide #!2.1 models |
| 3124 | | |
| 3125 | | > hide #!2.5 models |
| 3126 | | |
| 3127 | | > show #!2.2 models |
| 3128 | | |
| 3129 | | > select clear |
| 3130 | | |
| 3131 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 3132 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v11-M-M-color-SS |
| 3133 | | > assigned.cxs" |
| 3134 | | |
| 3135 | | ——— End of log from Mon May 23 12:04:10 2022 ——— |
| 3136 | | |
| 3137 | | opened ChimeraX session |
| 3138 | | |
| 3139 | | > color bfactor #!2.2 |
| 3140 | | |
| 3141 | | 21450 atoms, 2597 residues, atom bfactor range 1.74 to 269 |
| 3142 | | |
| 3143 | | > undo |
| 3144 | | |
| 3145 | | > hide #!2.2 models |
| 3146 | | |
| 3147 | | > show #!2.3 models |
| 3148 | | |
| 3149 | | > hide #!2.3 models |
| 3150 | | |
| 3151 | | > show #!2.1 models |
| 3152 | | |
| 3153 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 3154 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v12-M-M-color-SS |
| 3155 | | > assigned.cxs" |
| 3156 | | |
| 3157 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 3158 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_1/Fig1-v1.cxs" |
| 3159 | | |
| 3160 | | ——— End of log from Mon May 23 15:10:58 2022 ——— |
| 3161 | | |
| 3162 | | opened ChimeraX session |
| 3163 | | |
| 3164 | | > hide #!2.1 models |
| 3165 | | |
| 3166 | | > show #!2.2 models |
| 3167 | | |
| 3168 | | > hide #!2.2 models |
| 3169 | | |
| 3170 | | > show #!2.1 models |
| 3171 | | |
| 3172 | | > hide #!2.1 models |
| 3173 | | |
| 3174 | | > show #!2.2 models |
| 3175 | | |
| 3176 | | > hide #!2.2 models |
| 3177 | | |
| 3178 | | > show #!2.3 models |
| 3179 | | |
| 3180 | | > show #!1.3 models |
| 3181 | | |
| 3182 | | > hide #!1.5 models |
| 3183 | | |
| 3184 | | > volume #1.3 level 0.175 |
| 3185 | | |
| 3186 | | > color zone #1.3 near #2.3 distance 9 |
| 3187 | | |
| 3188 | | > hide #!1.3 models |
| 3189 | | |
| 3190 | | > undo |
| 3191 | | |
| 3192 | | > hide #!2.3 models |
| 3193 | | |
| 3194 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 3195 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_1/Fig1b-3.cxs" |
| 3196 | | |
| 3197 | | ——— End of log from Mon May 23 16:17:23 2022 ——— |
| 3198 | | |
| 3199 | | opened ChimeraX session |
| 3200 | | |
| 3201 | | > hide #!1 models |
| 3202 | | |
| 3203 | | > show #!2.1 models |
| 3204 | | |
| 3205 | | > hide #!2.1 models |
| 3206 | | |
| 3207 | | > show #!2.2 models |
| 3208 | | |
| 3209 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 3210 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_2/Fig2-1.cxs" |
| 3211 | | |
| 3212 | | ——— End of log from Tue May 24 12:29:31 2022 ——— |
| 3213 | | |
| 3214 | | opened ChimeraX session |
| 3215 | | |
| 3216 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 3217 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v1.cxs" |
| 3218 | | |
| 3219 | | ——— End of log from Thu May 26 14:32:30 2022 ——— |
| 3220 | | |
| 3221 | | opened ChimeraX session |
| 3222 | | |
| 3223 | | > show #!2.5 models |
| 3224 | | |
| 3225 | | > hide #!2.5 models |
| 3226 | | |
| 3227 | | > show #!2.5 models |
| 3228 | | |
| 3229 | | > hide #!2.5 models |
| 3230 | | |
| 3231 | | > hide #!2.2 models |
| 3232 | | |
| 3233 | | > show #!2.5 models |
| 3234 | | |
| 3235 | | > view name v1 |
| 3236 | | |
| 3237 | | > view v1 |
| 3238 | | |
| 3239 | | > show #!2.3 models |
| 3240 | | |
| 3241 | | > hide #!2.3 models |
| 3242 | | |
| 3243 | | > show #!2.3 models |
| 3244 | | |
| 3245 | | > hide #!2.3 models |
| 3246 | | |
| 3247 | | > show #!2.3 models |
| 3248 | | |
| 3249 | | > hide #!2.5 models |
| 3250 | | |
| 3251 | | > show #!2.5 models |
| 3252 | | |
| 3253 | | > hide #!2.3 models |
| 3254 | | |
| 3255 | | > show #!2.3 models |
| 3256 | | |
| 3257 | | > hide #!2.3 models |
| 3258 | | |
| 3259 | | > show #!2.2 models |
| 3260 | | |
| 3261 | | > hide #!2.2 models |
| 3262 | | |
| 3263 | | > show #!2.4 models |
| 3264 | | |
| 3265 | | > hide #!2.4 models |
| 3266 | | |
| 3267 | | > view v1 |
| 3268 | | |
| 3269 | | [Repeated 1 time(s)] |
| 3270 | | |
| 3271 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 3272 | | > Institute/Documents/Draft/ScRPD/Deposite/J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3273 | | > Rsf090-v11.pdb" |
| 3274 | | |
| 3275 | | Chain information for J100-ScRFC-PCNA-2DNA-wBRCT-Rsf090-v11.pdb #3 |
| 3276 | | --- |
| 3277 | | Chain | Description |
| 3278 | | A | No description available |
| 3279 | | B | No description available |
| 3280 | | C | No description available |
| 3281 | | D | No description available |
| 3282 | | E | No description available |
| 3283 | | F | No description available |
| 3284 | | G | No description available |
| 3285 | | H | No description available |
| 3286 | | I | No description available |
| 3287 | | J | No description available |
| 3288 | | K | No description available |
| 3289 | | L | No description available |
| 3290 | | |
| 3291 | | |
| 3292 | | > open 3GLF |
| 3293 | | |
| 3294 | | Summary of feedback from opening 3GLF fetched from pdb |
| 3295 | | --- |
| 3296 | | notes | Fetching compressed mmCIF 3glf from |
| 3297 | | http://files.rcsb.org/download/3glf.cif |
| 3298 | | Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif |
| 3299 | | Fetching CCD BEF from http://ligand-expo.rcsb.org/reports/B/BEF/BEF.cif |
| 3300 | | Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif |
| 3301 | | Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif |
| 3302 | | |
| 3303 | | 3glf title: |
| 3304 | | Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA [more |
| 3305 | | info...] |
| 3306 | | |
| 3307 | | Chain information for 3glf #4 |
| 3308 | | --- |
| 3309 | | Chain | Description | UniProt |
| 3310 | | A F | DNA polymerase III subunit δ | HOLA_ECOLI |
| 3311 | | B C D G H I | DNA polymerase III subunit τ | DPO3X_ECOLI |
| 3312 | | E J | DNA polymerase III subunit delta' | HOLB_ECOLI |
| 3313 | | K M | DNA (5'-D(*TP*TP*TP*TP*TP*TP*ap*TP*ap*GP*GP*CP*CP*ap*G)-3') | |
| 3314 | | L N | DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*ap*TP*A)-3') | |
| 3315 | | |
| 3316 | | Non-standard residues in 3glf #4 |
| 3317 | | --- |
| 3318 | | ADP — adenosine-5'-diphosphate |
| 3319 | | BEF — beryllium trifluoride ion |
| 3320 | | MG — magnesium ion |
| 3321 | | ZN — zinc ion |
| 3322 | | |
| 3323 | | 3glf mmCIF Assemblies |
| 3324 | | --- |
| 3325 | | 1| author_and_software_defined_assembly |
| 3326 | | 2| author_and_software_defined_assembly |
| 3327 | | |
| 3328 | | |
| 3329 | | > hide #!3 models |
| 3330 | | |
| 3331 | | > hide #!2.5 models |
| 3332 | | |
| 3333 | | > show #!3 models |
| 3334 | | |
| 3335 | | > hide #!4 models |
| 3336 | | |
| 3337 | | > show #!4 models |
| 3338 | | |
| 3339 | | > open 3U5Z |
| 3340 | | |
| 3341 | | Summary of feedback from opening 3U5Z fetched from pdb |
| 3342 | | --- |
| 3343 | | notes | Fetching compressed mmCIF 3u5z from |
| 3344 | | http://files.rcsb.org/download/3u5z.cif |
| 3345 | | Fetching CCD 08T from http://ligand-expo.rcsb.org/reports/0/08T/08T.cif |
| 3346 | | |
| 3347 | | 3u5z title: |
| 3348 | | Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer- |
| 3349 | | template DNA, and ATP analog [more info...] |
| 3350 | | |
| 3351 | | Chain information for 3u5z #5 |
| 3352 | | --- |
| 3353 | | Chain | Description | UniProt |
| 3354 | | A K | DNA polymerase accessory protein 62 | DPA62_BPT4 |
| 3355 | | B C D E L M N O | DNA polymerase accessory protein 44 | DPA44_BPT4 |
| 3356 | | F G H P Q R | DNA polymerase processivity component | DPA5_BPT4 |
| 3357 | | I S | Template DNA strand | |
| 3358 | | J T | Primer DNA strand | |
| 3359 | | |
| 3360 | | Non-standard residues in 3u5z #5 |
| 3361 | | --- |
| 3362 | | 08T — |
| 3363 | | [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy- |
| 3364 | | oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium |
| 3365 | | ADP — adenosine-5'-diphosphate |
| 3366 | | MG — magnesium ion |
| 3367 | | |
| 3368 | | 3u5z mmCIF Assemblies |
| 3369 | | --- |
| 3370 | | 1| author_and_software_defined_assembly |
| 3371 | | 2| author_and_software_defined_assembly |
| 3372 | | |
| 3373 | | |
| 3374 | | > hide #3-5 |
| 3375 | | |
| 3376 | | > show #3-5 cartoons |
| 3377 | | |
| 3378 | | > mmaker #3 to #2.5 |
| 3379 | | |
| 3380 | | Parameters |
| 3381 | | --- |
| 3382 | | Chain pairing | bb |
| 3383 | | Alignment algorithm | Needleman-Wunsch |
| 3384 | | Similarity matrix | BLOSUM-62 |
| 3385 | | SS fraction | 0.3 |
| 3386 | | Gap open (HH/SS/other) | 18/18/6 |
| 3387 | | Gap extend | 1 |
| 3388 | | SS matrix | | | H | S | O |
| 3389 | | ---|---|---|--- |
| 3390 | | H | 6 | -9 | -6 |
| 3391 | | S | | 6 | -6 |
| 3392 | | O | | | 4 |
| 3393 | | Iteration cutoff | 2 |
| 3394 | | |
| 3395 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3396 | | Rsf090-v11.pdb, chain E (#3), sequence alignment score = 1658 |
| 3397 | | RMSD between 332 pruned atom pairs is 0.602 angstroms; (across all 338 pairs: |
| 3398 | | 0.694) |
| 3399 | | |
| 3400 | | |
| 3401 | | > mmaker #3 to #2.5 |
| 3402 | | |
| 3403 | | Parameters |
| 3404 | | --- |
| 3405 | | Chain pairing | bb |
| 3406 | | Alignment algorithm | Needleman-Wunsch |
| 3407 | | Similarity matrix | BLOSUM-62 |
| 3408 | | SS fraction | 0.3 |
| 3409 | | Gap open (HH/SS/other) | 18/18/6 |
| 3410 | | Gap extend | 1 |
| 3411 | | SS matrix | | | H | S | O |
| 3412 | | ---|---|---|--- |
| 3413 | | H | 6 | -9 | -6 |
| 3414 | | S | | 6 | -6 |
| 3415 | | O | | | 4 |
| 3416 | | Iteration cutoff | 2 |
| 3417 | | |
| 3418 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3419 | | Rsf090-v11.pdb, chain E (#3), sequence alignment score = 1658 |
| 3420 | | RMSD between 332 pruned atom pairs is 0.602 angstroms; (across all 338 pairs: |
| 3421 | | 0.694) |
| 3422 | | |
| 3423 | | |
| 3424 | | > mmaker #4 to #2.5 |
| 3425 | | |
| 3426 | | Parameters |
| 3427 | | --- |
| 3428 | | Chain pairing | bb |
| 3429 | | Alignment algorithm | Needleman-Wunsch |
| 3430 | | Similarity matrix | BLOSUM-62 |
| 3431 | | SS fraction | 0.3 |
| 3432 | | Gap open (HH/SS/other) | 18/18/6 |
| 3433 | | Gap extend | 1 |
| 3434 | | SS matrix | | | H | S | O |
| 3435 | | ---|---|---|--- |
| 3436 | | H | 6 | -9 | -6 |
| 3437 | | S | | 6 | -6 |
| 3438 | | O | | | 4 |
| 3439 | | Iteration cutoff | 2 |
| 3440 | | |
| 3441 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain I (#4), |
| 3442 | | sequence alignment score = 531.7 |
| 3443 | | RMSD between 146 pruned atom pairs is 1.105 angstroms; (across all 312 pairs: |
| 3444 | | 9.621) |
| 3445 | | |
| 3446 | | |
| 3447 | | > mmaker #5 to #2.5 |
| 3448 | | |
| 3449 | | Parameters |
| 3450 | | --- |
| 3451 | | Chain pairing | bb |
| 3452 | | Alignment algorithm | Needleman-Wunsch |
| 3453 | | Similarity matrix | BLOSUM-62 |
| 3454 | | SS fraction | 0.3 |
| 3455 | | Gap open (HH/SS/other) | 18/18/6 |
| 3456 | | Gap extend | 1 |
| 3457 | | SS matrix | | | H | S | O |
| 3458 | | ---|---|---|--- |
| 3459 | | H | 6 | -9 | -6 |
| 3460 | | S | | 6 | -6 |
| 3461 | | O | | | 4 |
| 3462 | | Iteration cutoff | 2 |
| 3463 | | |
| 3464 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3u5z, chain B (#5), |
| 3465 | | sequence alignment score = 465.7 |
| 3466 | | RMSD between 141 pruned atom pairs is 1.038 angstroms; (across all 293 pairs: |
| 3467 | | 13.080) |
| 3468 | | |
| 3469 | | |
| 3470 | | > hide #!4 models |
| 3471 | | |
| 3472 | | > hide #!5 models |
| 3473 | | |
| 3474 | | > show #!2.5 models |
| 3475 | | |
| 3476 | | > hide #!2.5 models |
| 3477 | | |
| 3478 | | > mmaker #3/A-H to #2.5/A-H pair ss |
| 3479 | | |
| 3480 | | Parameters |
| 3481 | | --- |
| 3482 | | Chain pairing | ss |
| 3483 | | Alignment algorithm | Needleman-Wunsch |
| 3484 | | Similarity matrix | BLOSUM-62 |
| 3485 | | SS fraction | 0.3 |
| 3486 | | Gap open (HH/SS/other) | 18/18/6 |
| 3487 | | Gap extend | 1 |
| 3488 | | SS matrix | | | H | S | O |
| 3489 | | ---|---|---|--- |
| 3490 | | H | 6 | -9 | -6 |
| 3491 | | S | | 6 | -6 |
| 3492 | | O | | | 4 |
| 3493 | | Iteration cutoff | 2 |
| 3494 | | |
| 3495 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3496 | | Rsf090-v11.pdb, chain A (#3), sequence alignment score = 362.9 |
| 3497 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3498 | | Rsf090-v11.pdb, chain B (#3), sequence alignment score = 1555.9 |
| 3499 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3500 | | Rsf090-v11.pdb, chain C (#3), sequence alignment score = 1652.7 |
| 3501 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3502 | | Rsf090-v11.pdb, chain D (#3), sequence alignment score = 1650.9 |
| 3503 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3504 | | Rsf090-v11.pdb, chain E (#3), sequence alignment score = 1658 |
| 3505 | | Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3506 | | Rsf090-v11.pdb, chain F (#3), sequence alignment score = 201.1 |
| 3507 | | Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3508 | | Rsf090-v11.pdb, chain G (#3), sequence alignment score = 216.7 |
| 3509 | | Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3510 | | Rsf090-v11.pdb, chain H (#3), sequence alignment score = 177.6 |
| 3511 | | RMSD between 1467 pruned atom pairs is 0.714 angstroms; (across all 2392 |
| 3512 | | pairs: 6.053) |
| 3513 | | |
| 3514 | | |
| 3515 | | > dssp #3 |
| 3516 | | |
| 3517 | | > undo |
| 3518 | | |
| 3519 | | > dssp #3/A |
| 3520 | | |
| 3521 | | > undo |
| 3522 | | |
| 3523 | | > hide #!3 models |
| 3524 | | |
| 3525 | | > show #!4 models |
| 3526 | | |
| 3527 | | > show #!2.5 models |
| 3528 | | |
| 3529 | | > hide #!2.5 models |
| 3530 | | |
| 3531 | | > show #!2.5 models |
| 3532 | | |
| 3533 | | > hide #!2.5 models |
| 3534 | | |
| 3535 | | > mmaker #4/A-E to #2.5/A-E pair ss |
| 3536 | | |
| 3537 | | Parameters |
| 3538 | | --- |
| 3539 | | Chain pairing | ss |
| 3540 | | Alignment algorithm | Needleman-Wunsch |
| 3541 | | Similarity matrix | BLOSUM-62 |
| 3542 | | SS fraction | 0.3 |
| 3543 | | Gap open (HH/SS/other) | 18/18/6 |
| 3544 | | Gap extend | 1 |
| 3545 | | SS matrix | | | H | S | O |
| 3546 | | ---|---|---|--- |
| 3547 | | H | 6 | -9 | -6 |
| 3548 | | S | | 6 | -6 |
| 3549 | | O | | | 4 |
| 3550 | | Iteration cutoff | 2 |
| 3551 | | |
| 3552 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4), |
| 3553 | | sequence alignment score = 176.6 |
| 3554 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4), |
| 3555 | | sequence alignment score = 462.2 |
| 3556 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 3557 | | sequence alignment score = 507.5 |
| 3558 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 3559 | | sequence alignment score = 497.7 |
| 3560 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 3561 | | sequence alignment score = 285.9 |
| 3562 | | RMSD between 454 pruned atom pairs is 1.226 angstroms; (across all 1515 pairs: |
| 3563 | | 13.805) |
| 3564 | | |
| 3565 | | |
| 3566 | | > show #!2.5 models |
| 3567 | | |
| 3568 | | > view v1 |
| 3569 | | |
| 3570 | | > mmaker #4/F-J to #2.5/A-E pair ss |
| 3571 | | |
| 3572 | | Parameters |
| 3573 | | --- |
| 3574 | | Chain pairing | ss |
| 3575 | | Alignment algorithm | Needleman-Wunsch |
| 3576 | | Similarity matrix | BLOSUM-62 |
| 3577 | | SS fraction | 0.3 |
| 3578 | | Gap open (HH/SS/other) | 18/18/6 |
| 3579 | | Gap extend | 1 |
| 3580 | | SS matrix | | | H | S | O |
| 3581 | | ---|---|---|--- |
| 3582 | | H | 6 | -9 | -6 |
| 3583 | | S | | 6 | -6 |
| 3584 | | O | | | 4 |
| 3585 | | Iteration cutoff | 2 |
| 3586 | | |
| 3587 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain F (#4), |
| 3588 | | sequence alignment score = 175.7 |
| 3589 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain G (#4), |
| 3590 | | sequence alignment score = 469.4 |
| 3591 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain H (#4), |
| 3592 | | sequence alignment score = 511.1 |
| 3593 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain I (#4), |
| 3594 | | sequence alignment score = 497.7 |
| 3595 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain J (#4), |
| 3596 | | sequence alignment score = 267.9 |
| 3597 | | RMSD between 449 pruned atom pairs is 1.205 angstroms; (across all 1521 pairs: |
| 3598 | | 13.864) |
| 3599 | | |
| 3600 | | |
| 3601 | | > mmaker #4/A-E to #2.5/A-E pair ss |
| 3602 | | |
| 3603 | | Parameters |
| 3604 | | --- |
| 3605 | | Chain pairing | ss |
| 3606 | | Alignment algorithm | Needleman-Wunsch |
| 3607 | | Similarity matrix | BLOSUM-62 |
| 3608 | | SS fraction | 0.3 |
| 3609 | | Gap open (HH/SS/other) | 18/18/6 |
| 3610 | | Gap extend | 1 |
| 3611 | | SS matrix | | | H | S | O |
| 3612 | | ---|---|---|--- |
| 3613 | | H | 6 | -9 | -6 |
| 3614 | | S | | 6 | -6 |
| 3615 | | O | | | 4 |
| 3616 | | Iteration cutoff | 2 |
| 3617 | | |
| 3618 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4), |
| 3619 | | sequence alignment score = 176.6 |
| 3620 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4), |
| 3621 | | sequence alignment score = 462.2 |
| 3622 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 3623 | | sequence alignment score = 507.5 |
| 3624 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 3625 | | sequence alignment score = 497.7 |
| 3626 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 3627 | | sequence alignment score = 285.9 |
| 3628 | | RMSD between 454 pruned atom pairs is 1.226 angstroms; (across all 1515 pairs: |
| 3629 | | 13.805) |
| 3630 | | |
| 3631 | | |
| 3632 | | > select #4/F-J |
| 3633 | | |
| 3634 | | 13948 atoms, 14199 bonds, 23 pseudobonds, 1785 residues, 2 models selected |
| 3635 | | |
| 3636 | | > delete sel |
| 3637 | | |
| 3638 | | > delete #4/M-N |
| 3639 | | |
| 3640 | | > view v1 |
| 3641 | | |
| 3642 | | > hide #!2.5 models |
| 3643 | | |
| 3644 | | > hide #!4 models |
| 3645 | | |
| 3646 | | > show #!4 models |
| 3647 | | |
| 3648 | | > show #!2.5 models |
| 3649 | | |
| 3650 | | > hide #!2.5 models |
| 3651 | | |
| 3652 | | > show #!2.5 models |
| 3653 | | |
| 3654 | | > mmaker #4 to #2.5 |
| 3655 | | |
| 3656 | | Parameters |
| 3657 | | --- |
| 3658 | | Chain pairing | bb |
| 3659 | | Alignment algorithm | Needleman-Wunsch |
| 3660 | | Similarity matrix | BLOSUM-62 |
| 3661 | | SS fraction | 0.3 |
| 3662 | | Gap open (HH/SS/other) | 18/18/6 |
| 3663 | | Gap extend | 1 |
| 3664 | | SS matrix | | | H | S | O |
| 3665 | | ---|---|---|--- |
| 3666 | | H | 6 | -9 | -6 |
| 3667 | | S | | 6 | -6 |
| 3668 | | O | | | 4 |
| 3669 | | Iteration cutoff | 2 |
| 3670 | | |
| 3671 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain D (#4), |
| 3672 | | sequence alignment score = 525.7 |
| 3673 | | RMSD between 144 pruned atom pairs is 1.091 angstroms; (across all 312 pairs: |
| 3674 | | 9.612) |
| 3675 | | |
| 3676 | | |
| 3677 | | > mmaker #4/A to #2.5/A |
| 3678 | | |
| 3679 | | Parameters |
| 3680 | | --- |
| 3681 | | Chain pairing | bb |
| 3682 | | Alignment algorithm | Needleman-Wunsch |
| 3683 | | Similarity matrix | BLOSUM-62 |
| 3684 | | SS fraction | 0.3 |
| 3685 | | Gap open (HH/SS/other) | 18/18/6 |
| 3686 | | Gap extend | 1 |
| 3687 | | SS matrix | | | H | S | O |
| 3688 | | ---|---|---|--- |
| 3689 | | H | 6 | -9 | -6 |
| 3690 | | S | | 6 | -6 |
| 3691 | | O | | | 4 |
| 3692 | | Iteration cutoff | 2 |
| 3693 | | |
| 3694 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4), |
| 3695 | | sequence alignment score = 176.6 |
| 3696 | | RMSD between 19 pruned atom pairs is 1.035 angstroms; (across all 307 pairs: |
| 3697 | | 25.477) |
| 3698 | | |
| 3699 | | |
| 3700 | | > hide #!2.5 models |
| 3701 | | |
| 3702 | | > show #!2.5 models |
| 3703 | | |
| 3704 | | > mmaker #4/E to #2.5/E |
| 3705 | | |
| 3706 | | Parameters |
| 3707 | | --- |
| 3708 | | Chain pairing | bb |
| 3709 | | Alignment algorithm | Needleman-Wunsch |
| 3710 | | Similarity matrix | BLOSUM-62 |
| 3711 | | SS fraction | 0.3 |
| 3712 | | Gap open (HH/SS/other) | 18/18/6 |
| 3713 | | Gap extend | 1 |
| 3714 | | SS matrix | | | H | S | O |
| 3715 | | ---|---|---|--- |
| 3716 | | H | 6 | -9 | -6 |
| 3717 | | S | | 6 | -6 |
| 3718 | | O | | | 4 |
| 3719 | | Iteration cutoff | 2 |
| 3720 | | |
| 3721 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 3722 | | sequence alignment score = 285.9 |
| 3723 | | RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs: |
| 3724 | | 12.269) |
| 3725 | | |
| 3726 | | |
| 3727 | | > mmaker #4/C-E to #2.5/C-E pair ss |
| 3728 | | |
| 3729 | | Parameters |
| 3730 | | --- |
| 3731 | | Chain pairing | ss |
| 3732 | | Alignment algorithm | Needleman-Wunsch |
| 3733 | | Similarity matrix | BLOSUM-62 |
| 3734 | | SS fraction | 0.3 |
| 3735 | | Gap open (HH/SS/other) | 18/18/6 |
| 3736 | | Gap extend | 1 |
| 3737 | | SS matrix | | | H | S | O |
| 3738 | | ---|---|---|--- |
| 3739 | | H | 6 | -9 | -6 |
| 3740 | | S | | 6 | -6 |
| 3741 | | O | | | 4 |
| 3742 | | Iteration cutoff | 2 |
| 3743 | | |
| 3744 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 3745 | | sequence alignment score = 507.5 |
| 3746 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 3747 | | sequence alignment score = 497.7 |
| 3748 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 3749 | | sequence alignment score = 285.9 |
| 3750 | | RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs: |
| 3751 | | 10.786) |
| 3752 | | |
| 3753 | | |
| 3754 | | > mmaker #4/C-E to #2.5/C-E |
| 3755 | | |
| 3756 | | Parameters |
| 3757 | | --- |
| 3758 | | Chain pairing | bb |
| 3759 | | Alignment algorithm | Needleman-Wunsch |
| 3760 | | Similarity matrix | BLOSUM-62 |
| 3761 | | SS fraction | 0.3 |
| 3762 | | Gap open (HH/SS/other) | 18/18/6 |
| 3763 | | Gap extend | 1 |
| 3764 | | SS matrix | | | H | S | O |
| 3765 | | ---|---|---|--- |
| 3766 | | H | 6 | -9 | -6 |
| 3767 | | S | | 6 | -6 |
| 3768 | | O | | | 4 |
| 3769 | | Iteration cutoff | 2 |
| 3770 | | |
| 3771 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain D (#4), |
| 3772 | | sequence alignment score = 525.7 |
| 3773 | | RMSD between 144 pruned atom pairs is 1.091 angstroms; (across all 312 pairs: |
| 3774 | | 9.612) |
| 3775 | | |
| 3776 | | |
| 3777 | | > mmaker #4/C-E to #2.5/C-E pair ss |
| 3778 | | |
| 3779 | | Parameters |
| 3780 | | --- |
| 3781 | | Chain pairing | ss |
| 3782 | | Alignment algorithm | Needleman-Wunsch |
| 3783 | | Similarity matrix | BLOSUM-62 |
| 3784 | | SS fraction | 0.3 |
| 3785 | | Gap open (HH/SS/other) | 18/18/6 |
| 3786 | | Gap extend | 1 |
| 3787 | | SS matrix | | | H | S | O |
| 3788 | | ---|---|---|--- |
| 3789 | | H | 6 | -9 | -6 |
| 3790 | | S | | 6 | -6 |
| 3791 | | O | | | 4 |
| 3792 | | Iteration cutoff | 2 |
| 3793 | | |
| 3794 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 3795 | | sequence alignment score = 507.5 |
| 3796 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 3797 | | sequence alignment score = 497.7 |
| 3798 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 3799 | | sequence alignment score = 285.9 |
| 3800 | | RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs: |
| 3801 | | 10.786) |
| 3802 | | |
| 3803 | | |
| 3804 | | > mmaker #4/E to #2.5/E pair ss |
| 3805 | | |
| 3806 | | Parameters |
| 3807 | | --- |
| 3808 | | Chain pairing | ss |
| 3809 | | Alignment algorithm | Needleman-Wunsch |
| 3810 | | Similarity matrix | BLOSUM-62 |
| 3811 | | SS fraction | 0.3 |
| 3812 | | Gap open (HH/SS/other) | 18/18/6 |
| 3813 | | Gap extend | 1 |
| 3814 | | SS matrix | | | H | S | O |
| 3815 | | ---|---|---|--- |
| 3816 | | H | 6 | -9 | -6 |
| 3817 | | S | | 6 | -6 |
| 3818 | | O | | | 4 |
| 3819 | | Iteration cutoff | 2 |
| 3820 | | |
| 3821 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 3822 | | sequence alignment score = 285.9 |
| 3823 | | RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs: |
| 3824 | | 12.269) |
| 3825 | | |
| 3826 | | |
| 3827 | | > mmaker #4/D-E to #2.5/D-E pair ss |
| 3828 | | |
| 3829 | | Parameters |
| 3830 | | --- |
| 3831 | | Chain pairing | ss |
| 3832 | | Alignment algorithm | Needleman-Wunsch |
| 3833 | | Similarity matrix | BLOSUM-62 |
| 3834 | | SS fraction | 0.3 |
| 3835 | | Gap open (HH/SS/other) | 18/18/6 |
| 3836 | | Gap extend | 1 |
| 3837 | | SS matrix | | | H | S | O |
| 3838 | | ---|---|---|--- |
| 3839 | | H | 6 | -9 | -6 |
| 3840 | | S | | 6 | -6 |
| 3841 | | O | | | 4 |
| 3842 | | Iteration cutoff | 2 |
| 3843 | | |
| 3844 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 3845 | | sequence alignment score = 497.7 |
| 3846 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 3847 | | sequence alignment score = 285.9 |
| 3848 | | RMSD between 188 pruned atom pairs is 1.174 angstroms; (across all 593 pairs: |
| 3849 | | 11.216) |
| 3850 | | |
| 3851 | | |
| 3852 | | > hide #!2.5 models |
| 3853 | | |
| 3854 | | > show #!2.5 models |
| 3855 | | |
| 3856 | | > hide #!2.5 models |
| 3857 | | |
| 3858 | | > show #!3 models |
| 3859 | | |
| 3860 | | > hide #!4 models |
| 3861 | | |
| 3862 | | > show #!2.5 models |
| 3863 | | |
| 3864 | | > mmaker #3/A-H to #2.5/A-H pair ss |
| 3865 | | |
| 3866 | | Parameters |
| 3867 | | --- |
| 3868 | | Chain pairing | ss |
| 3869 | | Alignment algorithm | Needleman-Wunsch |
| 3870 | | Similarity matrix | BLOSUM-62 |
| 3871 | | SS fraction | 0.3 |
| 3872 | | Gap open (HH/SS/other) | 18/18/6 |
| 3873 | | Gap extend | 1 |
| 3874 | | SS matrix | | | H | S | O |
| 3875 | | ---|---|---|--- |
| 3876 | | H | 6 | -9 | -6 |
| 3877 | | S | | 6 | -6 |
| 3878 | | O | | | 4 |
| 3879 | | Iteration cutoff | 2 |
| 3880 | | |
| 3881 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3882 | | Rsf090-v11.pdb, chain A (#3), sequence alignment score = 362.9 |
| 3883 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3884 | | Rsf090-v11.pdb, chain B (#3), sequence alignment score = 1555.9 |
| 3885 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3886 | | Rsf090-v11.pdb, chain C (#3), sequence alignment score = 1652.7 |
| 3887 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3888 | | Rsf090-v11.pdb, chain D (#3), sequence alignment score = 1650.9 |
| 3889 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3890 | | Rsf090-v11.pdb, chain E (#3), sequence alignment score = 1658 |
| 3891 | | Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3892 | | Rsf090-v11.pdb, chain F (#3), sequence alignment score = 201.1 |
| 3893 | | Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3894 | | Rsf090-v11.pdb, chain G (#3), sequence alignment score = 216.7 |
| 3895 | | Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT- |
| 3896 | | Rsf090-v11.pdb, chain H (#3), sequence alignment score = 177.6 |
| 3897 | | RMSD between 1467 pruned atom pairs is 0.714 angstroms; (across all 2392 |
| 3898 | | pairs: 6.053) |
| 3899 | | |
| 3900 | | |
| 3901 | | > hide #!3 models |
| 3902 | | |
| 3903 | | > show #!4 models |
| 3904 | | |
| 3905 | | > mmaker #4/B-E to #2.5/B-E pair ss |
| 3906 | | |
| 3907 | | Parameters |
| 3908 | | --- |
| 3909 | | Chain pairing | ss |
| 3910 | | Alignment algorithm | Needleman-Wunsch |
| 3911 | | Similarity matrix | BLOSUM-62 |
| 3912 | | SS fraction | 0.3 |
| 3913 | | Gap open (HH/SS/other) | 18/18/6 |
| 3914 | | Gap extend | 1 |
| 3915 | | SS matrix | | | H | S | O |
| 3916 | | ---|---|---|--- |
| 3917 | | H | 6 | -9 | -6 |
| 3918 | | S | | 6 | -6 |
| 3919 | | O | | | 4 |
| 3920 | | Iteration cutoff | 2 |
| 3921 | | |
| 3922 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4), |
| 3923 | | sequence alignment score = 462.2 |
| 3924 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 3925 | | sequence alignment score = 507.5 |
| 3926 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 3927 | | sequence alignment score = 497.7 |
| 3928 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 3929 | | sequence alignment score = 285.9 |
| 3930 | | RMSD between 454 pruned atom pairs is 1.226 angstroms; (across all 1208 pairs: |
| 3931 | | 10.605) |
| 3932 | | |
| 3933 | | |
| 3934 | | > hide #!2.5 models |
| 3935 | | |
| 3936 | | > show #!2.5 models |
| 3937 | | |
| 3938 | | > mmaker #4/E to #2.5/E |
| 3939 | | |
| 3940 | | Parameters |
| 3941 | | --- |
| 3942 | | Chain pairing | bb |
| 3943 | | Alignment algorithm | Needleman-Wunsch |
| 3944 | | Similarity matrix | BLOSUM-62 |
| 3945 | | SS fraction | 0.3 |
| 3946 | | Gap open (HH/SS/other) | 18/18/6 |
| 3947 | | Gap extend | 1 |
| 3948 | | SS matrix | | | H | S | O |
| 3949 | | ---|---|---|--- |
| 3950 | | H | 6 | -9 | -6 |
| 3951 | | S | | 6 | -6 |
| 3952 | | O | | | 4 |
| 3953 | | Iteration cutoff | 2 |
| 3954 | | |
| 3955 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 3956 | | sequence alignment score = 285.9 |
| 3957 | | RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs: |
| 3958 | | 12.269) |
| 3959 | | |
| 3960 | | |
| 3961 | | > mmaker #4/E to #2.5/E pair ss |
| 3962 | | |
| 3963 | | Parameters |
| 3964 | | --- |
| 3965 | | Chain pairing | ss |
| 3966 | | Alignment algorithm | Needleman-Wunsch |
| 3967 | | Similarity matrix | BLOSUM-62 |
| 3968 | | SS fraction | 0.3 |
| 3969 | | Gap open (HH/SS/other) | 18/18/6 |
| 3970 | | Gap extend | 1 |
| 3971 | | SS matrix | | | H | S | O |
| 3972 | | ---|---|---|--- |
| 3973 | | H | 6 | -9 | -6 |
| 3974 | | S | | 6 | -6 |
| 3975 | | O | | | 4 |
| 3976 | | Iteration cutoff | 2 |
| 3977 | | |
| 3978 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 3979 | | sequence alignment score = 285.9 |
| 3980 | | RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs: |
| 3981 | | 12.269) |
| 3982 | | |
| 3983 | | |
| 3984 | | > mmaker #4/E to #2.5/E pair ss |
| 3985 | | |
| 3986 | | Parameters |
| 3987 | | --- |
| 3988 | | Chain pairing | ss |
| 3989 | | Alignment algorithm | Needleman-Wunsch |
| 3990 | | Similarity matrix | BLOSUM-62 |
| 3991 | | SS fraction | 0.3 |
| 3992 | | Gap open (HH/SS/other) | 18/18/6 |
| 3993 | | Gap extend | 1 |
| 3994 | | SS matrix | | | H | S | O |
| 3995 | | ---|---|---|--- |
| 3996 | | H | 6 | -9 | -6 |
| 3997 | | S | | 6 | -6 |
| 3998 | | O | | | 4 |
| 3999 | | Iteration cutoff | 2 |
| 4000 | | |
| 4001 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 4002 | | sequence alignment score = 285.9 |
| 4003 | | RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs: |
| 4004 | | 12.269) |
| 4005 | | |
| 4006 | | |
| 4007 | | > mmaker #4/C-E to #2.5/C-E pair ss |
| 4008 | | |
| 4009 | | Parameters |
| 4010 | | --- |
| 4011 | | Chain pairing | ss |
| 4012 | | Alignment algorithm | Needleman-Wunsch |
| 4013 | | Similarity matrix | BLOSUM-62 |
| 4014 | | SS fraction | 0.3 |
| 4015 | | Gap open (HH/SS/other) | 18/18/6 |
| 4016 | | Gap extend | 1 |
| 4017 | | SS matrix | | | H | S | O |
| 4018 | | ---|---|---|--- |
| 4019 | | H | 6 | -9 | -6 |
| 4020 | | S | | 6 | -6 |
| 4021 | | O | | | 4 |
| 4022 | | Iteration cutoff | 2 |
| 4023 | | |
| 4024 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 4025 | | sequence alignment score = 507.5 |
| 4026 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 4027 | | sequence alignment score = 497.7 |
| 4028 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 4029 | | sequence alignment score = 285.9 |
| 4030 | | RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs: |
| 4031 | | 10.786) |
| 4032 | | |
| 4033 | | |
| 4034 | | > hide #!2.5 models |
| 4035 | | |
| 4036 | | > hide #!1.3 models |
| 4037 | | |
| 4038 | | > show #!1.5 models |
| 4039 | | |
| 4040 | | > fitmap #4 inMap #1.5 |
| 4041 | | |
| 4042 | | Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using |
| 4043 | | 14323 atoms |
| 4044 | | average map value = 0.1428, steps = 80 |
| 4045 | | shifted from previous position = 0.269 |
| 4046 | | rotated from previous position = 1.09 degrees |
| 4047 | | atoms outside contour = 10008, contour level = 0.2 |
| 4048 | | |
| 4049 | | Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5) |
| 4050 | | coordinates: |
| 4051 | | Matrix rotation and translation |
| 4052 | | -0.79349866 -0.60576978 0.05833393 208.05381819 |
| 4053 | | -0.43311966 0.49479544 -0.75338227 232.74167460 |
| 4054 | | 0.42751285 -0.62307339 -0.65499032 198.11036122 |
| 4055 | | Axis 0.30454517 -0.86280889 0.40350099 |
| 4056 | | Axis point 131.22228743 0.00000000 167.62379289 |
| 4057 | | Rotation angle (degrees) 167.64664469 |
| 4058 | | Shift along axis -57.51207455 |
| 4059 | | |
| 4060 | | |
| 4061 | | > ui mousemode right "translate selected models" |
| 4062 | | |
| 4063 | | > select #4 |
| 4064 | | |
| 4065 | | 14323 atoms, 14626 bonds, 46 pseudobonds, 1795 residues, 3 models selected |
| 4066 | | |
| 4067 | | > view matrix models |
| 4068 | | > #4,-0.7935,-0.60577,0.058334,210.2,-0.43312,0.4948,-0.75338,232.2,0.42751,-0.62307,-0.65499,199.53 |
| 4069 | | |
| 4070 | | Drag select of 1.5 polish-stat5-cs_P24_J261_sharp.mrc , 10 residues |
| 4071 | | |
| 4072 | | > select clear |
| 4073 | | |
| 4074 | | > select #4 |
| 4075 | | |
| 4076 | | 14323 atoms, 14626 bonds, 46 pseudobonds, 1795 residues, 3 models selected |
| 4077 | | |
| 4078 | | > select clear |
| 4079 | | |
| 4080 | | > select #4 |
| 4081 | | |
| 4082 | | 14323 atoms, 14626 bonds, 46 pseudobonds, 1795 residues, 3 models selected |
| 4083 | | |
| 4084 | | > view matrix models |
| 4085 | | > #4,-0.7935,-0.60577,0.058334,209.26,-0.43312,0.4948,-0.75338,231.89,0.42751,-0.62307,-0.65499,199.67 |
| 4086 | | |
| 4087 | | > view matrix models |
| 4088 | | > #4,-0.7935,-0.60577,0.058334,210.12,-0.43312,0.4948,-0.75338,232.09,0.42751,-0.62307,-0.65499,199.65 |
| 4089 | | |
| 4090 | | > select clear |
| 4091 | | |
| 4092 | | > select #4 |
| 4093 | | |
| 4094 | | 14323 atoms, 14626 bonds, 46 pseudobonds, 1795 residues, 3 models selected |
| 4095 | | |
| 4096 | | > view matrix models |
| 4097 | | > #4,-0.7935,-0.60577,0.058334,208.96,-0.43312,0.4948,-0.75338,230.66,0.42751,-0.62307,-0.65499,193.64 |
| 4098 | | |
| 4099 | | > view matrix models |
| 4100 | | > #4,-0.7935,-0.60577,0.058334,210.09,-0.43312,0.4948,-0.75338,229.74,0.42751,-0.62307,-0.65499,195.04 |
| 4101 | | |
| 4102 | | > fitmap #4 inMap #1.5 |
| 4103 | | |
| 4104 | | Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using |
| 4105 | | 14323 atoms |
| 4106 | | average map value = 0.08317, steps = 72 |
| 4107 | | shifted from previous position = 1.87 |
| 4108 | | rotated from previous position = 1.5 degrees |
| 4109 | | atoms outside contour = 10998, contour level = 0.2 |
| 4110 | | |
| 4111 | | Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5) |
| 4112 | | coordinates: |
| 4113 | | Matrix rotation and translation |
| 4114 | | -0.79699414 -0.60310036 0.03271555 210.44525036 |
| 4115 | | -0.41423841 0.50638850 -0.75629176 227.30908388 |
| 4116 | | 0.43955305 -0.61631214 -0.65341600 195.03082143 |
| 4117 | | Axis 0.29791000 -0.86584715 0.40194322 |
| 4118 | | Axis point 129.36888139 0.00000000 165.89627059 |
| 4119 | | Rotation angle (degrees) 166.41214410 |
| 4120 | | Shift along axis -55.72986120 |
| 4121 | | |
| 4122 | | |
| 4123 | | > select clear |
| 4124 | | |
| 4125 | | > hide #!1.5 models |
| 4126 | | |
| 4127 | | > show #!2.5 models |
| 4128 | | |
| 4129 | | > mmaker #4/C-E to #2.5/C-E |
| 4130 | | |
| 4131 | | Parameters |
| 4132 | | --- |
| 4133 | | Chain pairing | bb |
| 4134 | | Alignment algorithm | Needleman-Wunsch |
| 4135 | | Similarity matrix | BLOSUM-62 |
| 4136 | | SS fraction | 0.3 |
| 4137 | | Gap open (HH/SS/other) | 18/18/6 |
| 4138 | | Gap extend | 1 |
| 4139 | | SS matrix | | | H | S | O |
| 4140 | | ---|---|---|--- |
| 4141 | | H | 6 | -9 | -6 |
| 4142 | | S | | 6 | -6 |
| 4143 | | O | | | 4 |
| 4144 | | Iteration cutoff | 2 |
| 4145 | | |
| 4146 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain D (#4), |
| 4147 | | sequence alignment score = 525.7 |
| 4148 | | RMSD between 144 pruned atom pairs is 1.091 angstroms; (across all 312 pairs: |
| 4149 | | 9.612) |
| 4150 | | |
| 4151 | | |
| 4152 | | > mmaker #4/C-E to #2.5/C-E pair ss |
| 4153 | | |
| 4154 | | Parameters |
| 4155 | | --- |
| 4156 | | Chain pairing | ss |
| 4157 | | Alignment algorithm | Needleman-Wunsch |
| 4158 | | Similarity matrix | BLOSUM-62 |
| 4159 | | SS fraction | 0.3 |
| 4160 | | Gap open (HH/SS/other) | 18/18/6 |
| 4161 | | Gap extend | 1 |
| 4162 | | SS matrix | | | H | S | O |
| 4163 | | ---|---|---|--- |
| 4164 | | H | 6 | -9 | -6 |
| 4165 | | S | | 6 | -6 |
| 4166 | | O | | | 4 |
| 4167 | | Iteration cutoff | 2 |
| 4168 | | |
| 4169 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 4170 | | sequence alignment score = 507.5 |
| 4171 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 4172 | | sequence alignment score = 497.7 |
| 4173 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 4174 | | sequence alignment score = 285.9 |
| 4175 | | RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs: |
| 4176 | | 10.786) |
| 4177 | | |
| 4178 | | |
| 4179 | | > mmaker #4/C to #2.5/C pair ss |
| 4180 | | |
| 4181 | | Parameters |
| 4182 | | --- |
| 4183 | | Chain pairing | ss |
| 4184 | | Alignment algorithm | Needleman-Wunsch |
| 4185 | | Similarity matrix | BLOSUM-62 |
| 4186 | | SS fraction | 0.3 |
| 4187 | | Gap open (HH/SS/other) | 18/18/6 |
| 4188 | | Gap extend | 1 |
| 4189 | | SS matrix | | | H | S | O |
| 4190 | | ---|---|---|--- |
| 4191 | | H | 6 | -9 | -6 |
| 4192 | | S | | 6 | -6 |
| 4193 | | O | | | 4 |
| 4194 | | Iteration cutoff | 2 |
| 4195 | | |
| 4196 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 4197 | | sequence alignment score = 507.5 |
| 4198 | | RMSD between 153 pruned atom pairs is 1.180 angstroms; (across all 310 pairs: |
| 4199 | | 8.065) |
| 4200 | | |
| 4201 | | |
| 4202 | | > mmaker #4/D to #2.5/D pair ss |
| 4203 | | |
| 4204 | | Parameters |
| 4205 | | --- |
| 4206 | | Chain pairing | ss |
| 4207 | | Alignment algorithm | Needleman-Wunsch |
| 4208 | | Similarity matrix | BLOSUM-62 |
| 4209 | | SS fraction | 0.3 |
| 4210 | | Gap open (HH/SS/other) | 18/18/6 |
| 4211 | | Gap extend | 1 |
| 4212 | | SS matrix | | | H | S | O |
| 4213 | | ---|---|---|--- |
| 4214 | | H | 6 | -9 | -6 |
| 4215 | | S | | 6 | -6 |
| 4216 | | O | | | 4 |
| 4217 | | Iteration cutoff | 2 |
| 4218 | | |
| 4219 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 4220 | | sequence alignment score = 497.7 |
| 4221 | | RMSD between 140 pruned atom pairs is 1.150 angstroms; (across all 312 pairs: |
| 4222 | | 10.303) |
| 4223 | | |
| 4224 | | |
| 4225 | | > mmaker #4/E to #2.5/E pair ss |
| 4226 | | |
| 4227 | | Parameters |
| 4228 | | --- |
| 4229 | | Chain pairing | ss |
| 4230 | | Alignment algorithm | Needleman-Wunsch |
| 4231 | | Similarity matrix | BLOSUM-62 |
| 4232 | | SS fraction | 0.3 |
| 4233 | | Gap open (HH/SS/other) | 18/18/6 |
| 4234 | | Gap extend | 1 |
| 4235 | | SS matrix | | | H | S | O |
| 4236 | | ---|---|---|--- |
| 4237 | | H | 6 | -9 | -6 |
| 4238 | | S | | 6 | -6 |
| 4239 | | O | | | 4 |
| 4240 | | Iteration cutoff | 2 |
| 4241 | | |
| 4242 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 4243 | | sequence alignment score = 285.9 |
| 4244 | | RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs: |
| 4245 | | 12.269) |
| 4246 | | |
| 4247 | | |
| 4248 | | > mmaker #4/A-E to #2.5/A-E pair ss |
| 4249 | | |
| 4250 | | Parameters |
| 4251 | | --- |
| 4252 | | Chain pairing | ss |
| 4253 | | Alignment algorithm | Needleman-Wunsch |
| 4254 | | Similarity matrix | BLOSUM-62 |
| 4255 | | SS fraction | 0.3 |
| 4256 | | Gap open (HH/SS/other) | 18/18/6 |
| 4257 | | Gap extend | 1 |
| 4258 | | SS matrix | | | H | S | O |
| 4259 | | ---|---|---|--- |
| 4260 | | H | 6 | -9 | -6 |
| 4261 | | S | | 6 | -6 |
| 4262 | | O | | | 4 |
| 4263 | | Iteration cutoff | 2 |
| 4264 | | |
| 4265 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4), |
| 4266 | | sequence alignment score = 176.6 |
| 4267 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4), |
| 4268 | | sequence alignment score = 462.2 |
| 4269 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 4270 | | sequence alignment score = 507.5 |
| 4271 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 4272 | | sequence alignment score = 497.7 |
| 4273 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 4274 | | sequence alignment score = 285.9 |
| 4275 | | RMSD between 454 pruned atom pairs is 1.226 angstroms; (across all 1515 pairs: |
| 4276 | | 13.805) |
| 4277 | | |
| 4278 | | |
| 4279 | | > mmaker #4/A-B to #2.5/A-B pair ss |
| 4280 | | |
| 4281 | | Parameters |
| 4282 | | --- |
| 4283 | | Chain pairing | ss |
| 4284 | | Alignment algorithm | Needleman-Wunsch |
| 4285 | | Similarity matrix | BLOSUM-62 |
| 4286 | | SS fraction | 0.3 |
| 4287 | | Gap open (HH/SS/other) | 18/18/6 |
| 4288 | | Gap extend | 1 |
| 4289 | | SS matrix | | | H | S | O |
| 4290 | | ---|---|---|--- |
| 4291 | | H | 6 | -9 | -6 |
| 4292 | | S | | 6 | -6 |
| 4293 | | O | | | 4 |
| 4294 | | Iteration cutoff | 2 |
| 4295 | | |
| 4296 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4), |
| 4297 | | sequence alignment score = 176.6 |
| 4298 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4), |
| 4299 | | sequence alignment score = 462.2 |
| 4300 | | RMSD between 160 pruned atom pairs is 1.140 angstroms; (across all 612 pairs: |
| 4301 | | 17.477) |
| 4302 | | |
| 4303 | | |
| 4304 | | > hide #!2.5 models |
| 4305 | | |
| 4306 | | > show #!2.5 models |
| 4307 | | |
| 4308 | | > hide #!4 models |
| 4309 | | |
| 4310 | | > show #!4 models |
| 4311 | | |
| 4312 | | > mmaker #4/A:1-204 to #2.5/A:63-303 pair ss |
| 4313 | | |
| 4314 | | Parameters |
| 4315 | | --- |
| 4316 | | Chain pairing | ss |
| 4317 | | Alignment algorithm | Needleman-Wunsch |
| 4318 | | Similarity matrix | BLOSUM-62 |
| 4319 | | SS fraction | 0.3 |
| 4320 | | Gap open (HH/SS/other) | 18/18/6 |
| 4321 | | Gap extend | 1 |
| 4322 | | SS matrix | | | H | S | O |
| 4323 | | ---|---|---|--- |
| 4324 | | H | 6 | -9 | -6 |
| 4325 | | S | | 6 | -6 |
| 4326 | | O | | | 4 |
| 4327 | | Iteration cutoff | 2 |
| 4328 | | |
| 4329 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4), |
| 4330 | | sequence alignment score = 74 |
| 4331 | | RMSD between 23 pruned atom pairs is 0.868 angstroms; (across all 163 pairs: |
| 4332 | | 12.128) |
| 4333 | | |
| 4334 | | |
| 4335 | | > mmaker #4/A:1-204 to #2.5/A:63-303 |
| 4336 | | |
| 4337 | | Parameters |
| 4338 | | --- |
| 4339 | | Chain pairing | bb |
| 4340 | | Alignment algorithm | Needleman-Wunsch |
| 4341 | | Similarity matrix | BLOSUM-62 |
| 4342 | | SS fraction | 0.3 |
| 4343 | | Gap open (HH/SS/other) | 18/18/6 |
| 4344 | | Gap extend | 1 |
| 4345 | | SS matrix | | | H | S | O |
| 4346 | | ---|---|---|--- |
| 4347 | | H | 6 | -9 | -6 |
| 4348 | | S | | 6 | -6 |
| 4349 | | O | | | 4 |
| 4350 | | Iteration cutoff | 2 |
| 4351 | | |
| 4352 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4), |
| 4353 | | sequence alignment score = 74 |
| 4354 | | RMSD between 23 pruned atom pairs is 0.868 angstroms; (across all 163 pairs: |
| 4355 | | 12.128) |
| 4356 | | |
| 4357 | | |
| 4358 | | > mmaker #4/C-E to #2.5/C-E |
| 4359 | | |
| 4360 | | Parameters |
| 4361 | | --- |
| 4362 | | Chain pairing | bb |
| 4363 | | Alignment algorithm | Needleman-Wunsch |
| 4364 | | Similarity matrix | BLOSUM-62 |
| 4365 | | SS fraction | 0.3 |
| 4366 | | Gap open (HH/SS/other) | 18/18/6 |
| 4367 | | Gap extend | 1 |
| 4368 | | SS matrix | | | H | S | O |
| 4369 | | ---|---|---|--- |
| 4370 | | H | 6 | -9 | -6 |
| 4371 | | S | | 6 | -6 |
| 4372 | | O | | | 4 |
| 4373 | | Iteration cutoff | 2 |
| 4374 | | |
| 4375 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain D (#4), |
| 4376 | | sequence alignment score = 525.7 |
| 4377 | | RMSD between 144 pruned atom pairs is 1.091 angstroms; (across all 312 pairs: |
| 4378 | | 9.612) |
| 4379 | | |
| 4380 | | |
| 4381 | | > mmaker #4/C-E to #2.5/C-E pair ss |
| 4382 | | |
| 4383 | | Parameters |
| 4384 | | --- |
| 4385 | | Chain pairing | ss |
| 4386 | | Alignment algorithm | Needleman-Wunsch |
| 4387 | | Similarity matrix | BLOSUM-62 |
| 4388 | | SS fraction | 0.3 |
| 4389 | | Gap open (HH/SS/other) | 18/18/6 |
| 4390 | | Gap extend | 1 |
| 4391 | | SS matrix | | | H | S | O |
| 4392 | | ---|---|---|--- |
| 4393 | | H | 6 | -9 | -6 |
| 4394 | | S | | 6 | -6 |
| 4395 | | O | | | 4 |
| 4396 | | Iteration cutoff | 2 |
| 4397 | | |
| 4398 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 4399 | | sequence alignment score = 507.5 |
| 4400 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 4401 | | sequence alignment score = 497.7 |
| 4402 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 4403 | | sequence alignment score = 285.9 |
| 4404 | | RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs: |
| 4405 | | 10.786) |
| 4406 | | |
| 4407 | | |
| 4408 | | > select #4 |
| 4409 | | |
| 4410 | | 14323 atoms, 14626 bonds, 46 pseudobonds, 1795 residues, 3 models selected |
| 4411 | | |
| 4412 | | > view matrix models |
| 4413 | | > #4,-0.79798,-0.5982,0.073302,205.84,-0.43439,0.48658,-0.75799,227.51,0.41776,-0.6367,-0.64814,194.31 |
| 4414 | | |
| 4415 | | > mmaker #4/C-E to #2.5/C-E pair ss |
| 4416 | | |
| 4417 | | Parameters |
| 4418 | | --- |
| 4419 | | Chain pairing | ss |
| 4420 | | Alignment algorithm | Needleman-Wunsch |
| 4421 | | Similarity matrix | BLOSUM-62 |
| 4422 | | SS fraction | 0.3 |
| 4423 | | Gap open (HH/SS/other) | 18/18/6 |
| 4424 | | Gap extend | 1 |
| 4425 | | SS matrix | | | H | S | O |
| 4426 | | ---|---|---|--- |
| 4427 | | H | 6 | -9 | -6 |
| 4428 | | S | | 6 | -6 |
| 4429 | | O | | | 4 |
| 4430 | | Iteration cutoff | 2 |
| 4431 | | |
| 4432 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 4433 | | sequence alignment score = 507.5 |
| 4434 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 4435 | | sequence alignment score = 497.7 |
| 4436 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 4437 | | sequence alignment score = 285.9 |
| 4438 | | RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs: |
| 4439 | | 10.786) |
| 4440 | | |
| 4441 | | |
| 4442 | | > view matrix models |
| 4443 | | > #4,-0.79798,-0.5982,0.073302,205.45,-0.43439,0.48658,-0.75799,226.22,0.41776,-0.6367,-0.64814,191.98 |
| 4444 | | |
| 4445 | | > view matrix models |
| 4446 | | > #4,-0.79798,-0.5982,0.073302,209.93,-0.43439,0.48658,-0.75799,227.2,0.41776,-0.6367,-0.64814,192.41 |
| 4447 | | |
| 4448 | | > fitmap #4 inMap #1.5 |
| 4449 | | |
| 4450 | | Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using |
| 4451 | | 14323 atoms |
| 4452 | | average map value = 0.07625, steps = 56 |
| 4453 | | shifted from previous position = 1.91 |
| 4454 | | rotated from previous position = 2.48 degrees |
| 4455 | | atoms outside contour = 11210, contour level = 0.2 |
| 4456 | | |
| 4457 | | Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5) |
| 4458 | | coordinates: |
| 4459 | | Matrix rotation and translation |
| 4460 | | -0.78474199 -0.61127299 0.10259313 209.87320078 |
| 4461 | | -0.47212854 0.48226270 -0.73791418 227.94133822 |
| 4462 | | 0.40159016 -0.62750938 -0.66705121 194.81853846 |
| 4463 | | Axis 0.31745756 -0.85973503 0.40009546 |
| 4464 | | Axis point 136.04597759 0.00000000 161.97288425 |
| 4465 | | Rotation angle (degrees) 169.98598502 |
| 4466 | | Shift along axis -51.39730412 |
| 4467 | | |
| 4468 | | |
| 4469 | | > fitmap #4 inMap #1.5 |
| 4470 | | |
| 4471 | | Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using |
| 4472 | | 14323 atoms |
| 4473 | | average map value = 0.07625, steps = 64 |
| 4474 | | shifted from previous position = 0.00132 |
| 4475 | | rotated from previous position = 0.0023 degrees |
| 4476 | | atoms outside contour = 11209, contour level = 0.2 |
| 4477 | | |
| 4478 | | Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5) |
| 4479 | | coordinates: |
| 4480 | | Matrix rotation and translation |
| 4481 | | -0.78473683 -0.61128584 0.10255597 209.87514322 |
| 4482 | | -0.47211620 0.48227795 -0.73791210 227.93970756 |
| 4483 | | 0.40161474 -0.62748514 -0.66705922 194.81680740 |
| 4484 | | Axis 0.31745723 -0.85973902 0.40008714 |
| 4485 | | Axis point 136.04429405 0.00000000 161.97271727 |
| 4486 | | Rotation angle (degrees) 169.98394312 |
| 4487 | | Shift along axis -51.39857903 |
| 4488 | | |
| 4489 | | |
| 4490 | | > hide #!2.5 models |
| 4491 | | |
| 4492 | | > show #!1.5 models |
| 4493 | | |
| 4494 | | > fitmap #4 inMap #1.5 |
| 4495 | | |
| 4496 | | Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using |
| 4497 | | 14323 atoms |
| 4498 | | average map value = 0.07626, steps = 44 |
| 4499 | | shifted from previous position = 0.012 |
| 4500 | | rotated from previous position = 0.00626 degrees |
| 4501 | | atoms outside contour = 11205, contour level = 0.2 |
| 4502 | | |
| 4503 | | Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5) |
| 4504 | | coordinates: |
| 4505 | | Matrix rotation and translation |
| 4506 | | -0.78471421 -0.61130779 0.10259825 209.88442579 |
| 4507 | | -0.47211893 0.48218581 -0.73797057 227.94307476 |
| 4508 | | 0.40165574 -0.62753457 -0.66698803 194.81451864 |
| 4509 | | Axis 0.31747459 -0.85971196 0.40013152 |
| 4510 | | Axis point 136.05289318 0.00000000 161.98082407 |
| 4511 | | Rotation angle (degrees) 169.98366802 |
| 4512 | | Shift along axis -51.38098601 |
| 4513 | | |
| 4514 | | |
| 4515 | | > view matrix models |
| 4516 | | > #4,-0.78471,-0.61131,0.1026,212.73,-0.47212,0.48219,-0.73797,223.43,0.40166,-0.62753,-0.66699,199.43 |
| 4517 | | |
| 4518 | | > view matrix models |
| 4519 | | > #4,-0.78471,-0.61131,0.1026,214.46,-0.47212,0.48219,-0.73797,230.2,0.40166,-0.62753,-0.66699,198.56 |
| 4520 | | |
| 4521 | | > view matrix models |
| 4522 | | > #4,-0.78471,-0.61131,0.1026,209.59,-0.47212,0.48219,-0.73797,230.98,0.40166,-0.62753,-0.66699,193.11 |
| 4523 | | |
| 4524 | | > ui mousemode right "rotate selected models" |
| 4525 | | |
| 4526 | | > view matrix models |
| 4527 | | > #4,-0.80188,-0.57899,0.14748,208.53,-0.52884,0.57293,-0.62616,228.87,0.27805,-0.5801,-0.76562,201.45 |
| 4528 | | |
| 4529 | | > fitmap #4 inMap #1.5 |
| 4530 | | |
| 4531 | | Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using |
| 4532 | | 14323 atoms |
| 4533 | | average map value = 0.07399, steps = 56 |
| 4534 | | shifted from previous position = 0.632 |
| 4535 | | rotated from previous position = 3.13 degrees |
| 4536 | | atoms outside contour = 11308, contour level = 0.2 |
| 4537 | | |
| 4538 | | Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5) |
| 4539 | | coordinates: |
| 4540 | | Matrix rotation and translation |
| 4541 | | -0.79223731 -0.58148948 0.18501356 206.95607859 |
| 4542 | | -0.54247696 0.53230593 -0.64989933 230.84620856 |
| 4543 | | 0.27942581 -0.61524010 -0.73715727 199.98606046 |
| 4544 | | Axis 0.32129214 -0.87520434 0.36164723 |
| 4545 | | Axis point 142.41452013 0.00000000 151.19162562 |
| 4546 | | Rotation angle (degrees) 176.90812245 |
| 4547 | | Shift along axis -63.21983717 |
| 4548 | | |
| 4549 | | |
| 4550 | | > hide #!1.5 models |
| 4551 | | |
| 4552 | | > show #!2.5 models |
| 4553 | | |
| 4554 | | > view matrix models |
| 4555 | | > #4,-0.79223,-0.58171,0.18435,206.98,-0.54159,0.53107,-0.65165,230.88,0.28117,-0.6161,-0.73578,199.87 |
| 4556 | | |
| 4557 | | > select clear |
| 4558 | | |
| 4559 | | > mmaker #4/C-E to #2.5/C-E pair ss |
| 4560 | | |
| 4561 | | Parameters |
| 4562 | | --- |
| 4563 | | Chain pairing | ss |
| 4564 | | Alignment algorithm | Needleman-Wunsch |
| 4565 | | Similarity matrix | BLOSUM-62 |
| 4566 | | SS fraction | 0.3 |
| 4567 | | Gap open (HH/SS/other) | 18/18/6 |
| 4568 | | Gap extend | 1 |
| 4569 | | SS matrix | | | H | S | O |
| 4570 | | ---|---|---|--- |
| 4571 | | H | 6 | -9 | -6 |
| 4572 | | S | | 6 | -6 |
| 4573 | | O | | | 4 |
| 4574 | | Iteration cutoff | 2 |
| 4575 | | |
| 4576 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 4577 | | sequence alignment score = 507.5 |
| 4578 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 4579 | | sequence alignment score = 497.7 |
| 4580 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 4581 | | sequence alignment score = 285.9 |
| 4582 | | RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs: |
| 4583 | | 10.786) |
| 4584 | | |
| 4585 | | |
| 4586 | | > hide #!2.5 models |
| 4587 | | |
| 4588 | | > show #!2.5 models |
| 4589 | | |
| 4590 | | > hide #!2.5 models |
| 4591 | | |
| 4592 | | > show #!3 models |
| 4593 | | |
| 4594 | | > hide #!4 models |
| 4595 | | |
| 4596 | | > hide #!3 models |
| 4597 | | |
| 4598 | | > show #!3 models |
| 4599 | | |
| 4600 | | > show #!2.5 models |
| 4601 | | |
| 4602 | | > hide #!2.5 models |
| 4603 | | |
| 4604 | | > show #!4 models |
| 4605 | | |
| 4606 | | > mmaker #4/C-E to #3/C-E pair ss |
| 4607 | | |
| 4608 | | Parameters |
| 4609 | | --- |
| 4610 | | Chain pairing | ss |
| 4611 | | Alignment algorithm | Needleman-Wunsch |
| 4612 | | Similarity matrix | BLOSUM-62 |
| 4613 | | SS fraction | 0.3 |
| 4614 | | Gap open (HH/SS/other) | 18/18/6 |
| 4615 | | Gap extend | 1 |
| 4616 | | SS matrix | | | H | S | O |
| 4617 | | ---|---|---|--- |
| 4618 | | H | 6 | -9 | -6 |
| 4619 | | S | | 6 | -6 |
| 4620 | | O | | | 4 |
| 4621 | | Iteration cutoff | 2 |
| 4622 | | |
| 4623 | | Matchmaker J100-ScRFC-PCNA-2DNA-wBRCT-Rsf090-v11.pdb, chain C (#3) with 3glf, |
| 4624 | | chain C (#4), sequence alignment score = 513.1 |
| 4625 | | Matchmaker J100-ScRFC-PCNA-2DNA-wBRCT-Rsf090-v11.pdb, chain D (#3) with 3glf, |
| 4626 | | chain D (#4), sequence alignment score = 484.7 |
| 4627 | | Matchmaker J100-ScRFC-PCNA-2DNA-wBRCT-Rsf090-v11.pdb, chain E (#3) with 3glf, |
| 4628 | | chain E (#4), sequence alignment score = 300 |
| 4629 | | RMSD between 303 pruned atom pairs is 1.218 angstroms; (across all 919 pairs: |
| 4630 | | 10.954) |
| 4631 | | |
| 4632 | | |
| 4633 | | > mmaker #4/C-E to #2.5/C-E pair ss |
| 4634 | | |
| 4635 | | Parameters |
| 4636 | | --- |
| 4637 | | Chain pairing | ss |
| 4638 | | Alignment algorithm | Needleman-Wunsch |
| 4639 | | Similarity matrix | BLOSUM-62 |
| 4640 | | SS fraction | 0.3 |
| 4641 | | Gap open (HH/SS/other) | 18/18/6 |
| 4642 | | Gap extend | 1 |
| 4643 | | SS matrix | | | H | S | O |
| 4644 | | ---|---|---|--- |
| 4645 | | H | 6 | -9 | -6 |
| 4646 | | S | | 6 | -6 |
| 4647 | | O | | | 4 |
| 4648 | | Iteration cutoff | 2 |
| 4649 | | |
| 4650 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 4651 | | sequence alignment score = 507.5 |
| 4652 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 4653 | | sequence alignment score = 497.7 |
| 4654 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 4655 | | sequence alignment score = 285.9 |
| 4656 | | RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs: |
| 4657 | | 10.786) |
| 4658 | | |
| 4659 | | |
| 4660 | | > mmaker #4/A-E to #2.5/A-E pair ss |
| 4661 | | |
| 4662 | | Parameters |
| 4663 | | --- |
| 4664 | | Chain pairing | ss |
| 4665 | | Alignment algorithm | Needleman-Wunsch |
| 4666 | | Similarity matrix | BLOSUM-62 |
| 4667 | | SS fraction | 0.3 |
| 4668 | | Gap open (HH/SS/other) | 18/18/6 |
| 4669 | | Gap extend | 1 |
| 4670 | | SS matrix | | | H | S | O |
| 4671 | | ---|---|---|--- |
| 4672 | | H | 6 | -9 | -6 |
| 4673 | | S | | 6 | -6 |
| 4674 | | O | | | 4 |
| 4675 | | Iteration cutoff | 2 |
| 4676 | | |
| 4677 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4), |
| 4678 | | sequence alignment score = 176.6 |
| 4679 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4), |
| 4680 | | sequence alignment score = 462.2 |
| 4681 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4), |
| 4682 | | sequence alignment score = 507.5 |
| 4683 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4), |
| 4684 | | sequence alignment score = 497.7 |
| 4685 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4), |
| 4686 | | sequence alignment score = 285.9 |
| 4687 | | RMSD between 454 pruned atom pairs is 1.226 angstroms; (across all 1515 pairs: |
| 4688 | | 13.805) |
| 4689 | | |
| 4690 | | |
| 4691 | | > hide #!4 models |
| 4692 | | |
| 4693 | | > show #!4 models |
| 4694 | | |
| 4695 | | > hide #!3 models |
| 4696 | | |
| 4697 | | > show #!3 models |
| 4698 | | |
| 4699 | | > hide #!3 models |
| 4700 | | |
| 4701 | | > show #!3 models |
| 4702 | | |
| 4703 | | > hide #!3 models |
| 4704 | | |
| 4705 | | > show #!3 models |
| 4706 | | |
| 4707 | | > hide #!3 models |
| 4708 | | |
| 4709 | | > hide #!4 models |
| 4710 | | |
| 4711 | | > show #!2.5 models |
| 4712 | | |
| 4713 | | > show #!5 models |
| 4714 | | |
| 4715 | | > view v1 |
| 4716 | | |
| 4717 | | > hide #!2.5 models |
| 4718 | | |
| 4719 | | > mmaker #5/A-E to #2.5/A-E pair ss |
| 4720 | | |
| 4721 | | Parameters |
| 4722 | | --- |
| 4723 | | Chain pairing | ss |
| 4724 | | Alignment algorithm | Needleman-Wunsch |
| 4725 | | Similarity matrix | BLOSUM-62 |
| 4726 | | SS fraction | 0.3 |
| 4727 | | Gap open (HH/SS/other) | 18/18/6 |
| 4728 | | Gap extend | 1 |
| 4729 | | SS matrix | | | H | S | O |
| 4730 | | ---|---|---|--- |
| 4731 | | H | 6 | -9 | -6 |
| 4732 | | S | | 6 | -6 |
| 4733 | | O | | | 4 |
| 4734 | | Iteration cutoff | 2 |
| 4735 | | |
| 4736 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3u5z, chain B (#5), |
| 4737 | | sequence alignment score = 259.6 |
| 4738 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3u5z, chain C (#5), |
| 4739 | | sequence alignment score = 428.2 |
| 4740 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3u5z, chain D (#5), |
| 4741 | | sequence alignment score = 465.2 |
| 4742 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3u5z, chain E (#5), |
| 4743 | | sequence alignment score = 445.3 |
| 4744 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3u5z, chain A (#5), |
| 4745 | | sequence alignment score = 105.3 |
| 4746 | | RMSD between 389 pruned atom pairs is 1.180 angstroms; (across all 1350 pairs: |
| 4747 | | 20.754) |
| 4748 | | |
| 4749 | | |
| 4750 | | > show #!2.5 models |
| 4751 | | |
| 4752 | | > hide #!2.5 models |
| 4753 | | |
| 4754 | | > select #5/K-R |
| 4755 | | |
| 4756 | | 16812 atoms, 17103 bonds, 14 pseudobonds, 2143 residues, 3 models selected |
| 4757 | | |
| 4758 | | > delete sel |
| 4759 | | |
| 4760 | | > delete #5/S-T |
| 4761 | | |
| 4762 | | > view v1 |
| 4763 | | |
| 4764 | | > show #!2.5 models |
| 4765 | | |
| 4766 | | > hide #!2.5 models |
| 4767 | | |
| 4768 | | > hide #!5 models |
| 4769 | | |
| 4770 | | > show #!2.5 models |
| 4771 | | |
| 4772 | | > show #!3 models |
| 4773 | | |
| 4774 | | > hide #!2.5 models |
| 4775 | | |
| 4776 | | > show #!2.5 models |
| 4777 | | |
| 4778 | | > hide #!3 models |
| 4779 | | |
| 4780 | | > hide #!2.5 models |
| 4781 | | |
| 4782 | | > show #!3 models |
| 4783 | | |
| 4784 | | > hide #!3 models |
| 4785 | | |
| 4786 | | > show #!4 models |
| 4787 | | |
| 4788 | | > select #4/F |
| 4789 | | |
| 4790 | | Nothing selected |
| 4791 | | |
| 4792 | | > show #!2.5 models |
| 4793 | | |
| 4794 | | > hide #!2.5 models |
| 4795 | | |
| 4796 | | > hide #!4 models |
| 4797 | | |
| 4798 | | > show #!2.5 models |
| 4799 | | |
| 4800 | | > hide #!2.5 models |
| 4801 | | |
| 4802 | | > show #!3 models |
| 4803 | | |
| 4804 | | > hide #!3 models |
| 4805 | | |
| 4806 | | > show #!4 models |
| 4807 | | |
| 4808 | | > setattr #4/K c chain_id I |
| 4809 | | |
| 4810 | | Assigning chain_id attribute to 1 item |
| 4811 | | |
| 4812 | | > setattr #4/L c chain_id J |
| 4813 | | |
| 4814 | | Assigning chain_id attribute to 1 item |
| 4815 | | |
| 4816 | | > hide #!4 models |
| 4817 | | |
| 4818 | | > show #!5 models |
| 4819 | | |
| 4820 | | > view v1 |
| 4821 | | |
| 4822 | | > show #!2.5 models |
| 4823 | | |
| 4824 | | > hide #!5 models |
| 4825 | | |
| 4826 | | > hide #!2.5 models |
| 4827 | | |
| 4828 | | > show #!5 models |
| 4829 | | |
| 4830 | | > show #!2.5 models |
| 4831 | | |
| 4832 | | > hide #!2.5 models |
| 4833 | | |
| 4834 | | > setattr #5/F c chain_id Q |
| 4835 | | |
| 4836 | | Assigning chain_id attribute to 1 item |
| 4837 | | |
| 4838 | | > setattr #5/H c chain_id F |
| 4839 | | |
| 4840 | | Assigning chain_id attribute to 1 item |
| 4841 | | |
| 4842 | | > setattr #5/Q c chain_id H |
| 4843 | | |
| 4844 | | Assigning chain_id attribute to 1 item |
| 4845 | | |
| 4846 | | > show #!2.5 models |
| 4847 | | |
| 4848 | | > mmaker #5/A-H to #2.5/A-H pair ss |
| 4849 | | |
| 4850 | | Parameters |
| 4851 | | --- |
| 4852 | | Chain pairing | ss |
| 4853 | | Alignment algorithm | Needleman-Wunsch |
| 4854 | | Similarity matrix | BLOSUM-62 |
| 4855 | | SS fraction | 0.3 |
| 4856 | | Gap open (HH/SS/other) | 18/18/6 |
| 4857 | | Gap extend | 1 |
| 4858 | | SS matrix | | | H | S | O |
| 4859 | | ---|---|---|--- |
| 4860 | | H | 6 | -9 | -6 |
| 4861 | | S | | 6 | -6 |
| 4862 | | O | | | 4 |
| 4863 | | Iteration cutoff | 2 |
| 4864 | | |
| 4865 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3u5z, chain B (#5), |
| 4866 | | sequence alignment score = 259.6 |
| 4867 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3u5z, chain C (#5), |
| 4868 | | sequence alignment score = 428.2 |
| 4869 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3u5z, chain D (#5), |
| 4870 | | sequence alignment score = 465.2 |
| 4871 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3u5z, chain E (#5), |
| 4872 | | sequence alignment score = 445.3 |
| 4873 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3u5z, chain A (#5), |
| 4874 | | sequence alignment score = 105.3 |
| 4875 | | Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with 3u5z, chain G (#5), |
| 4876 | | sequence alignment score = 85.8 |
| 4877 | | Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with 3u5z, chain F (#5), |
| 4878 | | sequence alignment score = 162.6 |
| 4879 | | Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with 3u5z, chain H (#5), |
| 4880 | | sequence alignment score = 121.6 |
| 4881 | | RMSD between 390 pruned atom pairs is 1.184 angstroms; (across all 1959 pairs: |
| 4882 | | 30.640) |
| 4883 | | |
| 4884 | | |
| 4885 | | > hide #!2.5 models |
| 4886 | | |
| 4887 | | > show #!2.5 models |
| 4888 | | |
| 4889 | | > cartoon style nucleic xsection oval width 2.5 thickness 2.5 |
| 4890 | | |
| 4891 | | > cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true |
| 4892 | | > xsection oval width 2.75 thickness 1 arrowScale 1.5 |
| 4893 | | |
| 4894 | | > hide #!5 models |
| 4895 | | |
| 4896 | | > show #!4 models |
| 4897 | | |
| 4898 | | > hide #!4 models |
| 4899 | | |
| 4900 | | > show #!3 models |
| 4901 | | |
| 4902 | | > kssp #3-5 |
| 4903 | | |
| 4904 | | Unknown command: kssp #3-5 |
| 4905 | | |
| 4906 | | > hide #!2.5 models |
| 4907 | | |
| 4908 | | > show #!2.5 models |
| 4909 | | |
| 4910 | | > kssp #3 |
| 4911 | | |
| 4912 | | Unknown command: kssp #3 |
| 4913 | | |
| 4914 | | > dssp #3 |
| 4915 | | |
| 4916 | | > hide #!2.5 models |
| 4917 | | |
| 4918 | | > show #!2.5 models |
| 4919 | | |
| 4920 | | > hide #!3 models |
| 4921 | | |
| 4922 | | > show #!3 models |
| 4923 | | |
| 4924 | | > hide #!3 models |
| 4925 | | |
| 4926 | | > show #!4 models |
| 4927 | | |
| 4928 | | > hide #!2.5 models |
| 4929 | | |
| 4930 | | > dssp #4 |
| 4931 | | |
| 4932 | | > undo |
| 4933 | | |
| 4934 | | > dssp #4 |
| 4935 | | |
| 4936 | | > undo |
| 4937 | | |
| 4938 | | > hide #!4 models |
| 4939 | | |
| 4940 | | > show #!5 models |
| 4941 | | |
| 4942 | | > dssp #5 |
| 4943 | | |
| 4944 | | > undo |
| 4945 | | |
| 4946 | | > show #!2.5 models |
| 4947 | | |
| 4948 | | > view v1 |
| 4949 | | |
| 4950 | | [Repeated 1 time(s)] |
| 4951 | | |
| 4952 | | > ui mousemode right select |
| 4953 | | |
| 4954 | | > windowsize 1100 609 |
| 4955 | | |
| 4956 | | > view v1 |
| 4957 | | |
| 4958 | | > windowsize 1100 609 |
| 4959 | | |
| 4960 | | [Repeated 1 time(s)] |
| 4961 | | |
| 4962 | | > windowsize 1108 609 |
| 4963 | | |
| 4964 | | > windowsize 1100 609 |
| 4965 | | |
| 4966 | | > windowsize 1100 616 |
| 4967 | | |
| 4968 | | > windowsize 1100 609 |
| 4969 | | |
| 4970 | | > 00 |
| 4971 | | |
| 4972 | | Unknown command: 00 |
| 4973 | | |
| 4974 | | > windowsize 1100 609 |
| 4975 | | |
| 4976 | | [Repeated 2 time(s)] |
| 4977 | | |
| 4978 | | > view v1 |
| 4979 | | |
| 4980 | | [Repeated 1 time(s)] |
| 4981 | | |
| 4982 | | > windowsize 1100 609 |
| 4983 | | |
| 4984 | | [Repeated 1 time(s)] |
| 4985 | | |
| 4986 | | > view v1 |
| 4987 | | |
| 4988 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 4989 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v2.cxs" |
| 4990 | | |
| 4991 | | > color /A #FFB381 |
| 4992 | | |
| 4993 | | > color /B #D7819F |
| 4994 | | |
| 4995 | | > color /C #B48FE3 |
| 4996 | | |
| 4997 | | > color /D #D7CD85 |
| 4998 | | |
| 4999 | | > color /E salmon |
| 5000 | | |
| 5001 | | > color /F navajo white |
| 5002 | | |
| 5003 | | > color /G #CAC6FD |
| 5004 | | |
| 5005 | | > color /H plum |
| 5006 | | |
| 5007 | | > color /I medium orchid |
| 5008 | | |
| 5009 | | > color /J light sky blue |
| 5010 | | |
| 5011 | | > color /K #E7F981 |
| 5012 | | |
| 5013 | | > hide #!5 models |
| 5014 | | |
| 5015 | | > hide #!2.5 models |
| 5016 | | |
| 5017 | | > show #!3 models |
| 5018 | | |
| 5019 | | > hide #!3 models |
| 5020 | | |
| 5021 | | > show #!4 models |
| 5022 | | |
| 5023 | | > hide #!4 models |
| 5024 | | |
| 5025 | | > show #!5 models |
| 5026 | | |
| 5027 | | > show #!2.5 models |
| 5028 | | |
| 5029 | | > mmaker #5/A-H to #2.5/A-H pair ss |
| 5030 | | |
| 5031 | | Parameters |
| 5032 | | --- |
| 5033 | | Chain pairing | ss |
| 5034 | | Alignment algorithm | Needleman-Wunsch |
| 5035 | | Similarity matrix | BLOSUM-62 |
| 5036 | | SS fraction | 0.3 |
| 5037 | | Gap open (HH/SS/other) | 18/18/6 |
| 5038 | | Gap extend | 1 |
| 5039 | | SS matrix | | | H | S | O |
| 5040 | | ---|---|---|--- |
| 5041 | | H | 6 | -9 | -6 |
| 5042 | | S | | 6 | -6 |
| 5043 | | O | | | 4 |
| 5044 | | Iteration cutoff | 2 |
| 5045 | | |
| 5046 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3u5z, chain B (#5), |
| 5047 | | sequence alignment score = 259.6 |
| 5048 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3u5z, chain C (#5), |
| 5049 | | sequence alignment score = 428.2 |
| 5050 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3u5z, chain D (#5), |
| 5051 | | sequence alignment score = 465.2 |
| 5052 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3u5z, chain E (#5), |
| 5053 | | sequence alignment score = 445.3 |
| 5054 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3u5z, chain A (#5), |
| 5055 | | sequence alignment score = 105.3 |
| 5056 | | Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with 3u5z, chain G (#5), |
| 5057 | | sequence alignment score = 85.8 |
| 5058 | | Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with 3u5z, chain F (#5), |
| 5059 | | sequence alignment score = 162.6 |
| 5060 | | Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with 3u5z, chain H (#5), |
| 5061 | | sequence alignment score = 121.6 |
| 5062 | | RMSD between 390 pruned atom pairs is 1.184 angstroms; (across all 1959 pairs: |
| 5063 | | 30.640) |
| 5064 | | |
| 5065 | | |
| 5066 | | > hide #!2.5 models |
| 5067 | | |
| 5068 | | > show #!2.5 models |
| 5069 | | |
| 5070 | | > hide #!2.5 models |
| 5071 | | |
| 5072 | | > show #!2.5 models |
| 5073 | | |
| 5074 | | > hide #!2.5 models |
| 5075 | | |
| 5076 | | > show #!2.5 models |
| 5077 | | |
| 5078 | | > hide #!2.5 models |
| 5079 | | |
| 5080 | | > show #!2.5 models |
| 5081 | | |
| 5082 | | > hide #!5 models |
| 5083 | | |
| 5084 | | > show #!5 models |
| 5085 | | |
| 5086 | | > hide #!5 models |
| 5087 | | |
| 5088 | | > show #!5 models |
| 5089 | | |
| 5090 | | > hide #!2.5 models |
| 5091 | | |
| 5092 | | > show #!2.5 models |
| 5093 | | |
| 5094 | | > hide #!2.5 models |
| 5095 | | |
| 5096 | | > show #!2.5 models |
| 5097 | | |
| 5098 | | > view v1 |
| 5099 | | |
| 5100 | | > hide #!5 models |
| 5101 | | |
| 5102 | | > show #!5 models |
| 5103 | | |
| 5104 | | > hide #!2.5 models |
| 5105 | | |
| 5106 | | > show #!3 models |
| 5107 | | |
| 5108 | | > select #3-5/I-L |
| 5109 | | |
| 5110 | | 2677 atoms, 2991 bonds, 61 pseudobonds, 131 residues, 5 models selected |
| 5111 | | |
| 5112 | | > show sel & #!3,5 atoms |
| 5113 | | |
| 5114 | | > nucleotides sel & #!3,5 stubs |
| 5115 | | |
| 5116 | | > select clear |
| 5117 | | |
| 5118 | | > hide #!3 models |
| 5119 | | |
| 5120 | | > show #!4 models |
| 5121 | | |
| 5122 | | > hide #!5 models |
| 5123 | | |
| 5124 | | > select #4/I-L |
| 5125 | | |
| 5126 | | 487 atoms, 543 bonds, 22 pseudobonds, 24 residues, 2 models selected |
| 5127 | | |
| 5128 | | > nucleotides sel stubs |
| 5129 | | |
| 5130 | | > show sel atoms |
| 5131 | | |
| 5132 | | > select clear |
| 5133 | | |
| 5134 | | > show #!2.5 models |
| 5135 | | |
| 5136 | | > hide #!2.5 models |
| 5137 | | |
| 5138 | | > show #!2.5 models |
| 5139 | | |
| 5140 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 5141 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v2.cxs" |
| 5142 | | |
| 5143 | | > hide #!4 models |
| 5144 | | |
| 5145 | | > hide #!2.5 models |
| 5146 | | |
| 5147 | | > show #!3 models |
| 5148 | | |
| 5149 | | > view v1 |
| 5150 | | |
| 5151 | | [Repeated 1 time(s)] |
| 5152 | | |
| 5153 | | > select #3/F:87-94 |
| 5154 | | |
| 5155 | | 59 atoms, 58 bonds, 8 residues, 1 model selected |
| 5156 | | |
| 5157 | | > select #3/F:1-5,87-94 |
| 5158 | | |
| 5159 | | 98 atoms, 96 bonds, 13 residues, 1 model selected |
| 5160 | | |
| 5161 | | > select #3/F:1-5,59-64,87-94 |
| 5162 | | |
| 5163 | | 154 atoms, 153 bonds, 19 residues, 1 model selected |
| 5164 | | |
| 5165 | | > select #3/F:1-5,59-64,87-94/H:157-162 |
| 5166 | | |
| 5167 | | 200 atoms, 198 bonds, 25 residues, 1 model selected |
| 5168 | | |
| 5169 | | > select |
| 5170 | | > #3/H:1-6,58-63,87-92,110-117,176-181,168-173,157-161,196-199,203-207/F:87-93,2-6,58-62,46-52,34-40,111-117,196-199/G:3-6,59-62,157-162,167-172,176-182,203-207 |
| 5171 | | |
| 5172 | | 989 atoms, 979 bonds, 126 residues, 1 model selected |
| 5173 | | |
| 5174 | | > setattr sel res ss_type 2 |
| 5175 | | |
| 5176 | | Assigning ss_type attribute to 126 items |
| 5177 | | |
| 5178 | | > setattr sel res ss_id 88 |
| 5179 | | |
| 5180 | | Assigning ss_id attribute to 126 items |
| 5181 | | |
| 5182 | | > select clear |
| 5183 | | |
| 5184 | | > hide #!3 models |
| 5185 | | |
| 5186 | | > show #!3 models |
| 5187 | | |
| 5188 | | > hide #!3 models |
| 5189 | | |
| 5190 | | > show #!4 models |
| 5191 | | |
| 5192 | | > hide #!4 models |
| 5193 | | |
| 5194 | | > show #!5 models |
| 5195 | | |
| 5196 | | > view v1 |
| 5197 | | |
| 5198 | | > hide #!5 models |
| 5199 | | |
| 5200 | | > show #!4 models |
| 5201 | | |
| 5202 | | > select #4/A:61-69 |
| 5203 | | |
| 5204 | | 75 atoms, 77 bonds, 9 residues, 1 model selected |
| 5205 | | |
| 5206 | | > setattr sel res ss_type 1 |
| 5207 | | |
| 5208 | | Assigning ss_type attribute to 9 items |
| 5209 | | |
| 5210 | | > setattr sel res ss_id 88 |
| 5211 | | |
| 5212 | | Assigning ss_id attribute to 9 items |
| 5213 | | |
| 5214 | | > select clear |
| 5215 | | |
| 5216 | | > view v1 |
| 5217 | | |
| 5218 | | > show #!2.5 models |
| 5219 | | |
| 5220 | | > hide #!4 models |
| 5221 | | |
| 5222 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 5223 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v2.cxs" |
| 5224 | | |
| 5225 | | > rename #3 ScRFC-PCNA-2DNA-wBRCT #3.1 |
| 5226 | | |
| 5227 | | Expected a keyword |
| 5228 | | |
| 5229 | | > rename #3 ScRFC-PCNA-2DNA-wBRCT id #3.1 |
| 5230 | | |
| 5231 | | > rename #4 EcLoader-DNA-3GLF id #3.2 |
| 5232 | | |
| 5233 | | > rename #5 T4-Clamp-Loader-DNA-3U5Z id #3.3 |
| 5234 | | |
| 5235 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 5236 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v2.cxs" |
| 5237 | | |
| 5238 | | > hide #!3 models |
| 5239 | | |
| 5240 | | > show #!1.5 models |
| 5241 | | |
| 5242 | | > volume #1.5 level 0.15 |
| 5243 | | |
| 5244 | | > volume #1.5 level 0.12 |
| 5245 | | |
| 5246 | | > volume #1.5 level 0.2 |
| 5247 | | |
| 5248 | | > view v1 |
| 5249 | | |
| 5250 | | > hide #!1 models |
| 5251 | | |
| 5252 | | > view v1 |
| 5253 | | |
| 5254 | | > show #!3.1 models |
| 5255 | | |
| 5256 | | > hide #!3.1 models |
| 5257 | | |
| 5258 | | > show #!3.1 models |
| 5259 | | |
| 5260 | | > hide #!3.1 models |
| 5261 | | |
| 5262 | | > view v1 |
| 5263 | | |
| 5264 | | > select #2.5/I:27-45/J |
| 5265 | | |
| 5266 | | 699 atoms, 780 bonds, 35 residues, 1 model selected |
| 5267 | | |
| 5268 | | > ui tool show H-Bonds |
| 5269 | | |
| 5270 | | Invalid H-bond GUI 'slop_color' attrbute value, using default: Invalid color |
| 5271 | | name or specifier |
| 5272 | | |
| 5273 | | [Repeated 1 time(s)] |
| 5274 | | |
| 5275 | | > hbonds sel color #00fdff showDist true restrict cross interModel false |
| 5276 | | > distSlop 0.5 intraMol false intraRes false select true reveal true log true |
| 5277 | | |
| 5278 | | |
| 5279 | | Finding intramodel H-bonds |
| 5280 | | Constraints relaxed by 0.5 angstroms and 20 degrees |
| 5281 | | Models used: |
| 5282 | | 2.5 Stat5-ref59-v3.pdb |
| 5283 | | |
| 5284 | | 14 H-bonds |
| 5285 | | H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): |
| 5286 | | Stat5-ref59-v3.pdb #2.5/A MET 163 N Stat5-ref59-v3.pdb #2.5/I DT 34 OP1 no hydrogen 2.652 N/A |
| 5287 | | Stat5-ref59-v3.pdb #2.5/A ARG 199 NH2 Stat5-ref59-v3.pdb #2.5/J DG 20 O3' no hydrogen 2.742 N/A |
| 5288 | | Stat5-ref59-v3.pdb #2.5/B ARG 90 NH2 Stat5-ref59-v3.pdb #2.5/I DG 33 OP1 no hydrogen 3.214 N/A |
| 5289 | | Stat5-ref59-v3.pdb #2.5/C ILE 90 N Stat5-ref59-v3.pdb #2.5/I DT 30 OP1 no hydrogen 2.729 N/A |
| 5290 | | Stat5-ref59-v3.pdb #2.5/C ARG 94 NH1 Stat5-ref59-v3.pdb #2.5/I DC 31 OP2 no hydrogen 3.513 N/A |
| 5291 | | Stat5-ref59-v3.pdb #2.5/C ARG 94 NH2 Stat5-ref59-v3.pdb #2.5/I DC 31 OP2 no hydrogen 3.164 N/A |
| 5292 | | Stat5-ref59-v3.pdb #2.5/C THR 123 OG1 Stat5-ref59-v3.pdb #2.5/I DT 30 OP1 no hydrogen 3.454 N/A |
| 5293 | | Stat5-ref59-v3.pdb #2.5/D ILE 103 N Stat5-ref59-v3.pdb #2.5/I DT 28 OP1 no hydrogen 2.787 N/A |
| 5294 | | Stat5-ref59-v3.pdb #2.5/D ARG 107 NH1 Stat5-ref59-v3.pdb #2.5/I DT 29 OP1 no hydrogen 3.397 N/A |
| 5295 | | Stat5-ref59-v3.pdb #2.5/D ARG 107 NH2 Stat5-ref59-v3.pdb #2.5/I DT 29 OP1 no hydrogen 3.384 N/A |
| 5296 | | Stat5-ref59-v3.pdb #2.5/D ARG 107 NH2 Stat5-ref59-v3.pdb #2.5/I DT 29 OP2 no hydrogen 3.185 N/A |
| 5297 | | Stat5-ref59-v3.pdb #2.5/E ASN 80 ND2 Stat5-ref59-v3.pdb #2.5/J DG 20 OP2 no hydrogen 2.915 N/A |
| 5298 | | Stat5-ref59-v3.pdb #2.5/E ARG 106 NH2 Stat5-ref59-v3.pdb #2.5/I DT 27 OP1 no hydrogen 3.474 N/A |
| 5299 | | Stat5-ref59-v3.pdb #2.5/G LYS 34 NZ Stat5-ref59-v3.pdb #2.5/J DA 17 OP1 no hydrogen 3.049 N/A |
| 5300 | | |
| 5301 | | |
| 5302 | | |
| 5303 | | 14 hydrogen bonds found |
| 5304 | | |
| 5305 | | > select up |
| 5306 | | |
| 5307 | | 287 atoms, 293 bonds, 20 residues, 1 model selected |
| 5308 | | |
| 5309 | | > show sel atoms |
| 5310 | | |
| 5311 | | [Repeated 1 time(s)] |
| 5312 | | |
| 5313 | | > style sel stick |
| 5314 | | |
| 5315 | | Changed 287 atom styles |
| 5316 | | |
| 5317 | | > color sel byhetero |
| 5318 | | |
| 5319 | | > hide #!3 models |
| 5320 | | |
| 5321 | | > hide #!2 models |
| 5322 | | |
| 5323 | | > show #!3.1 models |
| 5324 | | |
| 5325 | | > hide #!3.1 models |
| 5326 | | |
| 5327 | | > show #!2 models |
| 5328 | | |
| 5329 | | > view v1 |
| 5330 | | |
| 5331 | | > select #2.5/A:162-164 |
| 5332 | | |
| 5333 | | 26 atoms, 25 bonds, 3 residues, 1 model selected |
| 5334 | | |
| 5335 | | > select #2.5/A:162-164,195-199 |
| 5336 | | |
| 5337 | | 71 atoms, 69 bonds, 8 residues, 1 model selected |
| 5338 | | |
| 5339 | | > select #2.5/A:162-164,195-199/B:86-90 |
| 5340 | | |
| 5341 | | 112 atoms, 109 bonds, 13 residues, 1 model selected |
| 5342 | | |
| 5343 | | > select #2.5/A:162-164,195-199/B:86-90,121-126 |
| 5344 | | |
| 5345 | | 149 atoms, 145 bonds, 19 residues, 1 model selected |
| 5346 | | |
| 5347 | | > select #2.5/A:162-164,195-199/B:86-90,121-125 |
| 5348 | | |
| 5349 | | 144 atoms, 140 bonds, 18 residues, 1 model selected |
| 5350 | | |
| 5351 | | > select #2.5/A:162-164,195-199/B:86-90,121-125/C:90-94 |
| 5352 | | |
| 5353 | | 185 atoms, 180 bonds, 23 residues, 1 model selected |
| 5354 | | |
| 5355 | | > select #2.5/A:162-164,195-199/B:86-90,121-125/C:90-94,123-126 |
| 5356 | | |
| 5357 | | 210 atoms, 204 bonds, 27 residues, 1 model selected |
| 5358 | | |
| 5359 | | > select #2.5/A:162-164,195-199/B:86-90,121-125/C:90-94,123-126/D:103-107 |
| 5360 | | |
| 5361 | | 250 atoms, 243 bonds, 32 residues, 1 model selected |
| 5362 | | |
| 5363 | | > select |
| 5364 | | > #2.5/A:162-164,195-199/B:86-90,121-125/C:90-94,123-126/D:103-107,147-152 |
| 5365 | | |
| 5366 | | 288 atoms, 280 bonds, 38 residues, 1 model selected |
| 5367 | | |
| 5368 | | > select |
| 5369 | | > #2.5/A:162-164,195-199/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151 |
| 5370 | | |
| 5371 | | 283 atoms, 275 bonds, 37 residues, 1 model selected |
| 5372 | | |
| 5373 | | > show #!3.1 models |
| 5374 | | |
| 5375 | | > hide #!3.1 models |
| 5376 | | |
| 5377 | | > select |
| 5378 | | > #2.5/A:162-164,195-199,228-243/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151 |
| 5379 | | |
| 5380 | | 421 atoms, 416 bonds, 53 residues, 1 model selected |
| 5381 | | |
| 5382 | | > select |
| 5383 | | > #2.5/A:162-164,195-199,228-243/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:106-109 |
| 5384 | | |
| 5385 | | 455 atoms, 449 bonds, 57 residues, 1 model selected |
| 5386 | | |
| 5387 | | > select |
| 5388 | | > #2.5/A:162-164,195-199,228-243/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:106-109,149-152 |
| 5389 | | |
| 5390 | | 482 atoms, 475 bonds, 61 residues, 1 model selected |
| 5391 | | |
| 5392 | | > view v1 |
| 5393 | | |
| 5394 | | [Repeated 1 time(s)] |
| 5395 | | |
| 5396 | | > hide #2.5 & (~sel | /I:27-45/J) cartoons |
| 5397 | | |
| 5398 | | > undo |
| 5399 | | |
| 5400 | | > hide #2.5 & ~(sel | /I:27-45/J) cartoons |
| 5401 | | |
| 5402 | | > hide #2.5/I:1-27/K |
| 5403 | | |
| 5404 | | > select clear |
| 5405 | | |
| 5406 | | > view v1 |
| 5407 | | |
| 5408 | | > select |
| 5409 | | > #2.5/A:162-164,195-199,228-243/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:76-84,106-109,149-152 |
| 5410 | | |
| 5411 | | 552 atoms, 544 bonds, 70 residues, 1 model selected |
| 5412 | | |
| 5413 | | > show sel cartoons |
| 5414 | | |
| 5415 | | > select |
| 5416 | | > #2.5/A:162-164,195-199,228-243/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:74-84,106-109,149-152 |
| 5417 | | |
| 5418 | | 572 atoms, 565 bonds, 72 residues, 1 model selected |
| 5419 | | |
| 5420 | | > show sel cartoons |
| 5421 | | |
| 5422 | | > select clear |
| 5423 | | |
| 5424 | | > select #2.5/A:194 |
| 5425 | | |
| 5426 | | 10 atoms, 10 bonds, 1 residue, 1 model selected |
| 5427 | | |
| 5428 | | > view v1 |
| 5429 | | |
| 5430 | | > show #!3.1 models |
| 5431 | | |
| 5432 | | > hide #!3.1 models |
| 5433 | | |
| 5434 | | > view v1 |
| 5435 | | |
| 5436 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 5437 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v4.cxs" |
| 5438 | | |
| 5439 | | > view v1 |
| 5440 | | |
| 5441 | | > select |
| 5442 | | > #2.5/A:162-164,195-199,226-245/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:74-84,106-109,149-152 |
| 5443 | | |
| 5444 | | 604 atoms, 598 bonds, 76 residues, 1 model selected |
| 5445 | | |
| 5446 | | > show sel cartoons |
| 5447 | | |
| 5448 | | > select |
| 5449 | | > #2.5/A:162-164,195-199,223-248/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:74-84,106-109,149-152 |
| 5450 | | |
| 5451 | | 649 atoms, 643 bonds, 82 residues, 1 model selected |
| 5452 | | |
| 5453 | | > show sel cartoons |
| 5454 | | |
| 5455 | | > select clear |
| 5456 | | |
| 5457 | | > show #!3.1 models |
| 5458 | | |
| 5459 | | > view v1 |
| 5460 | | |
| 5461 | | > hide #!3.1 models |
| 5462 | | |
| 5463 | | > view v1 |
| 5464 | | |
| 5465 | | > hide #!3 models |
| 5466 | | |
| 5467 | | > show #!3.1 models |
| 5468 | | |
| 5469 | | > hide #!2 models |
| 5470 | | |
| 5471 | | > hide #!3 models |
| 5472 | | |
| 5473 | | > show #!3 models |
| 5474 | | |
| 5475 | | > select #3.1/I-J |
| 5476 | | |
| 5477 | | 860 atoms, 962 bonds, 42 residues, 1 model selected |
| 5478 | | |
| 5479 | | > ui tool show H-Bonds |
| 5480 | | |
| 5481 | | Invalid H-bond GUI 'slop_color' attrbute value, using default: Invalid color |
| 5482 | | name or specifier |
| 5483 | | |
| 5484 | | [Repeated 1 time(s)] |
| 5485 | | |
| 5486 | | > hbonds sel color #00fdff showDist true restrict cross interModel false |
| 5487 | | > distSlop 0.5 intraMol false intraRes false select true reveal true log true |
| 5488 | | |
| 5489 | | |
| 5490 | | Finding intramodel H-bonds |
| 5491 | | Constraints relaxed by 0.5 angstroms and 20 degrees |
| 5492 | | Models used: |
| 5493 | | 3.1 ScRFC-PCNA-2DNA-wBRCT |
| 5494 | | |
| 5495 | | 11 H-bonds |
| 5496 | | H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): |
| 5497 | | ScRFC-PCNA-2DNA-wBRCT #3.1/A SER 384 OG ScRFC-PCNA-2DNA-wBRCT #3.1/I DG 20 OP1 no hydrogen 2.975 N/A |
| 5498 | | ScRFC-PCNA-2DNA-wBRCT #3.1/A ARG 434 NH1 ScRFC-PCNA-2DNA-wBRCT #3.1/J DG 14 N3 no hydrogen 3.579 N/A |
| 5499 | | ScRFC-PCNA-2DNA-wBRCT #3.1/A ARG 434 NH2 ScRFC-PCNA-2DNA-wBRCT #3.1/J DA 13 N3 no hydrogen 3.306 N/A |
| 5500 | | ScRFC-PCNA-2DNA-wBRCT #3.1/A GLN 636 NE2 ScRFC-PCNA-2DNA-wBRCT #3.1/I DA 12 N3 no hydrogen 2.550 N/A |
| 5501 | | ScRFC-PCNA-2DNA-wBRCT #3.1/C ILE 90 N ScRFC-PCNA-2DNA-wBRCT #3.1/I DA 16 OP1 no hydrogen 3.009 N/A |
| 5502 | | ScRFC-PCNA-2DNA-wBRCT #3.1/C ARG 94 NH1 ScRFC-PCNA-2DNA-wBRCT #3.1/I DC 17 OP1 no hydrogen 3.400 N/A |
| 5503 | | ScRFC-PCNA-2DNA-wBRCT #3.1/C ARG 94 NH2 ScRFC-PCNA-2DNA-wBRCT #3.1/I DC 17 OP2 no hydrogen 3.025 N/A |
| 5504 | | ScRFC-PCNA-2DNA-wBRCT #3.1/C THR 123 OG1 ScRFC-PCNA-2DNA-wBRCT #3.1/I DA 16 OP1 no hydrogen 3.383 N/A |
| 5505 | | ScRFC-PCNA-2DNA-wBRCT #3.1/D ILE 103 N ScRFC-PCNA-2DNA-wBRCT #3.1/I DG 14 OP1 no hydrogen 3.178 N/A |
| 5506 | | ScRFC-PCNA-2DNA-wBRCT #3.1/E ASN 80 ND2 ScRFC-PCNA-2DNA-wBRCT #3.1/J DG 14 OP2 no hydrogen 3.382 N/A |
| 5507 | | ScRFC-PCNA-2DNA-wBRCT #3.1/I DT 9 N3 ScRFC-PCNA-2DNA-wBRCT #3.1/A SER 674 OG no hydrogen 3.284 N/A |
| 5508 | | |
| 5509 | | |
| 5510 | | |
| 5511 | | 11 hydrogen bonds found |
| 5512 | | |
| 5513 | | > select up |
| 5514 | | |
| 5515 | | 242 atoms, 249 bonds, 17 residues, 1 model selected |
| 5516 | | |
| 5517 | | > style sel stick |
| 5518 | | |
| 5519 | | Changed 242 atom styles |
| 5520 | | |
| 5521 | | > color sel byhetero |
| 5522 | | |
| 5523 | | > select #3.1/A:384-387 |
| 5524 | | |
| 5525 | | 30 atoms, 29 bonds, 4 residues, 1 model selected |
| 5526 | | |
| 5527 | | > select #3.1/A:384-387,431-440 |
| 5528 | | |
| 5529 | | 93 atoms, 91 bonds, 14 residues, 1 model selected |
| 5530 | | |
| 5531 | | > show #!2 models |
| 5532 | | |
| 5533 | | > hide #!2 models |
| 5534 | | |
| 5535 | | > show #!2 models |
| 5536 | | |
| 5537 | | > hide #!2 models |
| 5538 | | |
| 5539 | | > show #!2 models |
| 5540 | | |
| 5541 | | > hide #!2 models |
| 5542 | | |
| 5543 | | > show #!2 models |
| 5544 | | |
| 5545 | | > hide #!2 models |
| 5546 | | |
| 5547 | | > show #!2 models |
| 5548 | | |
| 5549 | | > select #3.1/A:384-387,431-440,454-466 |
| 5550 | | |
| 5551 | | 204 atoms, 204 bonds, 27 residues, 1 model selected |
| 5552 | | |
| 5553 | | > hide #!2 models |
| 5554 | | |
| 5555 | | > select #3.1/A:384-387,431-440,454-466/B:87-90 |
| 5556 | | |
| 5557 | | 237 atoms, 236 bonds, 31 residues, 1 model selected |
| 5558 | | |
| 5559 | | > select #3.1/A:384-387,431-440,454-466/B:87-90,121-124 |
| 5560 | | |
| 5561 | | 260 atoms, 258 bonds, 35 residues, 1 model selected |
| 5562 | | |
| 5563 | | > select #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94 |
| 5564 | | |
| 5565 | | 301 atoms, 298 bonds, 40 residues, 1 model selected |
| 5566 | | |
| 5567 | | > select #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128 |
| 5568 | | |
| 5569 | | 336 atoms, 332 bonds, 45 residues, 1 model selected |
| 5570 | | |
| 5571 | | > select |
| 5572 | | > #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106 |
| 5573 | | |
| 5574 | | 365 atoms, 360 bonds, 49 residues, 1 model selected |
| 5575 | | |
| 5576 | | > select |
| 5577 | | > #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150 |
| 5578 | | |
| 5579 | | 392 atoms, 386 bonds, 53 residues, 1 model selected |
| 5580 | | |
| 5581 | | > select |
| 5582 | | > #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150/E:74-84 |
| 5583 | | |
| 5584 | | 482 atoms, 476 bonds, 64 residues, 1 model selected |
| 5585 | | |
| 5586 | | > show #!2 models |
| 5587 | | |
| 5588 | | > hide #!2 models |
| 5589 | | |
| 5590 | | > show #!2 models |
| 5591 | | |
| 5592 | | > hide #!2 models |
| 5593 | | |
| 5594 | | > select |
| 5595 | | > #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150/E:74-84,101-108 |
| 5596 | | |
| 5597 | | 544 atoms, 537 bonds, 72 residues, 1 model selected |
| 5598 | | |
| 5599 | | > select |
| 5600 | | > #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150/E:74-84,101-108,150-154 |
| 5601 | | |
| 5602 | | 576 atoms, 568 bonds, 77 residues, 1 model selected |
| 5603 | | |
| 5604 | | > hide #3.1 & protein cartoons |
| 5605 | | |
| 5606 | | > select |
| 5607 | | > #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150/E:74-84,101-108,150-154 |
| 5608 | | |
| 5609 | | 576 atoms, 568 bonds, 77 residues, 1 model selected |
| 5610 | | |
| 5611 | | > show sel cartoons |
| 5612 | | |
| 5613 | | > select #3.1/K-L |
| 5614 | | |
| 5615 | | 430 atoms, 480 bonds, 21 residues, 1 model selected |
| 5616 | | |
| 5617 | | > hide sel models |
| 5618 | | |
| 5619 | | > undo |
| 5620 | | |
| 5621 | | > hide sel & models |
| 5622 | | |
| 5623 | | Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', |
| 5624 | | 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword |
| 5625 | | |
| 5626 | | > hide sel cartoons | atom |
| 5627 | | |
| 5628 | | Expected ',' or a keyword |
| 5629 | | |
| 5630 | | > hide sel cartoons, atoms |
| 5631 | | |
| 5632 | | > view v1 |
| 5633 | | |
| 5634 | | > show #!2 models |
| 5635 | | |
| 5636 | | > hide #!2 models |
| 5637 | | |
| 5638 | | > show #!2 models |
| 5639 | | |
| 5640 | | > hide #!2 models |
| 5641 | | |
| 5642 | | > select |
| 5643 | | > #3.1/A:384-387,431-440,454-466,582,638/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150/E:74-84,101-108,150-154 |
| 5644 | | |
| 5645 | | 601 atoms, 594 bonds, 79 residues, 1 model selected |
| 5646 | | |
| 5647 | | > show sel cartoons |
| 5648 | | |
| 5649 | | > show sel atoms |
| 5650 | | |
| 5651 | | > style sel stick |
| 5652 | | |
| 5653 | | Changed 601 atom styles |
| 5654 | | |
| 5655 | | > color sel byhetero |
| 5656 | | |
| 5657 | | > undo |
| 5658 | | |
| 5659 | | [Repeated 2 time(s)] |
| 5660 | | |
| 5661 | | > select #3.1/A:582,638 |
| 5662 | | |
| 5663 | | 25 atoms, 26 bonds, 2 residues, 1 model selected |
| 5664 | | |
| 5665 | | > show sel atoms |
| 5666 | | |
| 5667 | | > nucleotides sel atoms |
| 5668 | | |
| 5669 | | > style nucleic & sel stick |
| 5670 | | |
| 5671 | | Changed 0 atom styles |
| 5672 | | |
| 5673 | | > style sel stick |
| 5674 | | |
| 5675 | | Changed 25 atom styles |
| 5676 | | |
| 5677 | | > color sel byhetero |
| 5678 | | |
| 5679 | | > view v1 |
| 5680 | | |
| 5681 | | > select clear |
| 5682 | | |
| 5683 | | > view v1 |
| 5684 | | |
| 5685 | | > show #!2 models |
| 5686 | | |
| 5687 | | > hide #!2 models |
| 5688 | | |
| 5689 | | > show #!2 models |
| 5690 | | |
| 5691 | | > view v1 |
| 5692 | | |
| 5693 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 5694 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v5.cxs" |
| 5695 | | |
| 5696 | | ——— End of log from Fri May 27 10:46:01 2022 ——— |
| 5697 | | |
| 5698 | | opened ChimeraX session |
| 5699 | | |
| 5700 | | > view v1 |
| 5701 | | |
| 5702 | | [Repeated 1 time(s)] |
| 5703 | | |
| 5704 | | > hide #!2 models |
| 5705 | | |
| 5706 | | > show #!2 models |
| 5707 | | |
| 5708 | | > hide #!3.1 models |
| 5709 | | |
| 5710 | | > show #!3.1 models |
| 5711 | | |
| 5712 | | > hide #!3.1 models |
| 5713 | | |
| 5714 | | > show #!3.1 models |
| 5715 | | |
| 5716 | | > hide #!2.5 models |
| 5717 | | |
| 5718 | | > show #!2.4 models |
| 5719 | | |
| 5720 | | > hide #!2.4 models |
| 5721 | | |
| 5722 | | > show #!2.4 models |
| 5723 | | |
| 5724 | | > hide #!3.1 models |
| 5725 | | |
| 5726 | | > show #!3.1 models |
| 5727 | | |
| 5728 | | > hide #!3.1 models |
| 5729 | | |
| 5730 | | > show #!3.1 models |
| 5731 | | |
| 5732 | | > hide #!2.4 models |
| 5733 | | |
| 5734 | | > show #!2.4 models |
| 5735 | | |
| 5736 | | > hide #!2.4 models |
| 5737 | | |
| 5738 | | > view v1 |
| 5739 | | |
| 5740 | | > show #!2.5 models |
| 5741 | | |
| 5742 | | > select #2.5/A:410-413 |
| 5743 | | |
| 5744 | | 25 atoms, 24 bonds, 4 residues, 1 model selected |
| 5745 | | |
| 5746 | | > show #2.5/A:410-413 cartoons |
| 5747 | | |
| 5748 | | > show #2.5/A:410-414 cartoons |
| 5749 | | |
| 5750 | | > select clear |
| 5751 | | |
| 5752 | | > hide #!2.5 models |
| 5753 | | |
| 5754 | | > show #3.1/A:636-638 cartoons |
| 5755 | | |
| 5756 | | > show #3.1/A:636-639 cartoons |
| 5757 | | |
| 5758 | | > select #3.1/A:582 |
| 5759 | | |
| 5760 | | 11 atoms, 11 bonds, 1 residue, 1 model selected |
| 5761 | | |
| 5762 | | > hide sel atoms |
| 5763 | | |
| 5764 | | > hide sel cartoons |
| 5765 | | |
| 5766 | | > undo |
| 5767 | | |
| 5768 | | [Repeated 1 time(s)] |
| 5769 | | |
| 5770 | | > color sel byhetero |
| 5771 | | |
| 5772 | | > select clear |
| 5773 | | |
| 5774 | | > select #3.1/A:674@CB |
| 5775 | | |
| 5776 | | 1 atom, 1 residue, 1 model selected |
| 5777 | | |
| 5778 | | > select up |
| 5779 | | |
| 5780 | | 6 atoms, 5 bonds, 1 residue, 1 model selected |
| 5781 | | |
| 5782 | | > show #!2.5 models |
| 5783 | | |
| 5784 | | > hide #!2.5 models |
| 5785 | | |
| 5786 | | > show #!2.5 models |
| 5787 | | |
| 5788 | | > hide #!2.5 models |
| 5789 | | |
| 5790 | | > select #3.1/A:582 |
| 5791 | | |
| 5792 | | 11 atoms, 11 bonds, 1 residue, 1 model selected |
| 5793 | | |
| 5794 | | > hide sel atoms |
| 5795 | | |
| 5796 | | > hide sel cartoons |
| 5797 | | |
| 5798 | | > select clear |
| 5799 | | |
| 5800 | | > show #!2.5 models |
| 5801 | | |
| 5802 | | > hide #!2.5 models |
| 5803 | | |
| 5804 | | > show #!2.5 models |
| 5805 | | |
| 5806 | | > hide #!2.5 models |
| 5807 | | |
| 5808 | | > show #!2.5 models |
| 5809 | | |
| 5810 | | > select #2.5/A:233 |
| 5811 | | |
| 5812 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 5813 | | |
| 5814 | | > select clear |
| 5815 | | |
| 5816 | | > hide #3.1/A:674 |
| 5817 | | |
| 5818 | | > view v1 |
| 5819 | | |
| 5820 | | > hide #!3.1 models |
| 5821 | | |
| 5822 | | > view v1 |
| 5823 | | |
| 5824 | | > show #!3.2 models |
| 5825 | | |
| 5826 | | > hide #!3.2 models |
| 5827 | | |
| 5828 | | > show #!3.2 models |
| 5829 | | |
| 5830 | | > hide #!2.5 models |
| 5831 | | |
| 5832 | | > show #!2.4 models |
| 5833 | | |
| 5834 | | > hide #!3 models |
| 5835 | | |
| 5836 | | > hide #!2.4 models |
| 5837 | | |
| 5838 | | > show #!3 models |
| 5839 | | |
| 5840 | | > select #3.2/A:61-63 |
| 5841 | | |
| 5842 | | 27 atoms, 28 bonds, 3 residues, 1 model selected |
| 5843 | | |
| 5844 | | > select #3.2/A:61-63,92-94 |
| 5845 | | |
| 5846 | | 48 atoms, 48 bonds, 6 residues, 1 model selected |
| 5847 | | |
| 5848 | | > select #3.2/A:61-64,92-94 |
| 5849 | | |
| 5850 | | 56 atoms, 56 bonds, 7 residues, 1 model selected |
| 5851 | | |
| 5852 | | > select #3.2/A:61-64,92-95 |
| 5853 | | |
| 5854 | | 65 atoms, 65 bonds, 8 residues, 1 model selected |
| 5855 | | |
| 5856 | | > show #!2.5 models |
| 5857 | | |
| 5858 | | > select #3.2/A:61-64,22-95 |
| 5859 | | |
| 5860 | | 571 atoms, 582 bonds, 74 residues, 1 model selected |
| 5861 | | |
| 5862 | | > select #3.2/A:61-64,82-95 |
| 5863 | | |
| 5864 | | 137 atoms, 139 bonds, 18 residues, 1 model selected |
| 5865 | | |
| 5866 | | > hide #!2.5 models |
| 5867 | | |
| 5868 | | > select #3.2/A:61-64,82-95/B:133-136 |
| 5869 | | |
| 5870 | | 175 atoms, 178 bonds, 22 residues, 1 model selected |
| 5871 | | |
| 5872 | | > select #3.2/A:61-64,82-95/B:132-136 |
| 5873 | | |
| 5874 | | 181 atoms, 184 bonds, 23 residues, 1 model selected |
| 5875 | | |
| 5876 | | > select #3.2/A:61-64,82-95/B:100-103,132-136 |
| 5877 | | |
| 5878 | | 214 atoms, 216 bonds, 27 residues, 1 model selected |
| 5879 | | |
| 5880 | | > select #3.2/A:61-64,82-95/B:100-103,132-136/C:132-136 |
| 5881 | | |
| 5882 | | 258 atoms, 261 bonds, 32 residues, 1 model selected |
| 5883 | | |
| 5884 | | > select #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136 |
| 5885 | | |
| 5886 | | 298 atoms, 300 bonds, 37 residues, 1 model selected |
| 5887 | | |
| 5888 | | > select #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104 |
| 5889 | | |
| 5890 | | 338 atoms, 339 bonds, 42 residues, 1 model selected |
| 5891 | | |
| 5892 | | > select |
| 5893 | | > #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,133-136 |
| 5894 | | |
| 5895 | | 376 atoms, 378 bonds, 46 residues, 1 model selected |
| 5896 | | |
| 5897 | | > select |
| 5898 | | > #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,132-136 |
| 5899 | | |
| 5900 | | 382 atoms, 384 bonds, 47 residues, 1 model selected |
| 5901 | | |
| 5902 | | > show #!2.5 models |
| 5903 | | |
| 5904 | | > hide #!2.5 models |
| 5905 | | |
| 5906 | | > select |
| 5907 | | > #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,132-136/E:89-94 |
| 5908 | | |
| 5909 | | 424 atoms, 425 bonds, 53 residues, 1 model selected |
| 5910 | | |
| 5911 | | > select |
| 5912 | | > #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,132-136/E:89-93 |
| 5913 | | |
| 5914 | | 413 atoms, 414 bonds, 52 residues, 1 model selected |
| 5915 | | |
| 5916 | | > select |
| 5917 | | > #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,132-136/E:89-93,121-125 |
| 5918 | | |
| 5919 | | 443 atoms, 443 bonds, 57 residues, 1 model selected |
| 5920 | | |
| 5921 | | > hide #3.2 & protein cartoons |
| 5922 | | |
| 5923 | | > select |
| 5924 | | > #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,132-136/E:89-93,121-125 |
| 5925 | | |
| 5926 | | 443 atoms, 443 bonds, 57 residues, 1 model selected |
| 5927 | | |
| 5928 | | > show sel cartoons |
| 5929 | | |
| 5930 | | > show #3.2/A:316 |
| 5931 | | |
| 5932 | | > style sel stick |
| 5933 | | |
| 5934 | | Changed 443 atom styles |
| 5935 | | |
| 5936 | | > style sel stick |
| 5937 | | |
| 5938 | | Changed 443 atom styles |
| 5939 | | |
| 5940 | | > select #3.2/A:316 |
| 5941 | | |
| 5942 | | 12 atoms, 12 bonds, 1 residue, 1 model selected |
| 5943 | | |
| 5944 | | > show sel cartoons |
| 5945 | | |
| 5946 | | > show sel atoms |
| 5947 | | |
| 5948 | | > style sel stick |
| 5949 | | |
| 5950 | | Changed 12 atom styles |
| 5951 | | |
| 5952 | | > color sel byhetero |
| 5953 | | |
| 5954 | | > show #3.2/A:313-319 cartoons |
| 5955 | | |
| 5956 | | > show #!3.1 models |
| 5957 | | |
| 5958 | | > hide #!3 models |
| 5959 | | |
| 5960 | | > show #!3 models |
| 5961 | | |
| 5962 | | > hide #!3.2 models |
| 5963 | | |
| 5964 | | > show #3.1/A:632-638 cartoons |
| 5965 | | |
| 5966 | | > view v1 |
| 5967 | | |
| 5968 | | > show #3.1/A:631-638 cartoons |
| 5969 | | |
| 5970 | | > hide #!3.1 models |
| 5971 | | |
| 5972 | | > show #!3.2 models |
| 5973 | | |
| 5974 | | > select clear |
| 5975 | | |
| 5976 | | > show #!2.5 models |
| 5977 | | |
| 5978 | | > hide #!2.5 models |
| 5979 | | |
| 5980 | | > view v1 |
| 5981 | | |
| 5982 | | > show #!2.5 models |
| 5983 | | |
| 5984 | | > hide #!2.5 models |
| 5985 | | |
| 5986 | | > show #!2.5 models |
| 5987 | | |
| 5988 | | > hide #!2.5 models |
| 5989 | | |
| 5990 | | > hide #!3.2 models |
| 5991 | | |
| 5992 | | > show #!3.3 models |
| 5993 | | |
| 5994 | | > select #3.3/A:15-20 |
| 5995 | | |
| 5996 | | 53 atoms, 55 bonds, 6 residues, 1 model selected |
| 5997 | | |
| 5998 | | > select #3.3/A:15-19 |
| 5999 | | |
| 6000 | | 44 atoms, 46 bonds, 5 residues, 1 model selected |
| 6001 | | |
| 6002 | | > select #3.3/A:15-20 |
| 6003 | | |
| 6004 | | 53 atoms, 55 bonds, 6 residues, 1 model selected |
| 6005 | | |
| 6006 | | > select #3.3/A:16-20 |
| 6007 | | |
| 6008 | | 46 atoms, 48 bonds, 5 residues, 1 model selected |
| 6009 | | |
| 6010 | | > select #3.3/A:16-24 |
| 6011 | | |
| 6012 | | 80 atoms, 84 bonds, 9 residues, 1 model selected |
| 6013 | | |
| 6014 | | > select #3.3/A:16-24/B:80-85 |
| 6015 | | |
| 6016 | | 134 atoms, 138 bonds, 15 residues, 1 model selected |
| 6017 | | |
| 6018 | | > select #3.3/A:16-24/B:80-85,114-118 |
| 6019 | | |
| 6020 | | 171 atoms, 174 bonds, 20 residues, 1 model selected |
| 6021 | | |
| 6022 | | > select #3.3/A:16-24/B:80-84,114-118 |
| 6023 | | |
| 6024 | | 160 atoms, 163 bonds, 19 residues, 1 model selected |
| 6025 | | |
| 6026 | | > select #3.3/A:16-24/B:80-84,114-118/C:80-83 |
| 6027 | | |
| 6028 | | 196 atoms, 199 bonds, 23 residues, 1 model selected |
| 6029 | | |
| 6030 | | > select #3.3/A:16-24/B:80-84,114-118/C:80-84 |
| 6031 | | |
| 6032 | | 203 atoms, 206 bonds, 24 residues, 1 model selected |
| 6033 | | |
| 6034 | | > select #3.3/A:16-24/B:80-84,114-118/C:80-84,114-118 |
| 6035 | | |
| 6036 | | 240 atoms, 242 bonds, 29 residues, 1 model selected |
| 6037 | | |
| 6038 | | > select #3.3/A:16-24/B:80-84,114-118/C:80-84,114-118/D:114-118 |
| 6039 | | |
| 6040 | | 277 atoms, 278 bonds, 34 residues, 1 model selected |
| 6041 | | |
| 6042 | | > select #3.3/A:16-24/B:80-84,114-118/C:80-84,114-118/D:80-84,114-118 |
| 6043 | | |
| 6044 | | 320 atoms, 321 bonds, 39 residues, 1 model selected |
| 6045 | | |
| 6046 | | > select #3.3/A:16-24/B:80-84,114-118/C:80-84,114-118/D:80-84,114-118/E:80-84 |
| 6047 | | |
| 6048 | | 363 atoms, 364 bonds, 44 residues, 1 model selected |
| 6049 | | |
| 6050 | | > select |
| 6051 | | > #3.3/A:16-24/B:80-84,114-118/C:80-84,114-118/D:80-84,114-118/E:80-84,113-117 |
| 6052 | | |
| 6053 | | 395 atoms, 395 bonds, 49 residues, 1 model selected |
| 6054 | | |
| 6055 | | > view v1 |
| 6056 | | |
| 6057 | | > hide #3.3 & protein & ~sel cartoons |
| 6058 | | |
| 6059 | | > view v1 |
| 6060 | | |
| 6061 | | > select clear |
| 6062 | | |
| 6063 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6064 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v7.cxs" |
| 6065 | | |
| 6066 | | > hide #!3.3 models |
| 6067 | | |
| 6068 | | > show #!3.2 models |
| 6069 | | |
| 6070 | | > hide #!3.2 models |
| 6071 | | |
| 6072 | | > show #!3.1 models |
| 6073 | | |
| 6074 | | > select @@display & #3.1 |
| 6075 | | |
| 6076 | | 916 atoms, 1011 bonds, 10 pseudobonds, 51 residues, 2 models selected |
| 6077 | | |
| 6078 | | > select @@display & #3.1 & protein |
| 6079 | | |
| 6080 | | 56 atoms, 49 bonds, 9 residues, 1 model selected |
| 6081 | | |
| 6082 | | > hide sel atoms |
| 6083 | | |
| 6084 | | > select clear |
| 6085 | | |
| 6086 | | > select #3.1/A:638 |
| 6087 | | |
| 6088 | | 14 atoms, 15 bonds, 1 residue, 1 model selected |
| 6089 | | |
| 6090 | | > show sel atoms |
| 6091 | | |
| 6092 | | > color sel byhetero |
| 6093 | | |
| 6094 | | > select clear |
| 6095 | | |
| 6096 | | > view v1 |
| 6097 | | |
| 6098 | | > hide #!3.1.2 models |
| 6099 | | |
| 6100 | | > show #!2.5 models |
| 6101 | | |
| 6102 | | > hide #!3.1 models |
| 6103 | | |
| 6104 | | > hide pseduobond |
| 6105 | | |
| 6106 | | Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', |
| 6107 | | 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword |
| 6108 | | |
| 6109 | | > hide psedobond |
| 6110 | | |
| 6111 | | Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', |
| 6112 | | 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword |
| 6113 | | |
| 6114 | | > hide psedobonds |
| 6115 | | |
| 6116 | | Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', |
| 6117 | | 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword |
| 6118 | | |
| 6119 | | > ~psedobonds |
| 6120 | | |
| 6121 | | Unknown command: ~psedobonds |
| 6122 | | |
| 6123 | | > hide psedobonds |
| 6124 | | |
| 6125 | | Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', |
| 6126 | | 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword |
| 6127 | | |
| 6128 | | > hide pbonds |
| 6129 | | |
| 6130 | | > hide #2.5/G:34 |
| 6131 | | |
| 6132 | | > view v1 |
| 6133 | | |
| 6134 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6135 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v7.cxs" |
| 6136 | | |
| 6137 | | > show #!3.1 models |
| 6138 | | |
| 6139 | | > hide #!2.5 models |
| 6140 | | |
| 6141 | | > show #!2.5 models |
| 6142 | | |
| 6143 | | > hide #!3 models |
| 6144 | | |
| 6145 | | > show #!3 models |
| 6146 | | |
| 6147 | | > hide #!3.1 models |
| 6148 | | |
| 6149 | | > show #!3.2 models |
| 6150 | | |
| 6151 | | > hide #!3.2 models |
| 6152 | | |
| 6153 | | > show #!3.2 models |
| 6154 | | |
| 6155 | | > hide #!3.2 models |
| 6156 | | |
| 6157 | | > show #!3.3 models |
| 6158 | | |
| 6159 | | > hide #!3.3 models |
| 6160 | | |
| 6161 | | > view v1 |
| 6162 | | |
| 6163 | | > show #!3.1 models |
| 6164 | | |
| 6165 | | > show #!3.2 models |
| 6166 | | |
| 6167 | | > show #!3.3 models |
| 6168 | | |
| 6169 | | > hide #!3.3 models |
| 6170 | | |
| 6171 | | > hide #!3.2 models |
| 6172 | | |
| 6173 | | > hide #!3.1 models |
| 6174 | | |
| 6175 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6176 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v8.cxs" |
| 6177 | | |
| 6178 | | > view v1 |
| 6179 | | |
| 6180 | | > show #!3.3 models |
| 6181 | | |
| 6182 | | > hide #!3.3 models |
| 6183 | | |
| 6184 | | > select #2.5/A:225-244 |
| 6185 | | |
| 6186 | | 173 atoms, 177 bonds, 20 residues, 1 model selected |
| 6187 | | |
| 6188 | | > color sel yellow green |
| 6189 | | |
| 6190 | | > select clear |
| 6191 | | |
| 6192 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6193 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v8.cxs" |
| 6194 | | |
| 6195 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6196 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-1.jpg" width 1100 |
| 6197 | | > height 609 supersample 3 |
| 6198 | | |
| 6199 | | > hide #!3 models |
| 6200 | | |
| 6201 | | > show #!3 models |
| 6202 | | |
| 6203 | | > hide #!2 models |
| 6204 | | |
| 6205 | | > show #!3.1 models |
| 6206 | | |
| 6207 | | > select #3.1/I:12 |
| 6208 | | |
| 6209 | | 21 atoms, 23 bonds, 1 residue, 1 model selected |
| 6210 | | |
| 6211 | | > select #3.1/I:11 |
| 6212 | | |
| 6213 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 6214 | | |
| 6215 | | > select #3.1/I:9-12 |
| 6216 | | |
| 6217 | | 81 atoms, 89 bonds, 4 residues, 1 model selected |
| 6218 | | |
| 6219 | | > transparency sel 80 cartoons |
| 6220 | | |
| 6221 | | > select clear |
| 6222 | | |
| 6223 | | > show #!2 models |
| 6224 | | |
| 6225 | | > hide #!3 models |
| 6226 | | |
| 6227 | | > select #2.5/A:196 |
| 6228 | | |
| 6229 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 6230 | | |
| 6231 | | > select add #2.5/A:195 |
| 6232 | | |
| 6233 | | 16 atoms, 14 bonds, 2 residues, 1 model selected |
| 6234 | | |
| 6235 | | > transparency sel 80 cartoons |
| 6236 | | |
| 6237 | | > select clear |
| 6238 | | |
| 6239 | | > select add #2.5/I:31 |
| 6240 | | |
| 6241 | | 19 atoms, 20 bonds, 1 residue, 1 model selected |
| 6242 | | |
| 6243 | | > select add #2.5/I:33 |
| 6244 | | |
| 6245 | | 41 atoms, 44 bonds, 2 residues, 1 model selected |
| 6246 | | |
| 6247 | | > select #2.5/I:33 |
| 6248 | | |
| 6249 | | 22 atoms, 24 bonds, 1 residue, 1 model selected |
| 6250 | | |
| 6251 | | > select #2.5/I:31 |
| 6252 | | |
| 6253 | | 19 atoms, 20 bonds, 1 residue, 1 model selected |
| 6254 | | |
| 6255 | | > select clear |
| 6256 | | |
| 6257 | | > show #!3.2 models |
| 6258 | | |
| 6259 | | > hide #!3.1 models |
| 6260 | | |
| 6261 | | > hide #!2 models |
| 6262 | | |
| 6263 | | > select #3.2/I:7 |
| 6264 | | |
| 6265 | | 21 atoms, 23 bonds, 1 residue, 1 model selected |
| 6266 | | |
| 6267 | | > select add #3.2/I:6 |
| 6268 | | |
| 6269 | | 41 atoms, 44 bonds, 2 residues, 1 model selected |
| 6270 | | |
| 6271 | | > select add #3.2/I:5 |
| 6272 | | |
| 6273 | | 61 atoms, 65 bonds, 3 residues, 1 model selected |
| 6274 | | |
| 6275 | | > transparency sel 80 cartoons |
| 6276 | | |
| 6277 | | > select clear |
| 6278 | | |
| 6279 | | > hide #!3.2 models |
| 6280 | | |
| 6281 | | > show #!3.1 models |
| 6282 | | |
| 6283 | | > hide #!3.1 models |
| 6284 | | |
| 6285 | | > show #!3.3 models |
| 6286 | | |
| 6287 | | > select #3.3/I:10 |
| 6288 | | |
| 6289 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 6290 | | |
| 6291 | | > select add #3.3/I:9 |
| 6292 | | |
| 6293 | | 40 atoms, 42 bonds, 2 residues, 1 model selected |
| 6294 | | |
| 6295 | | > select add #3.3/I:7 |
| 6296 | | |
| 6297 | | 60 atoms, 63 bonds, 3 residues, 1 model selected |
| 6298 | | |
| 6299 | | > select add #3.3/I:8 |
| 6300 | | |
| 6301 | | 80 atoms, 84 bonds, 4 residues, 1 model selected |
| 6302 | | |
| 6303 | | > transparency sel 80 cartoons |
| 6304 | | |
| 6305 | | > select clear |
| 6306 | | |
| 6307 | | > hide #!3.3 models |
| 6308 | | |
| 6309 | | > show #!3.2 models |
| 6310 | | |
| 6311 | | > hide #!3.2 models |
| 6312 | | |
| 6313 | | > show #!3.1 models |
| 6314 | | |
| 6315 | | > hide #!3.1 models |
| 6316 | | |
| 6317 | | > show #!2 models |
| 6318 | | |
| 6319 | | > hide #!2 models |
| 6320 | | |
| 6321 | | > show #!3.1 models |
| 6322 | | |
| 6323 | | > select #3.1/J:14 |
| 6324 | | |
| 6325 | | 22 atoms, 24 bonds, 1 residue, 1 model selected |
| 6326 | | |
| 6327 | | > transparency sel 80 cartoons |
| 6328 | | |
| 6329 | | > select clear |
| 6330 | | |
| 6331 | | > select #3.1/I:12 |
| 6332 | | |
| 6333 | | 21 atoms, 23 bonds, 1 residue, 1 model selected |
| 6334 | | |
| 6335 | | > transparency sel 80 |
| 6336 | | |
| 6337 | | > select clear |
| 6338 | | |
| 6339 | | > view name v2 |
| 6340 | | |
| 6341 | | > show #!2 models |
| 6342 | | |
| 6343 | | > hide #!3 models |
| 6344 | | |
| 6345 | | > hide #!3.1 models |
| 6346 | | |
| 6347 | | > show #!3.1 models |
| 6348 | | |
| 6349 | | > hide #!2 models |
| 6350 | | |
| 6351 | | > view v2 |
| 6352 | | |
| 6353 | | > select #3.1/I:11 |
| 6354 | | |
| 6355 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 6356 | | |
| 6357 | | > hide sel atoms |
| 6358 | | |
| 6359 | | > select clear |
| 6360 | | |
| 6361 | | > select #3.1/I:10 |
| 6362 | | |
| 6363 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 6364 | | |
| 6365 | | > select add #3.1/I:9 |
| 6366 | | |
| 6367 | | 40 atoms, 42 bonds, 2 residues, 1 model selected |
| 6368 | | |
| 6369 | | > hide sel atoms |
| 6370 | | |
| 6371 | | > select clear |
| 6372 | | |
| 6373 | | > hide #!3.1 models |
| 6374 | | |
| 6375 | | > show #!3.2 models |
| 6376 | | |
| 6377 | | > hide #!3.2 models |
| 6378 | | |
| 6379 | | > show #!2 models |
| 6380 | | |
| 6381 | | > hide #!2 models |
| 6382 | | |
| 6383 | | > show #!3.1 models |
| 6384 | | |
| 6385 | | > hide #!3.1 models |
| 6386 | | |
| 6387 | | > show #!2 models |
| 6388 | | |
| 6389 | | > hide #!2 models |
| 6390 | | |
| 6391 | | > show #!3.2 models |
| 6392 | | |
| 6393 | | > hide #!3.2 models |
| 6394 | | |
| 6395 | | > show #!3.3 models |
| 6396 | | |
| 6397 | | > view v2 |
| 6398 | | |
| 6399 | | > hide #!3.3 models |
| 6400 | | |
| 6401 | | > show #!3.1 models |
| 6402 | | |
| 6403 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6404 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-2.jpg" width 1100 |
| 6405 | | > height 609 supersample 3 |
| 6406 | | |
| 6407 | | > hide #!3.1 models |
| 6408 | | |
| 6409 | | > show #!3.2 models |
| 6410 | | |
| 6411 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6412 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-3.jpg" width 1100 |
| 6413 | | > height 609 supersample 3 |
| 6414 | | |
| 6415 | | > hide #!3.2 models |
| 6416 | | |
| 6417 | | > show #!3.3 models |
| 6418 | | |
| 6419 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6420 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-4.jpg" width 1100 |
| 6421 | | > height 609 supersample 3 |
| 6422 | | |
| 6423 | | > hide #!3.3 models |
| 6424 | | |
| 6425 | | > show #!3.1 models |
| 6426 | | |
| 6427 | | > combine #3.1 id #3.4 |
| 6428 | | |
| 6429 | | Expected a keyword |
| 6430 | | |
| 6431 | | > combine #3.1 modelId id #3.4 |
| 6432 | | |
| 6433 | | Invalid "modelId" argument: Expected an integer |
| 6434 | | |
| 6435 | | > combine #3.1 Id #3.4 |
| 6436 | | |
| 6437 | | Expected a keyword |
| 6438 | | |
| 6439 | | > combine #3.1 modelId #3.4 |
| 6440 | | |
| 6441 | | > select #3.4 |
| 6442 | | |
| 6443 | | 22831 atoms, 23321 bonds, 15 pseudobonds, 2789 residues, 3 models selected |
| 6444 | | |
| 6445 | | > nucleotides sel stubs |
| 6446 | | |
| 6447 | | > hide #!3.1 models |
| 6448 | | |
| 6449 | | > close #3.4 |
| 6450 | | |
| 6451 | | > show #!3.1 models |
| 6452 | | |
| 6453 | | > show #!2 models |
| 6454 | | |
| 6455 | | > hide #!2 models |
| 6456 | | |
| 6457 | | > show #!2 models |
| 6458 | | |
| 6459 | | > hide #!2 models |
| 6460 | | |
| 6461 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6462 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v9.cxs" |
| 6463 | | |
| 6464 | | ——— End of log from Tue May 31 15:25:24 2022 ——— |
| 6465 | | |
| 6466 | | opened ChimeraX session |
| 6467 | | |
| 6468 | | > select #2.5/A:225-245 |
| 6469 | | |
| 6470 | | 179 atoms, 183 bonds, 21 residues, 1 model selected |
| 6471 | | |
| 6472 | | > color sel yellow green |
| 6473 | | |
| 6474 | | > view v2 |
| 6475 | | |
| 6476 | | > show #!2 models |
| 6477 | | |
| 6478 | | > select clear |
| 6479 | | |
| 6480 | | > hide #2.5 |
| 6481 | | |
| 6482 | | > hide #2.5 cartoons |
| 6483 | | |
| 6484 | | > select #2.5/A:225-245 |
| 6485 | | |
| 6486 | | 179 atoms, 183 bonds, 21 residues, 1 model selected |
| 6487 | | |
| 6488 | | > show sel cartoons |
| 6489 | | |
| 6490 | | > select clear |
| 6491 | | |
| 6492 | | > select #2.5/A:225-245 |
| 6493 | | |
| 6494 | | 179 atoms, 183 bonds, 21 residues, 1 model selected |
| 6495 | | |
| 6496 | | > color sel grey |
| 6497 | | |
| 6498 | | > select clear |
| 6499 | | |
| 6500 | | > view v2 |
| 6501 | | |
| 6502 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6503 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs" |
| 6504 | | |
| 6505 | | ——— End of log from Mon Jun 6 14:52:02 2022 ——— |
| 6506 | | |
| 6507 | | opened ChimeraX session |
| 6508 | | |
| 6509 | | > select up |
| 6510 | | |
| 6511 | | 2 atoms, 1 bond, 1 residue, 1 model selected |
| 6512 | | |
| 6513 | | > select up |
| 6514 | | |
| 6515 | | 14 atoms, 15 bonds, 1 residue, 1 model selected |
| 6516 | | |
| 6517 | | > color sel cyan target |
| 6518 | | |
| 6519 | | Missing "target" keyword's argument |
| 6520 | | |
| 6521 | | > color sel cyan target a |
| 6522 | | |
| 6523 | | > style sel sphere |
| 6524 | | |
| 6525 | | Changed 14 atom styles |
| 6526 | | |
| 6527 | | > color sel byhetero |
| 6528 | | |
| 6529 | | > style sel ball |
| 6530 | | |
| 6531 | | Changed 14 atom styles |
| 6532 | | |
| 6533 | | > style sel stick |
| 6534 | | |
| 6535 | | Changed 14 atom styles |
| 6536 | | |
| 6537 | | > style sel ball |
| 6538 | | |
| 6539 | | Changed 14 atom styles |
| 6540 | | |
| 6541 | | > color sel byhetero |
| 6542 | | |
| 6543 | | > select clear |
| 6544 | | |
| 6545 | | > select #3.1/A:638@CZ3 |
| 6546 | | |
| 6547 | | 1 atom, 1 residue, 1 model selected |
| 6548 | | |
| 6549 | | > select up |
| 6550 | | |
| 6551 | | 14 atoms, 15 bonds, 1 residue, 1 model selected |
| 6552 | | |
| 6553 | | > style sel stick |
| 6554 | | |
| 6555 | | Changed 14 atom styles |
| 6556 | | |
| 6557 | | > select clear |
| 6558 | | |
| 6559 | | > view v2 |
| 6560 | | |
| 6561 | | > select up |
| 6562 | | |
| 6563 | | 2 atoms, 1 bond, 1 residue, 1 model selected |
| 6564 | | |
| 6565 | | > select up |
| 6566 | | |
| 6567 | | 14 atoms, 15 bonds, 1 residue, 1 model selected |
| 6568 | | |
| 6569 | | > color sel green target a |
| 6570 | | |
| 6571 | | > select clear |
| 6572 | | |
| 6573 | | > select #3.1/A:638 |
| 6574 | | |
| 6575 | | 14 atoms, 15 bonds, 1 residue, 1 model selected |
| 6576 | | |
| 6577 | | > color sel lime target a |
| 6578 | | |
| 6579 | | > color sel byhetero |
| 6580 | | |
| 6581 | | > color sel yellow green target a |
| 6582 | | |
| 6583 | | > color sel green yellow target a |
| 6584 | | |
| 6585 | | > color sel lime target a |
| 6586 | | |
| 6587 | | > color sel byhetero |
| 6588 | | |
| 6589 | | > select clear |
| 6590 | | |
| 6591 | | > view v2 |
| 6592 | | |
| 6593 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6594 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-2_1.jpg" width |
| 6595 | | > 1100 height 609 supersample 3 |
| 6596 | | |
| 6597 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6598 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs" |
| 6599 | | |
| 6600 | | ——— End of log from Mon Jun 6 16:50:44 2022 ——— |
| 6601 | | |
| 6602 | | opened ChimeraX session |
| 6603 | | |
| 6604 | | > hide #!2 models |
| 6605 | | |
| 6606 | | > hide #!3.1 models |
| 6607 | | |
| 6608 | | > show #!3.2 models |
| 6609 | | |
| 6610 | | > select up |
| 6611 | | |
| 6612 | | 2 atoms, 1 bond, 1 residue, 1 model selected |
| 6613 | | |
| 6614 | | > select up |
| 6615 | | |
| 6616 | | 12 atoms, 12 bonds, 1 residue, 1 model selected |
| 6617 | | |
| 6618 | | > color sel lime target a |
| 6619 | | |
| 6620 | | > color sel byhetero |
| 6621 | | |
| 6622 | | > select clear |
| 6623 | | |
| 6624 | | > hide #!3.2 models |
| 6625 | | |
| 6626 | | > show #!3.3 models |
| 6627 | | |
| 6628 | | > show #3.3/A:61-63 cartoons |
| 6629 | | |
| 6630 | | > view v2 |
| 6631 | | |
| 6632 | | > select #3.3/A:63 |
| 6633 | | |
| 6634 | | 11 atoms, 11 bonds, 1 residue, 1 model selected |
| 6635 | | |
| 6636 | | > show sel atoms |
| 6637 | | |
| 6638 | | > style sel stick |
| 6639 | | |
| 6640 | | Changed 11 atom styles |
| 6641 | | |
| 6642 | | > color sel green yellow target a |
| 6643 | | |
| 6644 | | > color sel byhetero |
| 6645 | | |
| 6646 | | > select clear |
| 6647 | | |
| 6648 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6649 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-4.jpg" width 1100 |
| 6650 | | > height 609 supersample 3 |
| 6651 | | |
| 6652 | | > select #3.3/I:9 |
| 6653 | | |
| 6654 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 6655 | | |
| 6656 | | > hide sel atoms |
| 6657 | | |
| 6658 | | > select clear |
| 6659 | | |
| 6660 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6661 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-4.jpg" width 1100 |
| 6662 | | > height 609 supersample 3 |
| 6663 | | |
| 6664 | | > hide #!3.3 models |
| 6665 | | |
| 6666 | | > show #!3.2 models |
| 6667 | | |
| 6668 | | > hide #!3.2 models |
| 6669 | | |
| 6670 | | > show #!3.1 models |
| 6671 | | |
| 6672 | | > hide #!3.1 models |
| 6673 | | |
| 6674 | | > show #!3.2 models |
| 6675 | | |
| 6676 | | > hide #!3.2 models |
| 6677 | | |
| 6678 | | > show #!3.3 models |
| 6679 | | |
| 6680 | | > hide #!3.3 models |
| 6681 | | |
| 6682 | | > show #!2 models |
| 6683 | | |
| 6684 | | > hide #!3 models |
| 6685 | | |
| 6686 | | > show #!3 models |
| 6687 | | |
| 6688 | | > hide #!2 models |
| 6689 | | |
| 6690 | | > show #!2 models |
| 6691 | | |
| 6692 | | > show #!3.1 models |
| 6693 | | |
| 6694 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6695 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs" |
| 6696 | | |
| 6697 | | > hide #!2 models |
| 6698 | | |
| 6699 | | > hide #!3.1 models |
| 6700 | | |
| 6701 | | > show #!3.2 models |
| 6702 | | |
| 6703 | | > hide #!3.2 models |
| 6704 | | |
| 6705 | | > show #!3.3 models |
| 6706 | | |
| 6707 | | > hide #!3.3 models |
| 6708 | | |
| 6709 | | > show #!3.2 models |
| 6710 | | |
| 6711 | | > hide #!3.2 models |
| 6712 | | |
| 6713 | | > show #!3.1 models |
| 6714 | | |
| 6715 | | > hide #!3.1 models |
| 6716 | | |
| 6717 | | > show #!3.3 models |
| 6718 | | |
| 6719 | | > select #3.3/A:63 |
| 6720 | | |
| 6721 | | 11 atoms, 11 bonds, 1 residue, 1 model selected |
| 6722 | | |
| 6723 | | > color sel lime target a |
| 6724 | | |
| 6725 | | > color sel byhetero |
| 6726 | | |
| 6727 | | > select clear |
| 6728 | | |
| 6729 | | > view v2 |
| 6730 | | |
| 6731 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6732 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-4.jpg" width 1100 |
| 6733 | | > height 609 supersample 3 |
| 6734 | | |
| 6735 | | > hide #!3.3 models |
| 6736 | | |
| 6737 | | > show #!3.2 models |
| 6738 | | |
| 6739 | | > hide #!3.2 models |
| 6740 | | |
| 6741 | | > show #!3.1 models |
| 6742 | | |
| 6743 | | > show #!2 models |
| 6744 | | |
| 6745 | | > select #2.5/A:225-245 |
| 6746 | | |
| 6747 | | 179 atoms, 183 bonds, 21 residues, 1 model selected |
| 6748 | | |
| 6749 | | > transparency sel 80 cartoons |
| 6750 | | |
| 6751 | | > transparency sel 60 cartoons |
| 6752 | | |
| 6753 | | > transparency sel 50 cartoons |
| 6754 | | |
| 6755 | | > select clear |
| 6756 | | |
| 6757 | | > select #2.5/A:225-245 |
| 6758 | | |
| 6759 | | 179 atoms, 183 bonds, 21 residues, 1 model selected |
| 6760 | | |
| 6761 | | > transparency sel 0 cartoons |
| 6762 | | |
| 6763 | | > select clear |
| 6764 | | |
| 6765 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6766 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs" |
| 6767 | | |
| 6768 | | > hide #!3.1 models |
| 6769 | | |
| 6770 | | > show #!3.2 models |
| 6771 | | |
| 6772 | | > hide #!2 models |
| 6773 | | |
| 6774 | | > hide #!3.2 models |
| 6775 | | |
| 6776 | | > show #!3.3 models |
| 6777 | | |
| 6778 | | > hide #!3.3 models |
| 6779 | | |
| 6780 | | > show #!3.2 models |
| 6781 | | |
| 6782 | | > hide #!3.2 models |
| 6783 | | |
| 6784 | | > show #!3.1 models |
| 6785 | | |
| 6786 | | > hide #!3.1 models |
| 6787 | | |
| 6788 | | > show #!3.2 models |
| 6789 | | |
| 6790 | | > hide #!3.2 models |
| 6791 | | |
| 6792 | | > show #!3.3 models |
| 6793 | | |
| 6794 | | > hide #!3.3 models |
| 6795 | | |
| 6796 | | > show #!3.2 models |
| 6797 | | |
| 6798 | | > hide #!3.2 models |
| 6799 | | |
| 6800 | | > show #!3.1 models |
| 6801 | | |
| 6802 | | > ui windowfill toggle |
| 6803 | | |
| 6804 | | [Repeated 3 time(s)] |
| 6805 | | |
| 6806 | | > show #!2 models |
| 6807 | | |
| 6808 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6809 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs" |
| 6810 | | |
| 6811 | | > hide #!3 models |
| 6812 | | |
| 6813 | | > hide #!2 models |
| 6814 | | |
| 6815 | | > show #!3.2 models |
| 6816 | | |
| 6817 | | > hide #!3.1 models |
| 6818 | | |
| 6819 | | > show #!3.1 models |
| 6820 | | |
| 6821 | | > hide #!3.2 models |
| 6822 | | |
| 6823 | | > show #!3.3 models |
| 6824 | | |
| 6825 | | > hide #!3.3 models |
| 6826 | | |
| 6827 | | > show #!2 models |
| 6828 | | |
| 6829 | | > hide #!3.1 models |
| 6830 | | |
| 6831 | | > show #!3.1 models |
| 6832 | | |
| 6833 | | > select #3.1/A:431 |
| 6834 | | |
| 6835 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 6836 | | |
| 6837 | | > select #3.1/A:435 |
| 6838 | | |
| 6839 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 6840 | | |
| 6841 | | > select add #3.1/A:431 |
| 6842 | | |
| 6843 | | 8 atoms, 6 bonds, 2 residues, 1 model selected |
| 6844 | | |
| 6845 | | > select up |
| 6846 | | |
| 6847 | | 49 atoms, 48 bonds, 8 residues, 1 model selected |
| 6848 | | |
| 6849 | | > select clear |
| 6850 | | |
| 6851 | | > select #3.1/A:435 |
| 6852 | | |
| 6853 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 6854 | | |
| 6855 | | > select add #3.1/A:434 |
| 6856 | | |
| 6857 | | 15 atoms, 13 bonds, 2 residues, 1 model selected |
| 6858 | | |
| 6859 | | > select add #3.1/A:433 |
| 6860 | | |
| 6861 | | 23 atoms, 20 bonds, 3 residues, 1 model selected |
| 6862 | | |
| 6863 | | > select add #3.1/A:432 |
| 6864 | | |
| 6865 | | 27 atoms, 23 bonds, 4 residues, 1 model selected |
| 6866 | | |
| 6867 | | > select add #3.1/A:431 |
| 6868 | | |
| 6869 | | 31 atoms, 26 bonds, 5 residues, 1 model selected |
| 6870 | | |
| 6871 | | > view v2 |
| 6872 | | |
| 6873 | | > select add #3.1/A:436 |
| 6874 | | |
| 6875 | | 35 atoms, 29 bonds, 6 residues, 1 model selected |
| 6876 | | |
| 6877 | | > view v2 |
| 6878 | | |
| 6879 | | > hide sel cartoons |
| 6880 | | |
| 6881 | | > select #3.1/A:384 |
| 6882 | | |
| 6883 | | 6 atoms, 5 bonds, 1 residue, 1 model selected |
| 6884 | | |
| 6885 | | > hide sel cartoons |
| 6886 | | |
| 6887 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6888 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs" |
| 6889 | | |
| 6890 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6891 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-2_1.jpg" width |
| 6892 | | > 1100 height 609 supersample 3 |
| 6893 | | |
| 6894 | | > select #3.1/A:455-462 |
| 6895 | | |
| 6896 | | 66 atoms, 66 bonds, 8 residues, 1 model selected |
| 6897 | | |
| 6898 | | > select #3.1/A:456-462 |
| 6899 | | |
| 6900 | | 60 atoms, 60 bonds, 7 residues, 1 model selected |
| 6901 | | |
| 6902 | | > color sel yellow green |
| 6903 | | |
| 6904 | | > select clear |
| 6905 | | |
| 6906 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6907 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-2_1.jpg" width |
| 6908 | | > 1100 height 609 supersample 3 |
| 6909 | | |
| 6910 | | > hide #!2 models |
| 6911 | | |
| 6912 | | > hide #!3.1 models |
| 6913 | | |
| 6914 | | > show #!3.2 models |
| 6915 | | |
| 6916 | | > view v2 |
| 6917 | | |
| 6918 | | > select #3.2/A:83 |
| 6919 | | |
| 6920 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 6921 | | |
| 6922 | | > select #3.2/A:84 |
| 6923 | | |
| 6924 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 6925 | | |
| 6926 | | > select #3.2/A:91 |
| 6927 | | |
| 6928 | | 5 atoms, 4 bonds, 1 residue, 1 model selected |
| 6929 | | |
| 6930 | | > view v2 |
| 6931 | | |
| 6932 | | > select #3.2/A:84-91 |
| 6933 | | |
| 6934 | | 56 atoms, 57 bonds, 8 residues, 1 model selected |
| 6935 | | |
| 6936 | | > color sel yellow green |
| 6937 | | |
| 6938 | | > select clear |
| 6939 | | |
| 6940 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6941 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-3.jpg" width 1100 |
| 6942 | | > height 609 supersample 3 |
| 6943 | | |
| 6944 | | > hide #!3.2 models |
| 6945 | | |
| 6946 | | > show #!3.3 models |
| 6947 | | |
| 6948 | | > hide #!3.3 models |
| 6949 | | |
| 6950 | | > show #!2 models |
| 6951 | | |
| 6952 | | > show #!3.1 models |
| 6953 | | |
| 6954 | | > view v2 |
| 6955 | | |
| 6956 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 6957 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs" |
| 6958 | | |
| 6959 | | ——— End of log from Mon Jun 6 17:25:34 2022 ——— |
| 6960 | | |
| 6961 | | opened ChimeraX session |
| 6962 | | |
| 6963 | | > hide #!2.5 models |
| 6964 | | |
| 6965 | | > hide #!3.1 models |
| 6966 | | |
| 6967 | | > show #!3.2 models |
| 6968 | | |
| 6969 | | > hide #!3.2 models |
| 6970 | | |
| 6971 | | > show #!3.3 models |
| 6972 | | |
| 6973 | | > hide #!3.3 models |
| 6974 | | |
| 6975 | | > show #!3.1 models |
| 6976 | | |
| 6977 | | > view v1 |
| 6978 | | |
| 6979 | | > show #3.1 & protein cartoons |
| 6980 | | |
| 6981 | | > undo |
| 6982 | | |
| 6983 | | > show #3.1 & protein cartoons |
| 6984 | | |
| 6985 | | > hide #!3.1 models |
| 6986 | | |
| 6987 | | > show #!3.2 models |
| 6988 | | |
| 6989 | | > show #3.2 & protein cartoons |
| 6990 | | |
| 6991 | | > hide #!3.2 models |
| 6992 | | |
| 6993 | | > show #!3.1 models |
| 6994 | | |
| 6995 | | > hide #!3.1 models |
| 6996 | | |
| 6997 | | > show #!3.3 models |
| 6998 | | |
| 6999 | | > show #3.3 & protein cartoons |
| 7000 | | |
| 7001 | | > hide #!3 models |
| 7002 | | |
| 7003 | | > show #!2.5 models |
| 7004 | | |
| 7005 | | > show #!2.5 cartoons |
| 7006 | | |
| 7007 | | > select nucleo |
| 7008 | | |
| 7009 | | Expected an objects specifier or a keyword |
| 7010 | | |
| 7011 | | > select nucleotide |
| 7012 | | |
| 7013 | | Expected an objects specifier or a keyword |
| 7014 | | |
| 7015 | | > nucleotides stubs |
| 7016 | | |
| 7017 | | > hide #!2.5 models |
| 7018 | | |
| 7019 | | > show #!3 models |
| 7020 | | |
| 7021 | | > hide #!3 models |
| 7022 | | |
| 7023 | | > show #!2.4 models |
| 7024 | | |
| 7025 | | > hide #!2.4 models |
| 7026 | | |
| 7027 | | > show #!2.5 models |
| 7028 | | |
| 7029 | | > nucleotides #2.5 stubs |
| 7030 | | |
| 7031 | | > select #2.5 & nucleotides |
| 7032 | | |
| 7033 | | Expected a keyword |
| 7034 | | |
| 7035 | | > select #2.5/I-K |
| 7036 | | |
| 7037 | | 1166 atoms, 1301 bonds, 1 pseudobond, 58 residues, 2 models selected |
| 7038 | | |
| 7039 | | > nucleotides sel stubs |
| 7040 | | |
| 7041 | | > show sel atoms |
| 7042 | | |
| 7043 | | > select clear |
| 7044 | | |
| 7045 | | > select #2.5/A:225-245 |
| 7046 | | |
| 7047 | | 179 atoms, 183 bonds, 21 residues, 1 model selected |
| 7048 | | |
| 7049 | | > color sel yellow green |
| 7050 | | |
| 7051 | | > select clear |
| 7052 | | |
| 7053 | | > hide #!2.5 models |
| 7054 | | |
| 7055 | | > show #!2.4 models |
| 7056 | | |
| 7057 | | > hide #!2.4 models |
| 7058 | | |
| 7059 | | > show #!2.3 models |
| 7060 | | |
| 7061 | | > hide #!2.3 models |
| 7062 | | |
| 7063 | | > show #!2.2 models |
| 7064 | | |
| 7065 | | > hide #!2.2 models |
| 7066 | | |
| 7067 | | > show #!2.1 models |
| 7068 | | |
| 7069 | | > hide #!2.1 models |
| 7070 | | |
| 7071 | | > show #!2.2 models |
| 7072 | | |
| 7073 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7074 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v13-Models-Compare.cxs" |
| 7075 | | |
| 7076 | | ——— End of log from Wed Jun 29 10:57:53 2022 ——— |
| 7077 | | |
| 7078 | | opened ChimeraX session |
| 7079 | | |
| 7080 | | > select #2.2/I:35-37/J:14-18 |
| 7081 | | |
| 7082 | | 163 atoms, 181 bonds, 8 residues, 1 model selected |
| 7083 | | |
| 7084 | | > delete sel |
| 7085 | | |
| 7086 | | > view name v3 |
| 7087 | | |
| 7088 | | > view v1 |
| 7089 | | |
| 7090 | | > view v2 |
| 7091 | | |
| 7092 | | > view v3 |
| 7093 | | |
| 7094 | | > view v1 |
| 7095 | | |
| 7096 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7097 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v14-Models-Compare.cxs" |
| 7098 | | |
| 7099 | | ——— End of log from Wed Jun 29 11:25:52 2022 ——— |
| 7100 | | |
| 7101 | | opened ChimeraX session |
| 7102 | | |
| 7103 | | > hide #!2.2 models |
| 7104 | | |
| 7105 | | > show #!2.5 models |
| 7106 | | |
| 7107 | | > show #!3 models |
| 7108 | | |
| 7109 | | > hide #!3.3 models |
| 7110 | | |
| 7111 | | > show #!3.3 models |
| 7112 | | |
| 7113 | | > hide #!2 models |
| 7114 | | |
| 7115 | | > show #!2 models |
| 7116 | | |
| 7117 | | > hide #!2 models |
| 7118 | | |
| 7119 | | > show #!2 models |
| 7120 | | |
| 7121 | | > hide #!2 models |
| 7122 | | |
| 7123 | | > show #!2 models |
| 7124 | | |
| 7125 | | > hide #!2 models |
| 7126 | | |
| 7127 | | > show #!2 models |
| 7128 | | |
| 7129 | | > hide #!2 models |
| 7130 | | |
| 7131 | | > show #!2 models |
| 7132 | | |
| 7133 | | > hide #!2 models |
| 7134 | | |
| 7135 | | > show #!2 models |
| 7136 | | |
| 7137 | | > mmaker #3.3/B-H to #2.5/B-H pair ss |
| 7138 | | |
| 7139 | | Parameters |
| 7140 | | --- |
| 7141 | | Chain pairing | ss |
| 7142 | | Alignment algorithm | Needleman-Wunsch |
| 7143 | | Similarity matrix | BLOSUM-62 |
| 7144 | | SS fraction | 0.3 |
| 7145 | | Gap open (HH/SS/other) | 18/18/6 |
| 7146 | | Gap extend | 1 |
| 7147 | | SS matrix | | | H | S | O |
| 7148 | | ---|---|---|--- |
| 7149 | | H | 6 | -9 | -6 |
| 7150 | | S | | 6 | -6 |
| 7151 | | O | | | 4 |
| 7152 | | Iteration cutoff | 2 |
| 7153 | | |
| 7154 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with T4-Clamp-Loader-DNA-3U5Z, |
| 7155 | | chain B (#3.3), sequence alignment score = 442.4 |
| 7156 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with T4-Clamp-Loader-DNA-3U5Z, |
| 7157 | | chain C (#3.3), sequence alignment score = 461.6 |
| 7158 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with T4-Clamp-Loader-DNA-3U5Z, |
| 7159 | | chain D (#3.3), sequence alignment score = 438.2 |
| 7160 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with T4-Clamp-Loader-DNA-3U5Z, |
| 7161 | | chain E (#3.3), sequence alignment score = 375.3 |
| 7162 | | Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with T4-Clamp-Loader-DNA-3U5Z, |
| 7163 | | chain G (#3.3), sequence alignment score = 85.8 |
| 7164 | | Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with T4-Clamp-Loader-DNA-3U5Z, |
| 7165 | | chain F (#3.3), sequence alignment score = 162.6 |
| 7166 | | Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with T4-Clamp-Loader-DNA-3U5Z, |
| 7167 | | chain H (#3.3), sequence alignment score = 121.6 |
| 7168 | | RMSD between 438 pruned atom pairs is 1.185 angstroms; (across all 1759 pairs: |
| 7169 | | 28.127) |
| 7170 | | |
| 7171 | | |
| 7172 | | > hide #!2 models |
| 7173 | | |
| 7174 | | > show #!2 models |
| 7175 | | |
| 7176 | | > hide #!2 models |
| 7177 | | |
| 7178 | | > show #!2 models |
| 7179 | | |
| 7180 | | > hide #!3.3 models |
| 7181 | | |
| 7182 | | > show #!3.3 models |
| 7183 | | |
| 7184 | | > hide #!3.3 models |
| 7185 | | |
| 7186 | | > show #!3.3 models |
| 7187 | | |
| 7188 | | > hide #!3.3 models |
| 7189 | | |
| 7190 | | > show #!3.3 models |
| 7191 | | |
| 7192 | | > hide #!2 models |
| 7193 | | |
| 7194 | | > show #!2 models |
| 7195 | | |
| 7196 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7197 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v13-Models-Compare.cxs" |
| 7198 | | |
| 7199 | | ——— End of log from Wed Jun 29 11:45:15 2022 ——— |
| 7200 | | |
| 7201 | | opened ChimeraX session |
| 7202 | | |
| 7203 | | > hide #!3 models |
| 7204 | | |
| 7205 | | > show #!3 models |
| 7206 | | |
| 7207 | | > hide #!2 models |
| 7208 | | |
| 7209 | | > show #!2 models |
| 7210 | | |
| 7211 | | > hide #!2 models |
| 7212 | | |
| 7213 | | > show #!2 models |
| 7214 | | |
| 7215 | | > hide #!2 models |
| 7216 | | |
| 7217 | | > show #!2 models |
| 7218 | | |
| 7219 | | > hide #!3 models |
| 7220 | | |
| 7221 | | > hide #!2 models |
| 7222 | | |
| 7223 | | > show #!3 models |
| 7224 | | |
| 7225 | | > hide #!3.3 models |
| 7226 | | |
| 7227 | | > show #!3.2 models |
| 7228 | | |
| 7229 | | > hide #!3.2 models |
| 7230 | | |
| 7231 | | > show #!3.1 models |
| 7232 | | |
| 7233 | | > hide #!3.1 models |
| 7234 | | |
| 7235 | | > show #!3.2 models |
| 7236 | | |
| 7237 | | > hide #!3.2 models |
| 7238 | | |
| 7239 | | > show #!3.3 models |
| 7240 | | |
| 7241 | | > show #!2 models |
| 7242 | | |
| 7243 | | > hide #!3 models |
| 7244 | | |
| 7245 | | > show #!3 models |
| 7246 | | |
| 7247 | | > hide #!3.3 models |
| 7248 | | |
| 7249 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7250 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v1.cxs" |
| 7251 | | |
| 7252 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7253 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/Step5-v1.jpg" width |
| 7254 | | > 1100 height 609 supersample 3 |
| 7255 | | |
| 7256 | | > hide #!2 models |
| 7257 | | |
| 7258 | | > show #!3.1 models |
| 7259 | | |
| 7260 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7261 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/RFC-v1.jpg" width 1100 |
| 7262 | | > height 609 supersample 3 |
| 7263 | | |
| 7264 | | > hide #!3.1 models |
| 7265 | | |
| 7266 | | > show #!3.2 models |
| 7267 | | |
| 7268 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7269 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/Ecoli-v1.jpg" width |
| 7270 | | > 1100 height 609 supersample 3 |
| 7271 | | |
| 7272 | | > hide #!3.2 models |
| 7273 | | |
| 7274 | | > show #!3.3 models |
| 7275 | | |
| 7276 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7277 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/T4-v1.jpg" width 1100 |
| 7278 | | > height 609 supersample 3 |
| 7279 | | |
| 7280 | | > transparency #2-3 0 cartoons |
| 7281 | | |
| 7282 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7283 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v2.cxs" |
| 7284 | | |
| 7285 | | ——— End of log from Fri Jul 1 16:33:56 2022 ——— |
| 7286 | | |
| 7287 | | opened ChimeraX session |
| 7288 | | |
| 7289 | | > hide #!3.3 models |
| 7290 | | |
| 7291 | | > show #!3.1 models |
| 7292 | | |
| 7293 | | > show #3.1/I-L target ca |
| 7294 | | |
| 7295 | | > color #3.1/K plum cartoons |
| 7296 | | |
| 7297 | | > color #3.1/L #E7F981 cartoons |
| 7298 | | |
| 7299 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7300 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/RFC-v2.jpg" width 1100 |
| 7301 | | > height 609 supersample 3 |
| 7302 | | |
| 7303 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7304 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v3.cxs" |
| 7305 | | |
| 7306 | | > hide #!3 models |
| 7307 | | |
| 7308 | | > show #!2 models |
| 7309 | | |
| 7310 | | > hide #!2 models |
| 7311 | | |
| 7312 | | > show #!3 models |
| 7313 | | |
| 7314 | | > hide #!3.1 models |
| 7315 | | |
| 7316 | | > show #!3.2 models |
| 7317 | | |
| 7318 | | > hide #!3.2 models |
| 7319 | | |
| 7320 | | > show #!3.3 models |
| 7321 | | |
| 7322 | | > hide #!3.3 models |
| 7323 | | |
| 7324 | | > show #!2 models |
| 7325 | | |
| 7326 | | > hide #!3 models |
| 7327 | | |
| 7328 | | > show #!3.1 models |
| 7329 | | |
| 7330 | | > hide #!2 models |
| 7331 | | |
| 7332 | | > hide #!3.1 models |
| 7333 | | |
| 7334 | | > show #!3.2 models |
| 7335 | | |
| 7336 | | > hide #!3.2 models |
| 7337 | | |
| 7338 | | > show #!3.3 models |
| 7339 | | |
| 7340 | | > select #3.3/I:10 |
| 7341 | | |
| 7342 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 7343 | | |
| 7344 | | > select add #3.3/I:11 |
| 7345 | | |
| 7346 | | 40 atoms, 42 bonds, 2 residues, 1 model selected |
| 7347 | | |
| 7348 | | > transparency sel 80 cartoons |
| 7349 | | |
| 7350 | | > select clear |
| 7351 | | |
| 7352 | | > hide #!3.3 models |
| 7353 | | |
| 7354 | | > show #!3.2 models |
| 7355 | | |
| 7356 | | > select #3.2/I:6 |
| 7357 | | |
| 7358 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 7359 | | |
| 7360 | | > transparency sel 80 cartoons |
| 7361 | | |
| 7362 | | > select clear |
| 7363 | | |
| 7364 | | > hide #!3.2 models |
| 7365 | | |
| 7366 | | > show #!3.1 models |
| 7367 | | |
| 7368 | | > select #3.1/I:10 |
| 7369 | | |
| 7370 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 7371 | | |
| 7372 | | > select add #3.1/I:9 |
| 7373 | | |
| 7374 | | 40 atoms, 42 bonds, 2 residues, 1 model selected |
| 7375 | | |
| 7376 | | > select #3.1/I:10 |
| 7377 | | |
| 7378 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 7379 | | |
| 7380 | | > select #3.1/I:9 |
| 7381 | | |
| 7382 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 7383 | | |
| 7384 | | > transparency sel 80 cartoons |
| 7385 | | |
| 7386 | | > select clear |
| 7387 | | |
| 7388 | | > select #3.1/I:10 |
| 7389 | | |
| 7390 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 7391 | | |
| 7392 | | > transparency sel 80 cartoons |
| 7393 | | |
| 7394 | | > select clear |
| 7395 | | |
| 7396 | | > select add #3.1/I:10 |
| 7397 | | |
| 7398 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 7399 | | |
| 7400 | | > select add #3.1/I:9 |
| 7401 | | |
| 7402 | | 40 atoms, 42 bonds, 2 residues, 1 model selected |
| 7403 | | |
| 7404 | | > transparency sel 80 target ca |
| 7405 | | |
| 7406 | | > transparency sel 100 target ca |
| 7407 | | |
| 7408 | | > select clear |
| 7409 | | |
| 7410 | | > select #3.1/I:10 |
| 7411 | | |
| 7412 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 7413 | | |
| 7414 | | > select add #3.1/I:9 |
| 7415 | | |
| 7416 | | 40 atoms, 42 bonds, 2 residues, 1 model selected |
| 7417 | | |
| 7418 | | > transparency sel 80 target ca |
| 7419 | | |
| 7420 | | > transparency sel 80 target atoms |
| 7421 | | |
| 7422 | | Invalid "target" argument: Character 't' is not an allowed target, must be one |
| 7423 | | of acrsbmpfl |
| 7424 | | |
| 7425 | | > transparency sel 80 target atom |
| 7426 | | |
| 7427 | | Invalid "target" argument: Character 't' is not an allowed target, must be one |
| 7428 | | of acrsbmpfl |
| 7429 | | |
| 7430 | | > transparency sel 80 atoms |
| 7431 | | |
| 7432 | | > transparency sel 100 atoms |
| 7433 | | |
| 7434 | | > transparency sel 80 atoms |
| 7435 | | |
| 7436 | | > transparency sel 80 cartoons |
| 7437 | | |
| 7438 | | > transparency sel 50 cartoons |
| 7439 | | |
| 7440 | | > transparency sel 70 cartoons |
| 7441 | | |
| 7442 | | > select clear |
| 7443 | | |
| 7444 | | > select #3.1/I:10 |
| 7445 | | |
| 7446 | | 20 atoms, 21 bonds, 1 residue, 1 model selected |
| 7447 | | |
| 7448 | | > select add #3.1/I:9 |
| 7449 | | |
| 7450 | | 40 atoms, 42 bonds, 2 residues, 1 model selected |
| 7451 | | |
| 7452 | | > transparency sel 80 cartoons |
| 7453 | | |
| 7454 | | > select clear |
| 7455 | | |
| 7456 | | > hide #!3.1 models |
| 7457 | | |
| 7458 | | > show #!3.2 models |
| 7459 | | |
| 7460 | | > hide #!3.2 models |
| 7461 | | |
| 7462 | | > show #!3.1 models |
| 7463 | | |
| 7464 | | > hide #!3.1 models |
| 7465 | | |
| 7466 | | > show #!3.3 models |
| 7467 | | |
| 7468 | | > show #!2 models |
| 7469 | | |
| 7470 | | > hide #!3 models |
| 7471 | | |
| 7472 | | > hide #!2 models |
| 7473 | | |
| 7474 | | > show #!3 models |
| 7475 | | |
| 7476 | | > hide #!3.3 models |
| 7477 | | |
| 7478 | | > show #!3.2 models |
| 7479 | | |
| 7480 | | > hide #!3.2 models |
| 7481 | | |
| 7482 | | > show #!3.1 models |
| 7483 | | |
| 7484 | | > hide #!3.1 models |
| 7485 | | |
| 7486 | | > show #!3.3 models |
| 7487 | | |
| 7488 | | > hide #!3.3 models |
| 7489 | | |
| 7490 | | > show #!2 models |
| 7491 | | |
| 7492 | | > hide #!3 models |
| 7493 | | |
| 7494 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7495 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v3.cxs" |
| 7496 | | |
| 7497 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7498 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/Step5-v3.jpg" width |
| 7499 | | > 1100 height 609 supersample 3 |
| 7500 | | |
| 7501 | | > hide #!2 models |
| 7502 | | |
| 7503 | | > show #!3 models |
| 7504 | | |
| 7505 | | > show #!3.1 models |
| 7506 | | |
| 7507 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7508 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/RFC-v3.jpg" width 1100 |
| 7509 | | > height 609 supersample 3 |
| 7510 | | |
| 7511 | | > hide #!3.1 models |
| 7512 | | |
| 7513 | | > show #!3.2 models |
| 7514 | | |
| 7515 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7516 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/Ecoli-v3.jpg" width |
| 7517 | | > 1100 height 609 supersample 3 |
| 7518 | | |
| 7519 | | > hide #!3.2 models |
| 7520 | | |
| 7521 | | > show #!3.3 models |
| 7522 | | |
| 7523 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7524 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/T4-v3.jpg" width 1100 |
| 7525 | | > height 609 supersample 3 |
| 7526 | | |
| 7527 | | > hide #!3.3 models |
| 7528 | | |
| 7529 | | > show #!3.1 models |
| 7530 | | |
| 7531 | | > color #3.1/L light sky blue cartoons |
| 7532 | | |
| 7533 | | [Repeated 1 time(s)] |
| 7534 | | |
| 7535 | | > color #3.1/L light sky blue target ca |
| 7536 | | |
| 7537 | | > color #3.1/L light sky blue target a |
| 7538 | | |
| 7539 | | > color #3.1/L light sky blue a |
| 7540 | | |
| 7541 | | Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', |
| 7542 | | 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword |
| 7543 | | |
| 7544 | | > color #3.1/L light sky blue atoms |
| 7545 | | |
| 7546 | | > color #3.1/L light sky blue |
| 7547 | | |
| 7548 | | > color #3.1/K plum |
| 7549 | | |
| 7550 | | > color #3.1/L light blue |
| 7551 | | |
| 7552 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7553 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/RFC-v3.jpg" width 1100 |
| 7554 | | > height 609 supersample 3 |
| 7555 | | |
| 7556 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7557 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v3.cxs" |
| 7558 | | |
| 7559 | | ——— End of log from Mon Jul 4 15:09:05 2022 ——— |
| 7560 | | |
| 7561 | | opened ChimeraX session |
| 7562 | | |
| 7563 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7564 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 7565 | | |
| 7566 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7567 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 7568 | | |
| 7569 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7570 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 7571 | | |
| 7572 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7573 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 7574 | | |
| 7575 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7576 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 7577 | | |
| 7578 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7579 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 7580 | | |
| 7581 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7582 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 7583 | | |
| 7584 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7585 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 7586 | | |
| 7587 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7588 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 7589 | | |
| 7590 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7591 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 7592 | | |
| 7593 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7594 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 7595 | | |
| 7596 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7597 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 7598 | | |
| 7599 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7600 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 7601 | | |
| 7602 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7603 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 7604 | | |
| 7605 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7606 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 7607 | | |
| 7608 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 7609 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 7610 | | |
| 7611 | | > open 7ti8 |
| 7612 | | |
| 7613 | | Summary of feedback from opening 7ti8 fetched from pdb |
| 7614 | | --- |
| 7615 | | notes | Fetching compressed mmCIF 7ti8 from |
| 7616 | | http://files.rcsb.org/download/7ti8.cif |
| 7617 | | Fetching CCD AGS from http://ligand-expo.rcsb.org/reports/A/AGS/AGS.cif |
| 7618 | | |
| 7619 | | 7ti8 title: |
| 7620 | | Structure of the yeast clamp loader (Replication Factor C RFC) bound to the |
| 7621 | | open sliding clamp (Proliferating Cell Nuclear Antigen PCNA) [more info...] |
| 7622 | | |
| 7623 | | Chain information for 7ti8 #4 |
| 7624 | | --- |
| 7625 | | Chain | Description | UniProt |
| 7626 | | A | Replication factor C subunit 1 | RFC1_YEAST |
| 7627 | | B | Replication factor C subunit 4 | RFC4_YEAST |
| 7628 | | C | Replication factor C subunit 3 | RFC3_YEAST |
| 7629 | | D | Replication factor C subunit 2 | RFC2_YEAST |
| 7630 | | E | Replication factor C subunit 5 | RFC5_YEAST |
| 7631 | | F G H | Proliferating cell nuclear antigen | PCNA_YEAST |
| 7632 | | |
| 7633 | | Non-standard residues in 7ti8 #4 |
| 7634 | | --- |
| 7635 | | ADP — adenosine-5'-diphosphate |
| 7636 | | AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine |
| 7637 | | 5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate); |
| 7638 | | adenosine-5'-diphosphate monothiophosphate) |
| 7639 | | MG — magnesium ion |
| 7640 | | |
| 7641 | | |
| 7642 | | > hide #4 |
| 7643 | | |
| 7644 | | > show #4 cartoons |
| 7645 | | |
| 7646 | | > rename #4 Id #3.4 name Sc-CL-Open-7TI8 |
| 7647 | | |
| 7648 | | Expected a keyword |
| 7649 | | |
| 7650 | | > rename #4 model Id #3.4 name Sc-CL-Open-7TI8 |
| 7651 | | |
| 7652 | | Expected a keyword |
| 7653 | | |
| 7654 | | > rename #4 Sc-CL-Open-7TI8 Id #3.4 name |
| 7655 | | |
| 7656 | | Expected a keyword |
| 7657 | | |
| 7658 | | > rename #4 Sc-CL-Open-7TI8 Id #3.4 |
| 7659 | | |
| 7660 | | Expected a keyword |
| 7661 | | |
| 7662 | | > rename #4 Sc-CL-Open-7TI8 id #3.4 |
| 7663 | | |
| 7664 | | > show #!2 models |
| 7665 | | |
| 7666 | | > hide #!3.1 models |
| 7667 | | |
| 7668 | | Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with |
| 7669 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 7670 | | |
| 7671 | | Mismatch between Cocoa '\x0' and Carbon 'M' for virtual key 46 with |
| 7672 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 7673 | | |
| 7674 | | Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with |
| 7675 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 7676 | | |
| 7677 | | Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with |
| 7678 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 7679 | | |
| 7680 | | Mismatch between Cocoa '\x0' and Carbon '\u00b5' for virtual key 46 with |
| 7681 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 7682 | | |
| 7683 | | Mismatch between Cocoa '\x0' and Carbon '\u00c2' for virtual key 46 with |
| 7684 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 7685 | | |
| 7686 | | Mismatch between Cocoa '\x0' and Carbon '\u00b5' for virtual key 46 with |
| 7687 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 7688 | | |
| 7689 | | Mismatch between Cocoa '\x0' and Carbon '\u00c2' for virtual key 46 with |
| 7690 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 7691 | | |
| 7692 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 7693 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 7694 | | |
| 7695 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 7696 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 7697 | | |
| 7698 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 7699 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 7700 | | |
| 7701 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 7702 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 7703 | | |
| 7704 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 7705 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 7706 | | |
| 7707 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 7708 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 7709 | | |
| 7710 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 7711 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 7712 | | |
| 7713 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 7714 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 7715 | | |
| 7716 | | > hide #!2.5 models |
| 7717 | | |
| 7718 | | > show #!2.1 models |
| 7719 | | |
| 7720 | | > mmaker #3.4 to #2.1 pair ss |
| 7721 | | |
| 7722 | | Different number of reference/match chains (10 ref, 8 match) |
| 7723 | | |
| 7724 | | > mmaker #3.4/A-E to #2.1/A-E pair ss |
| 7725 | | |
| 7726 | | Parameters |
| 7727 | | --- |
| 7728 | | Chain pairing | ss |
| 7729 | | Alignment algorithm | Needleman-Wunsch |
| 7730 | | Similarity matrix | BLOSUM-62 |
| 7731 | | SS fraction | 0.3 |
| 7732 | | Gap open (HH/SS/other) | 18/18/6 |
| 7733 | | Gap extend | 1 |
| 7734 | | SS matrix | | | H | S | O |
| 7735 | | ---|---|---|--- |
| 7736 | | H | 6 | -9 | -6 |
| 7737 | | S | | 6 | -6 |
| 7738 | | O | | | 4 |
| 7739 | | Iteration cutoff | 2 |
| 7740 | | |
| 7741 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with Sc-CL-Open-7TI8, chain A |
| 7742 | | (#3.4), sequence alignment score = 330.6 |
| 7743 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain B (#2.1) with Sc-CL-Open-7TI8, chain B |
| 7744 | | (#3.4), sequence alignment score = 1592.5 |
| 7745 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain C (#2.1) with Sc-CL-Open-7TI8, chain C |
| 7746 | | (#3.4), sequence alignment score = 1603.5 |
| 7747 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain D (#2.1) with Sc-CL-Open-7TI8, chain D |
| 7748 | | (#3.4), sequence alignment score = 1649.7 |
| 7749 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain E (#2.1) with Sc-CL-Open-7TI8, chain E |
| 7750 | | (#3.4), sequence alignment score = 1684.7 |
| 7751 | | RMSD between 1352 pruned atom pairs is 0.690 angstroms; (across all 1692 |
| 7752 | | pairs: 3.677) |
| 7753 | | |
| 7754 | | |
| 7755 | | > hide #!2.1 models |
| 7756 | | |
| 7757 | | > show #!2.1 models |
| 7758 | | |
| 7759 | | > hide #!2.1 models |
| 7760 | | |
| 7761 | | Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with |
| 7762 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 7763 | | |
| 7764 | | Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with |
| 7765 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 7766 | | |
| 7767 | | Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with |
| 7768 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 7769 | | |
| 7770 | | Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with |
| 7771 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 7772 | | |
| 7773 | | Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with |
| 7774 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 7775 | | |
| 7776 | | Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with |
| 7777 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 7778 | | |
| 7779 | | Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with |
| 7780 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 7781 | | |
| 7782 | | Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with |
| 7783 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 7784 | | |
| 7785 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 7786 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 7787 | | |
| 7788 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 7789 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 7790 | | |
| 7791 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 7792 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 7793 | | |
| 7794 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 7795 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 7796 | | |
| 7797 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 7798 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 7799 | | |
| 7800 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 7801 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 7802 | | |
| 7803 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 7804 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 7805 | | |
| 7806 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 7807 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 7808 | | |
| 7809 | | > setattr #3.4/F chain_id X |
| 7810 | | |
| 7811 | | Missing or invalid "attrValue" argument: Expected a text string |
| 7812 | | |
| 7813 | | > setattr #3.4/F c chain_id X |
| 7814 | | |
| 7815 | | Assigning chain_id attribute to 1 item |
| 7816 | | |
| 7817 | | > setattr #3.4/H c chain_id F |
| 7818 | | |
| 7819 | | Assigning chain_id attribute to 1 item |
| 7820 | | |
| 7821 | | > setattr #3.4/G c chain_id H |
| 7822 | | |
| 7823 | | Assigning chain_id attribute to 1 item |
| 7824 | | |
| 7825 | | > setattr #3.4/X c chain_id G |
| 7826 | | |
| 7827 | | Assigning chain_id attribute to 1 item |
| 7828 | | |
| 7829 | | > show #!2.1 models |
| 7830 | | |
| 7831 | | > mmaker #3.4/A-H to #2.1/A-H pair ss |
| 7832 | | |
| 7833 | | Parameters |
| 7834 | | --- |
| 7835 | | Chain pairing | ss |
| 7836 | | Alignment algorithm | Needleman-Wunsch |
| 7837 | | Similarity matrix | BLOSUM-62 |
| 7838 | | SS fraction | 0.3 |
| 7839 | | Gap open (HH/SS/other) | 18/18/6 |
| 7840 | | Gap extend | 1 |
| 7841 | | SS matrix | | | H | S | O |
| 7842 | | ---|---|---|--- |
| 7843 | | H | 6 | -9 | -6 |
| 7844 | | S | | 6 | -6 |
| 7845 | | O | | | 4 |
| 7846 | | Iteration cutoff | 2 |
| 7847 | | |
| 7848 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with Sc-CL-Open-7TI8, chain A |
| 7849 | | (#3.4), sequence alignment score = 330.6 |
| 7850 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain B (#2.1) with Sc-CL-Open-7TI8, chain B |
| 7851 | | (#3.4), sequence alignment score = 1592.5 |
| 7852 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain C (#2.1) with Sc-CL-Open-7TI8, chain C |
| 7853 | | (#3.4), sequence alignment score = 1603.5 |
| 7854 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain D (#2.1) with Sc-CL-Open-7TI8, chain D |
| 7855 | | (#3.4), sequence alignment score = 1649.7 |
| 7856 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain E (#2.1) with Sc-CL-Open-7TI8, chain E |
| 7857 | | (#3.4), sequence alignment score = 1684.7 |
| 7858 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain F (#2.1) with Sc-CL-Open-7TI8, chain G |
| 7859 | | (#3.4), sequence alignment score = 199.6 |
| 7860 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain G (#2.1) with Sc-CL-Open-7TI8, chain H |
| 7861 | | (#3.4), sequence alignment score = 221.2 |
| 7862 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain H (#2.1) with Sc-CL-Open-7TI8, chain F |
| 7863 | | (#3.4), sequence alignment score = 208 |
| 7864 | | RMSD between 1352 pruned atom pairs is 0.690 angstroms; (across all 2382 |
| 7865 | | pairs: 32.054) |
| 7866 | | |
| 7867 | | |
| 7868 | | > hide #!2 models |
| 7869 | | |
| 7870 | | > show #!2 models |
| 7871 | | |
| 7872 | | > cartoon style nucleic xsection oval width 2.5 thickness 2.5 |
| 7873 | | |
| 7874 | | > cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true |
| 7875 | | > xsection oval width 2.75 thickness 1 arrowScale 1.5 |
| 7876 | | |
| 7877 | | > color /A #FFB381 |
| 7878 | | |
| 7879 | | > color /B #D7819F |
| 7880 | | |
| 7881 | | > color /C #B48FE3 |
| 7882 | | |
| 7883 | | > color /D #D7CD85 |
| 7884 | | |
| 7885 | | > color /E salmon |
| 7886 | | |
| 7887 | | > color /F navajo white |
| 7888 | | |
| 7889 | | > color /G #CAC6FD |
| 7890 | | |
| 7891 | | > color /H plum |
| 7892 | | |
| 7893 | | > hide #!3 models |
| 7894 | | |
| 7895 | | Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with |
| 7896 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 7897 | | |
| 7898 | | Mismatch between Cocoa '\x0' and Carbon 'U' for virtual key 32 with |
| 7899 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 7900 | | |
| 7901 | | Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with |
| 7902 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 7903 | | |
| 7904 | | Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with |
| 7905 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 7906 | | |
| 7907 | | Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with |
| 7908 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 7909 | | |
| 7910 | | Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with |
| 7911 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 7912 | | |
| 7913 | | Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with |
| 7914 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 7915 | | |
| 7916 | | Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with |
| 7917 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 7918 | | |
| 7919 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 7920 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 7921 | | |
| 7922 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 7923 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 7924 | | |
| 7925 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 7926 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 7927 | | |
| 7928 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 7929 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 7930 | | |
| 7931 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 7932 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 7933 | | |
| 7934 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 7935 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 7936 | | |
| 7937 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 7938 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 7939 | | |
| 7940 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 7941 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 7942 | | |
| 7943 | | > show #!3 models |
| 7944 | | |
| 7945 | | > hide #!3 models |
| 7946 | | |
| 7947 | | > show #!3 models |
| 7948 | | |
| 7949 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 7950 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v14-Models-Compare.cxs" |
| 7951 | | |
| 7952 | | > hide #!2 models |
| 7953 | | |
| 7954 | | > show #!2 models |
| 7955 | | |
| 7956 | | > hide #!3 models |
| 7957 | | |
| 7958 | | > show #!3 models |
| 7959 | | |
| 7960 | | > view name v4 |
| 7961 | | |
| 7962 | | > view v1 |
| 7963 | | |
| 7964 | | > hide #!3.4 models |
| 7965 | | |
| 7966 | | > show #!3.1 models |
| 7967 | | |
| 7968 | | > hide #!3.1 models |
| 7969 | | |
| 7970 | | > show #!3.1 models |
| 7971 | | |
| 7972 | | > hide #!3.1 models |
| 7973 | | |
| 7974 | | > hide #!3 models |
| 7975 | | |
| 7976 | | > show #!3.1 models |
| 7977 | | |
| 7978 | | > hide #!2 models |
| 7979 | | |
| 7980 | | > show #!2 models |
| 7981 | | |
| 7982 | | > hide #!3 models |
| 7983 | | |
| 7984 | | > hide #!2 models |
| 7985 | | |
| 7986 | | > show #!3 models |
| 7987 | | |
| 7988 | | > show #!2 models |
| 7989 | | |
| 7990 | | > hide #!3 models |
| 7991 | | |
| 7992 | | > coulombic #!2.1 |
| 7993 | | |
| 7994 | | The following heavy (non-hydrogen) atoms are missing, which may result in |
| 7995 | | inaccurate electrostatics: |
| 7996 | | Stat1-Rsr115-Ct4.pdb #2.1/A ASP 396 OD1 |
| 7997 | | Stat1-Rsr115-Ct4.pdb #2.1/A ASP 396 CG |
| 7998 | | Stat1-Rsr115-Ct4.pdb #2.1/A ASP 396 OD2 |
| 7999 | | Stat1-Rsr115-Ct4.pdb #2.1/A LEU 413 CD2 |
| 8000 | | Stat1-Rsr115-Ct4.pdb #2.1/A LEU 413 CG |
| 8001 | | Stat1-Rsr115-Ct4.pdb #2.1/A LEU 413 CD1 |
| 8002 | | |
| 8003 | | Deleting 5' phosphates from: copy of Stat1-Rsr115-Ct4.pdb #/I DT 29, copy of |
| 8004 | | Stat1-Rsr115-Ct4.pdb #/I DG 11 |
| 8005 | | Using Amber 20 recommended default charges and atom types for standard |
| 8006 | | residues |
| 8007 | | Hydrogen copy of Stat1-Rsr115-Ct4.pdb #/F ARG 470 H bonded to atom that should |
| 8008 | | not have hydrogens (copy of Stat1-Rsr115-Ct4.pdb #/F ARG 470 C) |
| 8009 | | |
| 8010 | | > hide #!2 models |
| 8011 | | |
| 8012 | | > show #!2 models |
| 8013 | | |
| 8014 | | > show #!3 models |
| 8015 | | |
| 8016 | | > hide #!2 models |
| 8017 | | |
| 8018 | | > hide #!3 models |
| 8019 | | |
| 8020 | | > show #!2 models |
| 8021 | | |
| 8022 | | > show #!3 models |
| 8023 | | |
| 8024 | | > hide #!2 models |
| 8025 | | |
| 8026 | | > show #!2 models |
| 8027 | | |
| 8028 | | > hide #!3 models |
| 8029 | | |
| 8030 | | > show #!3 models |
| 8031 | | |
| 8032 | | > hide #!2 models |
| 8033 | | |
| 8034 | | > hide #!3 models |
| 8035 | | |
| 8036 | | > show #!2 models |
| 8037 | | |
| 8038 | | > show #!3 models |
| 8039 | | |
| 8040 | | > hide #!2 models |
| 8041 | | |
| 8042 | | > show #!2 models |
| 8043 | | |
| 8044 | | > hide #!2 models |
| 8045 | | |
| 8046 | | > show #!2 models |
| 8047 | | |
| 8048 | | > hide #!2 models |
| 8049 | | |
| 8050 | | > show #!2 models |
| 8051 | | |
| 8052 | | > hide #!3 models |
| 8053 | | |
| 8054 | | > show #!3 models |
| 8055 | | |
| 8056 | | > hide #!2 models |
| 8057 | | |
| 8058 | | > show #!2 models |
| 8059 | | |
| 8060 | | > hide #!3 models |
| 8061 | | |
| 8062 | | > open 7tiB |
| 8063 | | |
| 8064 | | Summary of feedback from opening 7tiB fetched from pdb |
| 8065 | | --- |
| 8066 | | note | Fetching compressed mmCIF 7tib from |
| 8067 | | http://files.rcsb.org/download/7tib.cif |
| 8068 | | |
| 8069 | | 7tib title: |
| 8070 | | Structure of the yeast clamp loader (Replication Factor C RFC) bound to the |
| 8071 | | open sliding clamp (Proliferating Cell Nuclear Antigen PCNA) and primer- |
| 8072 | | template DNA [more info...] |
| 8073 | | |
| 8074 | | Chain information for 7tib #4 |
| 8075 | | --- |
| 8076 | | Chain | Description | UniProt |
| 8077 | | A | Replication factor C subunit 1 | RFC1_YEAST |
| 8078 | | B | Replication factor C subunit 4 | RFC4_YEAST |
| 8079 | | C | Replication factor C subunit 3 | RFC3_YEAST |
| 8080 | | D | Replication factor C subunit 2 | RFC2_YEAST |
| 8081 | | E | Replication factor C subunit 5 | RFC5_YEAST |
| 8082 | | F G H | Proliferating cell nuclear antigen | PCNA_YEAST |
| 8083 | | I | DNA |
| 8084 | | (5'-D(P*TP*TP*TP*TP*TP*TP*TP*ap*TP*GP*TP*ap*CP*TP*CP*GP*TP*ap*GP*TP*GP*TP*CP*T)-3') |
| 8085 | | | |
| 8086 | | J | DNA (5'-D(*ap*GP*ap*CP*ap*CP*TP*ap*CP*GP*ap*GP*TP*ap*CP*ap*TP*A)-3') | |
| 8087 | | |
| 8088 | | Non-standard residues in 7tib #4 |
| 8089 | | --- |
| 8090 | | ADP — adenosine-5'-diphosphate |
| 8091 | | AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine |
| 8092 | | 5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate); |
| 8093 | | adenosine-5'-diphosphate monothiophosphate) |
| 8094 | | MG — magnesium ion |
| 8095 | | |
| 8096 | | |
| 8097 | | > hide #4 |
| 8098 | | |
| 8099 | | > show #4 cartoons |
| 8100 | | |
| 8101 | | > rename #4 Sc-CL-OpenDNA-7TIB id #3.5 |
| 8102 | | |
| 8103 | | > hide #!3.1 models |
| 8104 | | |
| 8105 | | > show #!3.1 models |
| 8106 | | |
| 8107 | | > hide #!3.1 models |
| 8108 | | |
| 8109 | | > hide #!3.5 models |
| 8110 | | |
| 8111 | | > show #!3.5 models |
| 8112 | | |
| 8113 | | > mmaker #3.4 to #2.3 |
| 8114 | | |
| 8115 | | Parameters |
| 8116 | | --- |
| 8117 | | Chain pairing | bb |
| 8118 | | Alignment algorithm | Needleman-Wunsch |
| 8119 | | Similarity matrix | BLOSUM-62 |
| 8120 | | SS fraction | 0.3 |
| 8121 | | Gap open (HH/SS/other) | 18/18/6 |
| 8122 | | Gap extend | 1 |
| 8123 | | SS matrix | | | H | S | O |
| 8124 | | ---|---|---|--- |
| 8125 | | H | 6 | -9 | -6 |
| 8126 | | S | | 6 | -6 |
| 8127 | | O | | | 4 |
| 8128 | | Iteration cutoff | 2 |
| 8129 | | |
| 8130 | | Matchmaker Stat3-Ref88-Ct3.pdb, chain E (#2.3) with Sc-CL-Open-7TI8, chain E |
| 8131 | | (#3.4), sequence alignment score = 1707.5 |
| 8132 | | RMSD between 336 pruned atom pairs is 0.625 angstroms; (across all 348 pairs: |
| 8133 | | 1.807) |
| 8134 | | |
| 8135 | | |
| 8136 | | > undo |
| 8137 | | |
| 8138 | | > hide #!3.5 models |
| 8139 | | |
| 8140 | | > show #!3.4 models |
| 8141 | | |
| 8142 | | > undo |
| 8143 | | |
| 8144 | | [Repeated 9 time(s)] |
| 8145 | | |
| 8146 | | > redo |
| 8147 | | |
| 8148 | | [Repeated 1 time(s)] |
| 8149 | | |
| 8150 | | > hide #!3.1 models |
| 8151 | | |
| 8152 | | > hide #!3 models |
| 8153 | | |
| 8154 | | > show #!3 models |
| 8155 | | |
| 8156 | | > hide #!3.5 models |
| 8157 | | |
| 8158 | | > show #!3.5 models |
| 8159 | | |
| 8160 | | > show #3.5 cartoons |
| 8161 | | |
| 8162 | | > hide #!3.5 models |
| 8163 | | |
| 8164 | | > show #!3.4 models |
| 8165 | | |
| 8166 | | > mmaker #3.4/A-H to #2.1/A-H pair ss |
| 8167 | | |
| 8168 | | Parameters |
| 8169 | | --- |
| 8170 | | Chain pairing | ss |
| 8171 | | Alignment algorithm | Needleman-Wunsch |
| 8172 | | Similarity matrix | BLOSUM-62 |
| 8173 | | SS fraction | 0.3 |
| 8174 | | Gap open (HH/SS/other) | 18/18/6 |
| 8175 | | Gap extend | 1 |
| 8176 | | SS matrix | | | H | S | O |
| 8177 | | ---|---|---|--- |
| 8178 | | H | 6 | -9 | -6 |
| 8179 | | S | | 6 | -6 |
| 8180 | | O | | | 4 |
| 8181 | | Iteration cutoff | 2 |
| 8182 | | |
| 8183 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with Sc-CL-Open-7TI8, chain A |
| 8184 | | (#3.4), sequence alignment score = 330.6 |
| 8185 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain B (#2.1) with Sc-CL-Open-7TI8, chain B |
| 8186 | | (#3.4), sequence alignment score = 1592.5 |
| 8187 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain C (#2.1) with Sc-CL-Open-7TI8, chain C |
| 8188 | | (#3.4), sequence alignment score = 1603.5 |
| 8189 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain D (#2.1) with Sc-CL-Open-7TI8, chain D |
| 8190 | | (#3.4), sequence alignment score = 1649.7 |
| 8191 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain E (#2.1) with Sc-CL-Open-7TI8, chain E |
| 8192 | | (#3.4), sequence alignment score = 1684.7 |
| 8193 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain F (#2.1) with Sc-CL-Open-7TI8, chain G |
| 8194 | | (#3.4), sequence alignment score = 199.6 |
| 8195 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain G (#2.1) with Sc-CL-Open-7TI8, chain H |
| 8196 | | (#3.4), sequence alignment score = 221.2 |
| 8197 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain H (#2.1) with Sc-CL-Open-7TI8, chain F |
| 8198 | | (#3.4), sequence alignment score = 208 |
| 8199 | | RMSD between 1352 pruned atom pairs is 0.690 angstroms; (across all 2382 |
| 8200 | | pairs: 32.054) |
| 8201 | | |
| 8202 | | |
| 8203 | | > hide #!3.4 models |
| 8204 | | |
| 8205 | | > show #!3.4 models |
| 8206 | | |
| 8207 | | > hide #!3.4 models |
| 8208 | | |
| 8209 | | > show #!3.5 models |
| 8210 | | |
| 8211 | | > hide #!2.1 models |
| 8212 | | |
| 8213 | | > show #!2.3 models |
| 8214 | | |
| 8215 | | > mmaker #3.5 to #2.3 |
| 8216 | | |
| 8217 | | Parameters |
| 8218 | | --- |
| 8219 | | Chain pairing | bb |
| 8220 | | Alignment algorithm | Needleman-Wunsch |
| 8221 | | Similarity matrix | BLOSUM-62 |
| 8222 | | SS fraction | 0.3 |
| 8223 | | Gap open (HH/SS/other) | 18/18/6 |
| 8224 | | Gap extend | 1 |
| 8225 | | SS matrix | | | H | S | O |
| 8226 | | ---|---|---|--- |
| 8227 | | H | 6 | -9 | -6 |
| 8228 | | S | | 6 | -6 |
| 8229 | | O | | | 4 |
| 8230 | | Iteration cutoff | 2 |
| 8231 | | |
| 8232 | | Matchmaker Stat3-Ref88-Ct3.pdb, chain E (#2.3) with Sc-CL-OpenDNA-7TIB, chain |
| 8233 | | E (#3.5), sequence alignment score = 1691.9 |
| 8234 | | RMSD between 336 pruned atom pairs is 0.661 angstroms; (across all 343 pairs: |
| 8235 | | 1.225) |
| 8236 | | |
| 8237 | | |
| 8238 | | > hide #!2.3 models |
| 8239 | | |
| 8240 | | > show #!2.4 models |
| 8241 | | |
| 8242 | | > mmaker #3.5 to #2.4 |
| 8243 | | |
| 8244 | | Parameters |
| 8245 | | --- |
| 8246 | | Chain pairing | bb |
| 8247 | | Alignment algorithm | Needleman-Wunsch |
| 8248 | | Similarity matrix | BLOSUM-62 |
| 8249 | | SS fraction | 0.3 |
| 8250 | | Gap open (HH/SS/other) | 18/18/6 |
| 8251 | | Gap extend | 1 |
| 8252 | | SS matrix | | | H | S | O |
| 8253 | | ---|---|---|--- |
| 8254 | | H | 6 | -9 | -6 |
| 8255 | | S | | 6 | -6 |
| 8256 | | O | | | 4 |
| 8257 | | Iteration cutoff | 2 |
| 8258 | | |
| 8259 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with Sc-CL-OpenDNA-7TIB, chain |
| 8260 | | D (#3.5), sequence alignment score = 1642.5 |
| 8261 | | RMSD between 329 pruned atom pairs is 0.462 angstroms; (across all 330 pairs: |
| 8262 | | 0.497) |
| 8263 | | |
| 8264 | | |
| 8265 | | > hide #!2.4 models |
| 8266 | | |
| 8267 | | > show #!2.4 models |
| 8268 | | |
| 8269 | | > hide #!2.4 models |
| 8270 | | |
| 8271 | | Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with |
| 8272 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 8273 | | |
| 8274 | | Mismatch between Cocoa '\x0' and Carbon 'O' for virtual key 31 with |
| 8275 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 8276 | | |
| 8277 | | Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with |
| 8278 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 8279 | | |
| 8280 | | Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with |
| 8281 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 8282 | | |
| 8283 | | Mismatch between Cocoa '\x0' and Carbon '\u00f8' for virtual key 31 with |
| 8284 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 8285 | | |
| 8286 | | Mismatch between Cocoa '\x0' and Carbon '\u00d8' for virtual key 31 with |
| 8287 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 8288 | | |
| 8289 | | Mismatch between Cocoa '\x0' and Carbon '\u00f8' for virtual key 31 with |
| 8290 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 8291 | | |
| 8292 | | Mismatch between Cocoa '\x0' and Carbon '\u00d8' for virtual key 31 with |
| 8293 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 8294 | | |
| 8295 | | Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with |
| 8296 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 8297 | | |
| 8298 | | Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with |
| 8299 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 8300 | | |
| 8301 | | Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with |
| 8302 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 8303 | | |
| 8304 | | Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with |
| 8305 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 8306 | | |
| 8307 | | Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with |
| 8308 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 8309 | | |
| 8310 | | Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with |
| 8311 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 8312 | | |
| 8313 | | Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with |
| 8314 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 8315 | | |
| 8316 | | Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with |
| 8317 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 8318 | | |
| 8319 | | > open 7SH2 |
| 8320 | | |
| 8321 | | Summary of feedback from opening 7SH2 fetched from pdb |
| 8322 | | --- |
| 8323 | | note | Fetching compressed mmCIF 7sh2 from |
| 8324 | | http://files.rcsb.org/download/7sh2.cif |
| 8325 | | |
| 8326 | | 7sh2 title: |
| 8327 | | Structure of the yeast Rad24-RFC loader bound to DNA and the open 9-1-1 clamp |
| 8328 | | [more info...] |
| 8329 | | |
| 8330 | | Chain information for 7sh2 #4 |
| 8331 | | --- |
| 8332 | | Chain | Description | UniProt |
| 8333 | | A | Checkpoint protein RAD24 | RAD24_YEAST |
| 8334 | | B | Replication factor C subunit 4 | RFC4_YEAST |
| 8335 | | C | Replication factor C subunit 3 | RFC3_YEAST |
| 8336 | | D | Replication factor C subunit 2 | RFC2_YEAST |
| 8337 | | E | Replication factor C subunit 5 | RFC5_YEAST |
| 8338 | | F | Mitosis Entry Checkpoint protein MEC3 | A0A6A5PTK1_YEASX |
| 8339 | | G | DNA damage checkpoint control protein RAD17 | RAD17_YEAST |
| 8340 | | H | DNA damage checkpoint protein DDC1 | DDC1_YEAST |
| 8341 | | P | Watson strand | |
| 8342 | | T | Crick strand | |
| 8343 | | |
| 8344 | | Non-standard residues in 7sh2 #4 |
| 8345 | | --- |
| 8346 | | ADP — adenosine-5'-diphosphate |
| 8347 | | AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine |
| 8348 | | 5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate); |
| 8349 | | adenosine-5'-diphosphate monothiophosphate) |
| 8350 | | MG — magnesium ion |
| 8351 | | |
| 8352 | | |
| 8353 | | Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with |
| 8354 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 8355 | | |
| 8356 | | Mismatch between Cocoa '\x0' and Carbon 'H' for virtual key 4 with |
| 8357 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 8358 | | |
| 8359 | | Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with |
| 8360 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 8361 | | |
| 8362 | | Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with |
| 8363 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 8364 | | |
| 8365 | | Mismatch between Cocoa '\x0' and Carbon '\u02d9' for virtual key 4 with |
| 8366 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 8367 | | |
| 8368 | | Mismatch between Cocoa '\x0' and Carbon '\u00d3' for virtual key 4 with |
| 8369 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 8370 | | |
| 8371 | | Mismatch between Cocoa '\x0' and Carbon '\u02d9' for virtual key 4 with |
| 8372 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 8373 | | |
| 8374 | | Mismatch between Cocoa '\x0' and Carbon '\u00d3' for virtual key 4 with |
| 8375 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 8376 | | |
| 8377 | | Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with |
| 8378 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 8379 | | |
| 8380 | | Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with |
| 8381 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 8382 | | |
| 8383 | | Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with |
| 8384 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 8385 | | |
| 8386 | | Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with |
| 8387 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 8388 | | |
| 8389 | | Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with |
| 8390 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 8391 | | |
| 8392 | | Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with |
| 8393 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 8394 | | |
| 8395 | | Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with |
| 8396 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 8397 | | |
| 8398 | | Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with |
| 8399 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 8400 | | |
| 8401 | | > hide #4 |
| 8402 | | |
| 8403 | | > show #4 cartoons |
| 8404 | | |
| 8405 | | > mmaker #4 to #2.4 |
| 8406 | | |
| 8407 | | Parameters |
| 8408 | | --- |
| 8409 | | Chain pairing | bb |
| 8410 | | Alignment algorithm | Needleman-Wunsch |
| 8411 | | Similarity matrix | BLOSUM-62 |
| 8412 | | SS fraction | 0.3 |
| 8413 | | Gap open (HH/SS/other) | 18/18/6 |
| 8414 | | Gap extend | 1 |
| 8415 | | SS matrix | | | H | S | O |
| 8416 | | ---|---|---|--- |
| 8417 | | H | 6 | -9 | -6 |
| 8418 | | S | | 6 | -6 |
| 8419 | | O | | | 4 |
| 8420 | | Iteration cutoff | 2 |
| 8421 | | |
| 8422 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain A (#2.4) with 7sh2, chain A (#4), |
| 8423 | | sequence alignment score = 2049.6 |
| 8424 | | RMSD between 397 pruned atom pairs is 0.760 angstroms; (across all 404 pairs: |
| 8425 | | 0.876) |
| 8426 | | |
| 8427 | | |
| 8428 | | > hide #!3 models |
| 8429 | | |
| 8430 | | > mmaker #4 to #2.1 |
| 8431 | | |
| 8432 | | Parameters |
| 8433 | | --- |
| 8434 | | Chain pairing | bb |
| 8435 | | Alignment algorithm | Needleman-Wunsch |
| 8436 | | Similarity matrix | BLOSUM-62 |
| 8437 | | SS fraction | 0.3 |
| 8438 | | Gap open (HH/SS/other) | 18/18/6 |
| 8439 | | Gap extend | 1 |
| 8440 | | SS matrix | | | H | S | O |
| 8441 | | ---|---|---|--- |
| 8442 | | H | 6 | -9 | -6 |
| 8443 | | S | | 6 | -6 |
| 8444 | | O | | | 4 |
| 8445 | | Iteration cutoff | 2 |
| 8446 | | |
| 8447 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with 7sh2, chain A (#4), |
| 8448 | | sequence alignment score = 2071.6 |
| 8449 | | RMSD between 394 pruned atom pairs is 0.767 angstroms; (across all 404 pairs: |
| 8450 | | 0.914) |
| 8451 | | |
| 8452 | | |
| 8453 | | > mmaker #4/A-H to #2.1/A-H pair ss |
| 8454 | | |
| 8455 | | Parameters |
| 8456 | | --- |
| 8457 | | Chain pairing | ss |
| 8458 | | Alignment algorithm | Needleman-Wunsch |
| 8459 | | Similarity matrix | BLOSUM-62 |
| 8460 | | SS fraction | 0.3 |
| 8461 | | Gap open (HH/SS/other) | 18/18/6 |
| 8462 | | Gap extend | 1 |
| 8463 | | SS matrix | | | H | S | O |
| 8464 | | ---|---|---|--- |
| 8465 | | H | 6 | -9 | -6 |
| 8466 | | S | | 6 | -6 |
| 8467 | | O | | | 4 |
| 8468 | | Iteration cutoff | 2 |
| 8469 | | |
| 8470 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with 7sh2, chain A (#4), |
| 8471 | | sequence alignment score = 2071.6 |
| 8472 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain B (#2.1) with 7sh2, chain B (#4), |
| 8473 | | sequence alignment score = 1549.3 |
| 8474 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain C (#2.1) with 7sh2, chain C (#4), |
| 8475 | | sequence alignment score = 1601.1 |
| 8476 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain D (#2.1) with 7sh2, chain D (#4), |
| 8477 | | sequence alignment score = 1653.9 |
| 8478 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain E (#2.1) with 7sh2, chain E (#4), |
| 8479 | | sequence alignment score = 1670.9 |
| 8480 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain F (#2.1) with 7sh2, chain F (#4), |
| 8481 | | sequence alignment score = 947.7 |
| 8482 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain G (#2.1) with 7sh2, chain G (#4), |
| 8483 | | sequence alignment score = 1277.2 |
| 8484 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain H (#2.1) with 7sh2, chain H (#4), |
| 8485 | | sequence alignment score = 988.1 |
| 8486 | | RMSD between 2240 pruned atom pairs is 0.786 angstroms; (across all 2492 |
| 8487 | | pairs: 1.429) |
| 8488 | | |
| 8489 | | |
| 8490 | | > rename #4 Sc-911-OpenDNA-7SH2 id #3.6 |
| 8491 | | |
| 8492 | | > show #!3 models |
| 8493 | | |
| 8494 | | > hide #!3.5 models |
| 8495 | | |
| 8496 | | > mmaker #3.6/A-H to #2.1/A-H pair ss |
| 8497 | | |
| 8498 | | Parameters |
| 8499 | | --- |
| 8500 | | Chain pairing | ss |
| 8501 | | Alignment algorithm | Needleman-Wunsch |
| 8502 | | Similarity matrix | BLOSUM-62 |
| 8503 | | SS fraction | 0.3 |
| 8504 | | Gap open (HH/SS/other) | 18/18/6 |
| 8505 | | Gap extend | 1 |
| 8506 | | SS matrix | | | H | S | O |
| 8507 | | ---|---|---|--- |
| 8508 | | H | 6 | -9 | -6 |
| 8509 | | S | | 6 | -6 |
| 8510 | | O | | | 4 |
| 8511 | | Iteration cutoff | 2 |
| 8512 | | |
| 8513 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with Sc-911-OpenDNA-7SH2, |
| 8514 | | chain A (#3.6), sequence alignment score = 2071.6 |
| 8515 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain B (#2.1) with Sc-911-OpenDNA-7SH2, |
| 8516 | | chain B (#3.6), sequence alignment score = 1549.3 |
| 8517 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain C (#2.1) with Sc-911-OpenDNA-7SH2, |
| 8518 | | chain C (#3.6), sequence alignment score = 1601.1 |
| 8519 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain D (#2.1) with Sc-911-OpenDNA-7SH2, |
| 8520 | | chain D (#3.6), sequence alignment score = 1653.9 |
| 8521 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain E (#2.1) with Sc-911-OpenDNA-7SH2, |
| 8522 | | chain E (#3.6), sequence alignment score = 1670.9 |
| 8523 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain F (#2.1) with Sc-911-OpenDNA-7SH2, |
| 8524 | | chain F (#3.6), sequence alignment score = 947.7 |
| 8525 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain G (#2.1) with Sc-911-OpenDNA-7SH2, |
| 8526 | | chain G (#3.6), sequence alignment score = 1277.2 |
| 8527 | | Matchmaker Stat1-Rsr115-Ct4.pdb, chain H (#2.1) with Sc-911-OpenDNA-7SH2, |
| 8528 | | chain H (#3.6), sequence alignment score = 988.1 |
| 8529 | | RMSD between 2240 pruned atom pairs is 0.786 angstroms; (across all 2492 |
| 8530 | | pairs: 1.429) |
| 8531 | | |
| 8532 | | |
| 8533 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 8534 | | > Institute/Documents/Draft/ScRPD/Deposite/eLife-77469_maps-models_Michael E. |
| 8535 | | > O'Donnell/RFC−DNA1−DNA2.pdb" |
| 8536 | | |
| 8537 | | Chain information for RFC−DNA1−DNA2.pdb #4 |
| 8538 | | --- |
| 8539 | | Chain | Description |
| 8540 | | A | No description available |
| 8541 | | B | No description available |
| 8542 | | C | No description available |
| 8543 | | D | No description available |
| 8544 | | E | No description available |
| 8545 | | I | No description available |
| 8546 | | J | No description available |
| 8547 | | K | No description available |
| 8548 | | L | No description available |
| 8549 | | |
| 8550 | | |
| 8551 | | > hide #4 |
| 8552 | | |
| 8553 | | > show #4 cartoons |
| 8554 | | |
| 8555 | | > hide #!3 models |
| 8556 | | |
| 8557 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8558 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 8559 | | |
| 8560 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8561 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 8562 | | |
| 8563 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8564 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 8565 | | |
| 8566 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8567 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 8568 | | |
| 8569 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8570 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 8571 | | |
| 8572 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8573 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 8574 | | |
| 8575 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8576 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 8577 | | |
| 8578 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8579 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 8580 | | |
| 8581 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8582 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 8583 | | |
| 8584 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8585 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 8586 | | |
| 8587 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8588 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 8589 | | |
| 8590 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8591 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 8592 | | |
| 8593 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8594 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 8595 | | |
| 8596 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8597 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 8598 | | |
| 8599 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8600 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 8601 | | |
| 8602 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 8603 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 8604 | | |
| 8605 | | > mmaker #4/A-H to #2.4/A-H pair ss |
| 8606 | | |
| 8607 | | Different number of reference/match chains (8 ref, 5 match) |
| 8608 | | |
| 8609 | | > mmaker #4/A- to #2.4/A-E pair ss |
| 8610 | | |
| 8611 | | > matchmaker #4/A- to #2.4/A-E pair ss |
| 8612 | | |
| 8613 | | Missing or invalid "matchAtoms" argument: only initial part "#4/A" of atom |
| 8614 | | specifier valid |
| 8615 | | |
| 8616 | | > mmaker #4/A-E to #2.4/A-E pair ss |
| 8617 | | |
| 8618 | | Parameters |
| 8619 | | --- |
| 8620 | | Chain pairing | ss |
| 8621 | | Alignment algorithm | Needleman-Wunsch |
| 8622 | | Similarity matrix | BLOSUM-62 |
| 8623 | | SS fraction | 0.3 |
| 8624 | | Gap open (HH/SS/other) | 18/18/6 |
| 8625 | | Gap extend | 1 |
| 8626 | | SS matrix | | | H | S | O |
| 8627 | | ---|---|---|--- |
| 8628 | | H | 6 | -9 | -6 |
| 8629 | | S | | 6 | -6 |
| 8630 | | O | | | 4 |
| 8631 | | Iteration cutoff | 2 |
| 8632 | | |
| 8633 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain A (#2.4) with RFC−DNA1−DNA2.pdb, chain A |
| 8634 | | (#4), sequence alignment score = 303.5 |
| 8635 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with RFC−DNA1−DNA2.pdb, chain B |
| 8636 | | (#4), sequence alignment score = 1535.5 |
| 8637 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain C (#2.4) with RFC−DNA1−DNA2.pdb, chain C |
| 8638 | | (#4), sequence alignment score = 1581.3 |
| 8639 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with RFC−DNA1−DNA2.pdb, chain D |
| 8640 | | (#4), sequence alignment score = 1624.5 |
| 8641 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain E (#2.4) with RFC−DNA1−DNA2.pdb, chain E |
| 8642 | | (#4), sequence alignment score = 1576.3 |
| 8643 | | RMSD between 1337 pruned atom pairs is 0.871 angstroms; (across all 1631 |
| 8644 | | pairs: 3.361) |
| 8645 | | |
| 8646 | | |
| 8647 | | > close #4 |
| 8648 | | |
| 8649 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 8650 | | > Institute/Documents/Draft/ScRPD/Deposite/eLife-77469_maps-models_Michael E. |
| 8651 | | > O'Donnell/RFC−closed PCNA−DNA1.pdb" |
| 8652 | | |
| 8653 | | Chain information for RFC−closed PCNA−DNA1.pdb #4 |
| 8654 | | --- |
| 8655 | | Chain | Description |
| 8656 | | A | No description available |
| 8657 | | B | No description available |
| 8658 | | C | No description available |
| 8659 | | D | No description available |
| 8660 | | E | No description available |
| 8661 | | F | No description available |
| 8662 | | G | No description available |
| 8663 | | H | No description available |
| 8664 | | I | No description available |
| 8665 | | J | No description available |
| 8666 | | |
| 8667 | | |
| 8668 | | > hide #4 |
| 8669 | | |
| 8670 | | > show #4 cartoons |
| 8671 | | |
| 8672 | | > mmaker #4/A-H to #2.4/A-H pair ss |
| 8673 | | |
| 8674 | | Parameters |
| 8675 | | --- |
| 8676 | | Chain pairing | ss |
| 8677 | | Alignment algorithm | Needleman-Wunsch |
| 8678 | | Similarity matrix | BLOSUM-62 |
| 8679 | | SS fraction | 0.3 |
| 8680 | | Gap open (HH/SS/other) | 18/18/6 |
| 8681 | | Gap extend | 1 |
| 8682 | | SS matrix | | | H | S | O |
| 8683 | | ---|---|---|--- |
| 8684 | | H | 6 | -9 | -6 |
| 8685 | | S | | 6 | -6 |
| 8686 | | O | | | 4 |
| 8687 | | Iteration cutoff | 2 |
| 8688 | | |
| 8689 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain A (#2.4) with RFC−closed PCNA−DNA1.pdb, |
| 8690 | | chain A (#4), sequence alignment score = 342.7 |
| 8691 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with RFC−closed PCNA−DNA1.pdb, |
| 8692 | | chain B (#4), sequence alignment score = 1559.5 |
| 8693 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain C (#2.4) with RFC−closed PCNA−DNA1.pdb, |
| 8694 | | chain C (#4), sequence alignment score = 1578.9 |
| 8695 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with RFC−closed PCNA−DNA1.pdb, |
| 8696 | | chain D (#4), sequence alignment score = 1611.9 |
| 8697 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain E (#2.4) with RFC−closed PCNA−DNA1.pdb, |
| 8698 | | chain E (#4), sequence alignment score = 1612.3 |
| 8699 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain F (#2.4) with RFC−closed PCNA−DNA1.pdb, |
| 8700 | | chain F (#4), sequence alignment score = 202.5 |
| 8701 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain G (#2.4) with RFC−closed PCNA−DNA1.pdb, |
| 8702 | | chain G (#4), sequence alignment score = 210.2 |
| 8703 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain H (#2.4) with RFC−closed PCNA−DNA1.pdb, |
| 8704 | | chain H (#4), sequence alignment score = 199.5 |
| 8705 | | RMSD between 1347 pruned atom pairs is 0.830 angstroms; (across all 2380 |
| 8706 | | pairs: 30.360) |
| 8707 | | |
| 8708 | | |
| 8709 | | > close #4 |
| 8710 | | |
| 8711 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 8712 | | > Institute/Documents/Draft/ScRPD/Deposite/eLife-77469_maps-models_Michael E. |
| 8713 | | > O'Donnell/RFC−open PCNA−DNA1.pdb" |
| 8714 | | |
| 8715 | | Chain information for RFC−open PCNA−DNA1.pdb #4 |
| 8716 | | --- |
| 8717 | | Chain | Description |
| 8718 | | A | No description available |
| 8719 | | B | No description available |
| 8720 | | C | No description available |
| 8721 | | D | No description available |
| 8722 | | E | No description available |
| 8723 | | F | No description available |
| 8724 | | G | No description available |
| 8725 | | H | No description available |
| 8726 | | I | No description available |
| 8727 | | J | No description available |
| 8728 | | |
| 8729 | | |
| 8730 | | > hide #4 |
| 8731 | | |
| 8732 | | > show #4 cartoons |
| 8733 | | |
| 8734 | | > mmaker #4/A-H to #2.4/A-H pair ss |
| 8735 | | |
| 8736 | | Parameters |
| 8737 | | --- |
| 8738 | | Chain pairing | ss |
| 8739 | | Alignment algorithm | Needleman-Wunsch |
| 8740 | | Similarity matrix | BLOSUM-62 |
| 8741 | | SS fraction | 0.3 |
| 8742 | | Gap open (HH/SS/other) | 18/18/6 |
| 8743 | | Gap extend | 1 |
| 8744 | | SS matrix | | | H | S | O |
| 8745 | | ---|---|---|--- |
| 8746 | | H | 6 | -9 | -6 |
| 8747 | | S | | 6 | -6 |
| 8748 | | O | | | 4 |
| 8749 | | Iteration cutoff | 2 |
| 8750 | | |
| 8751 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain A (#2.4) with RFC−open PCNA−DNA1.pdb, |
| 8752 | | chain A (#4), sequence alignment score = 345 |
| 8753 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with RFC−open PCNA−DNA1.pdb, |
| 8754 | | chain B (#4), sequence alignment score = 1561.9 |
| 8755 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain C (#2.4) with RFC−open PCNA−DNA1.pdb, |
| 8756 | | chain C (#4), sequence alignment score = 1577.7 |
| 8757 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with RFC−open PCNA−DNA1.pdb, |
| 8758 | | chain D (#4), sequence alignment score = 1613.1 |
| 8759 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain E (#2.4) with RFC−open PCNA−DNA1.pdb, |
| 8760 | | chain E (#4), sequence alignment score = 1620.7 |
| 8761 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain F (#2.4) with RFC−open PCNA−DNA1.pdb, |
| 8762 | | chain F (#4), sequence alignment score = 205.6 |
| 8763 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain G (#2.4) with RFC−open PCNA−DNA1.pdb, |
| 8764 | | chain G (#4), sequence alignment score = 203 |
| 8765 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain H (#2.4) with RFC−open PCNA−DNA1.pdb, |
| 8766 | | chain H (#4), sequence alignment score = 207.2 |
| 8767 | | RMSD between 1477 pruned atom pairs is 0.760 angstroms; (across all 2390 |
| 8768 | | pairs: 5.815) |
| 8769 | | |
| 8770 | | |
| 8771 | | > hide #!2 models |
| 8772 | | |
| 8773 | | > show #!3 models |
| 8774 | | |
| 8775 | | > hide #!3.6 models |
| 8776 | | |
| 8777 | | > show #!3.5 models |
| 8778 | | |
| 8779 | | > hide #!4 models |
| 8780 | | |
| 8781 | | > show #!4 models |
| 8782 | | |
| 8783 | | > hide #!4 models |
| 8784 | | |
| 8785 | | > show #!4 models |
| 8786 | | |
| 8787 | | > hide #!4 models |
| 8788 | | |
| 8789 | | > show #!4 models |
| 8790 | | |
| 8791 | | > hide #!4 models |
| 8792 | | |
| 8793 | | > show #!4 models |
| 8794 | | |
| 8795 | | > hide #!3.5 models |
| 8796 | | |
| 8797 | | > show #!3.5 models |
| 8798 | | |
| 8799 | | > hide #!3.5 models |
| 8800 | | |
| 8801 | | > show #!3.5 models |
| 8802 | | |
| 8803 | | > hide #!4 models |
| 8804 | | |
| 8805 | | > show #!4 models |
| 8806 | | |
| 8807 | | > hide #!4 models |
| 8808 | | |
| 8809 | | > show #!4 models |
| 8810 | | |
| 8811 | | > hide #!4 models |
| 8812 | | |
| 8813 | | > show #!4 models |
| 8814 | | |
| 8815 | | > hide #!4 models |
| 8816 | | |
| 8817 | | > show #!4 models |
| 8818 | | |
| 8819 | | > hide #!4 models |
| 8820 | | |
| 8821 | | > show #!4 models |
| 8822 | | |
| 8823 | | > hide #!3.5 models |
| 8824 | | |
| 8825 | | > close #4 |
| 8826 | | |
| 8827 | | > show #!3.5 models |
| 8828 | | |
| 8829 | | > hide #!3.5 models |
| 8830 | | |
| 8831 | | > show #!3.4 models |
| 8832 | | |
| 8833 | | > hide #!3.4 models |
| 8834 | | |
| 8835 | | > show #!3.5 models |
| 8836 | | |
| 8837 | | > show #!3.6 models |
| 8838 | | |
| 8839 | | > cartoon style nucleic xsection oval width 2.5 thickness 2.5 |
| 8840 | | |
| 8841 | | > cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true |
| 8842 | | > xsection oval width 2.75 thickness 1 arrowScale 1.5 |
| 8843 | | |
| 8844 | | > color /A #FFB381 |
| 8845 | | |
| 8846 | | > color /B #D7819F |
| 8847 | | |
| 8848 | | > color /C #B48FE3 |
| 8849 | | |
| 8850 | | > color /D #D7CD85 |
| 8851 | | |
| 8852 | | > color /E salmon |
| 8853 | | |
| 8854 | | > color /F navajo white |
| 8855 | | |
| 8856 | | > color /G #CAC6FD |
| 8857 | | |
| 8858 | | > color /H plum |
| 8859 | | |
| 8860 | | > hide #!3.6 models |
| 8861 | | |
| 8862 | | > hide #!3.5 models |
| 8863 | | |
| 8864 | | > show #!3.6 models |
| 8865 | | |
| 8866 | | > hide #!3.6 models |
| 8867 | | |
| 8868 | | > show #!3.5 models |
| 8869 | | |
| 8870 | | > setattr #3.5/F c chain_id X |
| 8871 | | |
| 8872 | | Assigning chain_id attribute to 1 item |
| 8873 | | |
| 8874 | | > setattr #3.5/H c chain_id F |
| 8875 | | |
| 8876 | | Assigning chain_id attribute to 1 item |
| 8877 | | |
| 8878 | | > setattr #3.5/G c chain_id H |
| 8879 | | |
| 8880 | | Assigning chain_id attribute to 1 item |
| 8881 | | |
| 8882 | | > setattr #3.5/X c chain_id G |
| 8883 | | |
| 8884 | | Assigning chain_id attribute to 1 item |
| 8885 | | |
| 8886 | | > hide #!3.5 models |
| 8887 | | |
| 8888 | | > show #!3.1 models |
| 8889 | | |
| 8890 | | > hide #!3.1 models |
| 8891 | | |
| 8892 | | > show #!3.2 models |
| 8893 | | |
| 8894 | | > hide #!3.2 models |
| 8895 | | |
| 8896 | | > show #!3.1 models |
| 8897 | | |
| 8898 | | > select #3.1/C:152 |
| 8899 | | |
| 8900 | | 9 atoms, 8 bonds, 1 residue, 1 model selected |
| 8901 | | |
| 8902 | | > select #3.1/A:638@CD2 |
| 8903 | | |
| 8904 | | 1 atom, 1 residue, 1 model selected |
| 8905 | | |
| 8906 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8907 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 8908 | | |
| 8909 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8910 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 8911 | | |
| 8912 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8913 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 8914 | | |
| 8915 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8916 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 8917 | | |
| 8918 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8919 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 8920 | | |
| 8921 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8922 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 8923 | | |
| 8924 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8925 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 8926 | | |
| 8927 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8928 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 8929 | | |
| 8930 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8931 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 8932 | | |
| 8933 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8934 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 8935 | | |
| 8936 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8937 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 8938 | | |
| 8939 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8940 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 8941 | | |
| 8942 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8943 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 8944 | | |
| 8945 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8946 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 8947 | | |
| 8948 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8949 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 8950 | | |
| 8951 | | Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with |
| 8952 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 8953 | | |
| 8954 | | > select up |
| 8955 | | |
| 8956 | | 14 atoms, 15 bonds, 1 residue, 1 model selected |
| 8957 | | |
| 8958 | | Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with |
| 8959 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 8960 | | |
| 8961 | | Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with |
| 8962 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 8963 | | |
| 8964 | | Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with |
| 8965 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 8966 | | |
| 8967 | | Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with |
| 8968 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 8969 | | |
| 8970 | | Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with |
| 8971 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 8972 | | |
| 8973 | | Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with |
| 8974 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 8975 | | |
| 8976 | | Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with |
| 8977 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 8978 | | |
| 8979 | | Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with |
| 8980 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 8981 | | |
| 8982 | | Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with |
| 8983 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 8984 | | |
| 8985 | | Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with |
| 8986 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 8987 | | |
| 8988 | | Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with |
| 8989 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 8990 | | |
| 8991 | | Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with |
| 8992 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 8993 | | |
| 8994 | | Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with |
| 8995 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 8996 | | |
| 8997 | | Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with |
| 8998 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 8999 | | |
| 9000 | | Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with |
| 9001 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 9002 | | |
| 9003 | | Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with |
| 9004 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 9005 | | |
| 9006 | | > color sel lime |
| 9007 | | |
| 9008 | | > undo |
| 9009 | | |
| 9010 | | > color sel lime atoms |
| 9011 | | |
| 9012 | | > color sel byhetero |
| 9013 | | |
| 9014 | | > select clear |
| 9015 | | |
| 9016 | | > show #!2 models |
| 9017 | | |
| 9018 | | > show #!2.5 models |
| 9019 | | |
| 9020 | | Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with |
| 9021 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 9022 | | |
| 9023 | | Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with |
| 9024 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 9025 | | |
| 9026 | | Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with |
| 9027 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 9028 | | |
| 9029 | | Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with |
| 9030 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 9031 | | |
| 9032 | | Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with |
| 9033 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 9034 | | |
| 9035 | | Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with |
| 9036 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 9037 | | |
| 9038 | | Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with |
| 9039 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 9040 | | |
| 9041 | | Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with |
| 9042 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 9043 | | |
| 9044 | | Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with |
| 9045 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 9046 | | |
| 9047 | | Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with |
| 9048 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 9049 | | |
| 9050 | | Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with |
| 9051 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 9052 | | |
| 9053 | | Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with |
| 9054 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 9055 | | |
| 9056 | | Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with |
| 9057 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 9058 | | |
| 9059 | | Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with |
| 9060 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 9061 | | |
| 9062 | | Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with |
| 9063 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 9064 | | |
| 9065 | | Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with |
| 9066 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 9067 | | |
| 9068 | | > select #2/A:225-245 |
| 9069 | | |
| 9070 | | 895 atoms, 915 bonds, 105 residues, 5 models selected |
| 9071 | | |
| 9072 | | > color sel yellow green cartoons |
| 9073 | | |
| 9074 | | > show #!2.1 models |
| 9075 | | |
| 9076 | | > hide #!2 models |
| 9077 | | |
| 9078 | | > show #!2.2 models |
| 9079 | | |
| 9080 | | > show #!2.3 models |
| 9081 | | |
| 9082 | | > show #!2.4 models |
| 9083 | | |
| 9084 | | > hide #!2.5 models |
| 9085 | | |
| 9086 | | > hide #!2.4 models |
| 9087 | | |
| 9088 | | > hide #!2.3 models |
| 9089 | | |
| 9090 | | > hide #!2.2 models |
| 9091 | | |
| 9092 | | > hide #!2.1 models |
| 9093 | | |
| 9094 | | > show #!2.1 models |
| 9095 | | |
| 9096 | | > select clear |
| 9097 | | |
| 9098 | | > select #2.1/A:239 |
| 9099 | | |
| 9100 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 9101 | | |
| 9102 | | > select add #2.1/A:240 |
| 9103 | | |
| 9104 | | 12 atoms, 10 bonds, 2 residues, 1 model selected |
| 9105 | | |
| 9106 | | > select add #2.1/A:241 |
| 9107 | | |
| 9108 | | 20 atoms, 17 bonds, 3 residues, 1 model selected |
| 9109 | | |
| 9110 | | > select add #2.1/A:242 |
| 9111 | | |
| 9112 | | 32 atoms, 29 bonds, 4 residues, 1 model selected |
| 9113 | | |
| 9114 | | > setattribute sel res ss_type 0 |
| 9115 | | |
| 9116 | | Unknown command: setattribute sel res ss_type 0 |
| 9117 | | |
| 9118 | | > setattri sel res ss_type 0 |
| 9119 | | |
| 9120 | | Unknown command: setattri sel res ss_type 0 |
| 9121 | | |
| 9122 | | > setattr sel res ss_type 0 |
| 9123 | | |
| 9124 | | Assigning ss_type attribute to 4 items |
| 9125 | | |
| 9126 | | > select clear |
| 9127 | | |
| 9128 | | > hide #!2 models |
| 9129 | | |
| 9130 | | > hide #!2.1 models |
| 9131 | | |
| 9132 | | > show #!2.5 models |
| 9133 | | |
| 9134 | | > hide #!2.5 models |
| 9135 | | |
| 9136 | | > show #!2.5 models |
| 9137 | | |
| 9138 | | > hide #!2.5 models |
| 9139 | | |
| 9140 | | > show #!2.5 models |
| 9141 | | |
| 9142 | | > hide #!2.5 models |
| 9143 | | |
| 9144 | | > show #!2.5 models |
| 9145 | | |
| 9146 | | > hide #!2.5 models |
| 9147 | | |
| 9148 | | > show #!2.5 models |
| 9149 | | |
| 9150 | | > hide #!2.5 models |
| 9151 | | |
| 9152 | | > show #!2.5 models |
| 9153 | | |
| 9154 | | > hide #!2.5 models |
| 9155 | | |
| 9156 | | > show #!2.5 models |
| 9157 | | |
| 9158 | | > hide #!2.5 models |
| 9159 | | |
| 9160 | | > show #!2.5 models |
| 9161 | | |
| 9162 | | > ui tool show "Side View" |
| 9163 | | |
| 9164 | | > hide #!2 models |
| 9165 | | |
| 9166 | | > show #!2 models |
| 9167 | | |
| 9168 | | > hide #!2 models |
| 9169 | | |
| 9170 | | > show #!2 models |
| 9171 | | |
| 9172 | | > hide #!2.5 models |
| 9173 | | |
| 9174 | | > show #!2.5 models |
| 9175 | | |
| 9176 | | > hide #!2.5 models |
| 9177 | | |
| 9178 | | > select #3.1/A:455 |
| 9179 | | |
| 9180 | | 6 atoms, 5 bonds, 1 residue, 1 model selected |
| 9181 | | |
| 9182 | | > select #3.1/A:456 |
| 9183 | | |
| 9184 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 9185 | | |
| 9186 | | > select add #3.1/A:463 |
| 9187 | | |
| 9188 | | 16 atoms, 14 bonds, 2 residues, 1 model selected |
| 9189 | | |
| 9190 | | > select up |
| 9191 | | |
| 9192 | | 68 atoms, 68 bonds, 8 residues, 1 model selected |
| 9193 | | |
| 9194 | | > color sel yellow green cartoons |
| 9195 | | |
| 9196 | | > select clear |
| 9197 | | |
| 9198 | | > show #!2.5 models |
| 9199 | | |
| 9200 | | > hide #!2.5 models |
| 9201 | | |
| 9202 | | > hide #!3.1 models |
| 9203 | | |
| 9204 | | > show #!3.2 models |
| 9205 | | |
| 9206 | | > select #3.2/A:316@CE2 |
| 9207 | | |
| 9208 | | 1 atom, 1 residue, 1 model selected |
| 9209 | | |
| 9210 | | > select up |
| 9211 | | |
| 9212 | | 12 atoms, 12 bonds, 1 residue, 1 model selected |
| 9213 | | |
| 9214 | | > color sel lime atoms |
| 9215 | | |
| 9216 | | > color sel byhetero |
| 9217 | | |
| 9218 | | > select clear |
| 9219 | | |
| 9220 | | > hide #!3.2 models |
| 9221 | | |
| 9222 | | > show #!3.3 models |
| 9223 | | |
| 9224 | | > select #3.3/C:175 |
| 9225 | | |
| 9226 | | 11 atoms, 10 bonds, 1 residue, 1 model selected |
| 9227 | | |
| 9228 | | > select #3.3/C:173 |
| 9229 | | |
| 9230 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 9231 | | |
| 9232 | | > select up |
| 9233 | | |
| 9234 | | 2 atoms, 1 bond, 1 residue, 1 model selected |
| 9235 | | |
| 9236 | | > select up |
| 9237 | | |
| 9238 | | 11 atoms, 11 bonds, 1 residue, 1 model selected |
| 9239 | | |
| 9240 | | > color sel yellow green cartoons |
| 9241 | | |
| 9242 | | > undo |
| 9243 | | |
| 9244 | | > color sel lime atoms |
| 9245 | | |
| 9246 | | > color sel byhetero |
| 9247 | | |
| 9248 | | > select clear |
| 9249 | | |
| 9250 | | > hide #!3.3 models |
| 9251 | | |
| 9252 | | > show #!3.3 models |
| 9253 | | |
| 9254 | | > hide #!3.3 models |
| 9255 | | |
| 9256 | | > show #!3.4 models |
| 9257 | | |
| 9258 | | > show #!3.1 models |
| 9259 | | |
| 9260 | | > hide #!3.4 models |
| 9261 | | |
| 9262 | | > hide #!3.1 models |
| 9263 | | |
| 9264 | | > show #!3.3 models |
| 9265 | | |
| 9266 | | > hide #!3.3 models |
| 9267 | | |
| 9268 | | > show #!3.4 models |
| 9269 | | |
| 9270 | | > select #3.4/A:638 |
| 9271 | | |
| 9272 | | 14 atoms, 15 bonds, 1 residue, 1 model selected |
| 9273 | | |
| 9274 | | > show sel atoms |
| 9275 | | |
| 9276 | | > style sel stick |
| 9277 | | |
| 9278 | | Changed 14 atom styles |
| 9279 | | |
| 9280 | | > color sel lime atoms |
| 9281 | | |
| 9282 | | > color sel byhetero |
| 9283 | | |
| 9284 | | > select clear |
| 9285 | | |
| 9286 | | > hide #!3.4 models |
| 9287 | | |
| 9288 | | > show #!3.4 models |
| 9289 | | |
| 9290 | | > show #!3.1 models |
| 9291 | | |
| 9292 | | > hide #!3.4 models |
| 9293 | | |
| 9294 | | > show #!3.4 models |
| 9295 | | |
| 9296 | | > hide #!3.4 models |
| 9297 | | |
| 9298 | | > show #!3.4 models |
| 9299 | | |
| 9300 | | > hide #!3.1 models |
| 9301 | | |
| 9302 | | > select #3.4/A:455 |
| 9303 | | |
| 9304 | | 6 atoms, 5 bonds, 1 residue, 1 model selected |
| 9305 | | |
| 9306 | | > select #3.4/A:456 |
| 9307 | | |
| 9308 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 9309 | | |
| 9310 | | > select add #3.4/A:459 |
| 9311 | | |
| 9312 | | 16 atoms, 14 bonds, 2 residues, 1 model selected |
| 9313 | | |
| 9314 | | > hide #!3.4 models |
| 9315 | | |
| 9316 | | > show #!3.1 models |
| 9317 | | |
| 9318 | | > hide #!3.1 models |
| 9319 | | |
| 9320 | | > show #!3.4 models |
| 9321 | | |
| 9322 | | > select add #3.4/A:458 |
| 9323 | | |
| 9324 | | 27 atoms, 24 bonds, 3 residues, 1 model selected |
| 9325 | | |
| 9326 | | > select add #3.4/A:457 |
| 9327 | | |
| 9328 | | 36 atoms, 32 bonds, 4 residues, 1 model selected |
| 9329 | | |
| 9330 | | > hide #!3.4 models |
| 9331 | | |
| 9332 | | > show #!3.1 models |
| 9333 | | |
| 9334 | | > select #3.1/A:463 |
| 9335 | | |
| 9336 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 9337 | | |
| 9338 | | > hide #!3.1 models |
| 9339 | | |
| 9340 | | > show #!3.2 models |
| 9341 | | |
| 9342 | | > hide #!3.2 models |
| 9343 | | |
| 9344 | | > show #!3.3 models |
| 9345 | | |
| 9346 | | > hide #!3.3 models |
| 9347 | | |
| 9348 | | > show #!3.4 models |
| 9349 | | |
| 9350 | | > select #3.4/A:459 |
| 9351 | | |
| 9352 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 9353 | | |
| 9354 | | > select add #3.4/A:458 |
| 9355 | | |
| 9356 | | 19 atoms, 17 bonds, 2 residues, 1 model selected |
| 9357 | | |
| 9358 | | > select add #3.4/A:457 |
| 9359 | | |
| 9360 | | 28 atoms, 25 bonds, 3 residues, 1 model selected |
| 9361 | | |
| 9362 | | > select add #3.4/A:456 |
| 9363 | | |
| 9364 | | 36 atoms, 32 bonds, 4 residues, 1 model selected |
| 9365 | | |
| 9366 | | > color sel yellow green cartoons |
| 9367 | | |
| 9368 | | > select clear |
| 9369 | | |
| 9370 | | > show #!3.1 models |
| 9371 | | |
| 9372 | | > hide #!3.1 models |
| 9373 | | |
| 9374 | | > show #!3.5 models |
| 9375 | | |
| 9376 | | > hide #!3.4 models |
| 9377 | | |
| 9378 | | > select #3.5/A:638 |
| 9379 | | |
| 9380 | | 14 atoms, 15 bonds, 1 residue, 1 model selected |
| 9381 | | |
| 9382 | | > show sel atoms |
| 9383 | | |
| 9384 | | > style sel stick |
| 9385 | | |
| 9386 | | Changed 14 atom styles |
| 9387 | | |
| 9388 | | > color sel lime atoms |
| 9389 | | |
| 9390 | | > color sel byhetero |
| 9391 | | |
| 9392 | | > select clear |
| 9393 | | |
| 9394 | | > select #3.5/A:455 |
| 9395 | | |
| 9396 | | 6 atoms, 5 bonds, 1 residue, 1 model selected |
| 9397 | | |
| 9398 | | > select #3.5/A:456-461 |
| 9399 | | |
| 9400 | | 51 atoms, 51 bonds, 6 residues, 1 model selected |
| 9401 | | |
| 9402 | | > select #3.5/A:456-462 |
| 9403 | | |
| 9404 | | 60 atoms, 60 bonds, 7 residues, 1 model selected |
| 9405 | | |
| 9406 | | > color sel yellow green cartoons |
| 9407 | | |
| 9408 | | > select clear |
| 9409 | | |
| 9410 | | > select #3.5/F:111 |
| 9411 | | |
| 9412 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 9413 | | |
| 9414 | | > select add #3.5/F:116 |
| 9415 | | |
| 9416 | | 16 atoms, 14 bonds, 2 residues, 1 model selected |
| 9417 | | |
| 9418 | | > select up |
| 9419 | | |
| 9420 | | 245 atoms, 247 bonds, 29 residues, 1 model selected |
| 9421 | | |
| 9422 | | > select clear |
| 9423 | | |
| 9424 | | > select #3.5/F:111 |
| 9425 | | |
| 9426 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 9427 | | |
| 9428 | | > select add #3.5/F:115 |
| 9429 | | |
| 9430 | | 14 atoms, 12 bonds, 2 residues, 1 model selected |
| 9431 | | |
| 9432 | | > setattri #3.5/F:111-115 res ss_type 2 |
| 9433 | | |
| 9434 | | Unknown command: setattri #3.5/F:111-115 res ss_type 2 |
| 9435 | | |
| 9436 | | > setattr #3.5/F:111-115 res ss_type 2 |
| 9437 | | |
| 9438 | | Assigning ss_type attribute to 5 items |
| 9439 | | |
| 9440 | | > select clear |
| 9441 | | |
| 9442 | | > hide #!3.5 models |
| 9443 | | |
| 9444 | | > show #!3.6 models |
| 9445 | | |
| 9446 | | > select #3.6/H:283 |
| 9447 | | |
| 9448 | | 6 atoms, 5 bonds, 1 residue, 1 model selected |
| 9449 | | |
| 9450 | | > select #3.6/H:287 |
| 9451 | | |
| 9452 | | 7 atoms, 6 bonds, 1 residue, 1 model selected |
| 9453 | | |
| 9454 | | > setattr #3.6/H:283-287 res ss_type 2 |
| 9455 | | |
| 9456 | | Assigning ss_type attribute to 5 items |
| 9457 | | |
| 9458 | | > setattr #3.6/H:283-287 res ss_id 88 |
| 9459 | | |
| 9460 | | Assigning ss_id attribute to 5 items |
| 9461 | | |
| 9462 | | > select clear |
| 9463 | | |
| 9464 | | Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with |
| 9465 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 9466 | | |
| 9467 | | Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with |
| 9468 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 9469 | | |
| 9470 | | Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with |
| 9471 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 9472 | | |
| 9473 | | Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with |
| 9474 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 9475 | | |
| 9476 | | Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with |
| 9477 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 9478 | | |
| 9479 | | Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with |
| 9480 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 9481 | | |
| 9482 | | Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with |
| 9483 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 9484 | | |
| 9485 | | Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with |
| 9486 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 9487 | | |
| 9488 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 9489 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 9490 | | |
| 9491 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 9492 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 9493 | | |
| 9494 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 9495 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 9496 | | |
| 9497 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 9498 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 9499 | | |
| 9500 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 9501 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 9502 | | |
| 9503 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 9504 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 9505 | | |
| 9506 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 9507 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 9508 | | |
| 9509 | | Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with |
| 9510 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 9511 | | |
| 9512 | | > view v2 |
| 9513 | | |
| 9514 | | > view v3 |
| 9515 | | |
| 9516 | | > hide #!3.6 models |
| 9517 | | |
| 9518 | | > hide #!3 models |
| 9519 | | |
| 9520 | | > show #!2.5 models |
| 9521 | | |
| 9522 | | > view v3 |
| 9523 | | |
| 9524 | | > show #!2.4 models |
| 9525 | | |
| 9526 | | > hide #!2.5 models |
| 9527 | | |
| 9528 | | > show #!2.5 models |
| 9529 | | |
| 9530 | | > hide #!2.4 models |
| 9531 | | |
| 9532 | | > hide #!2.5 models |
| 9533 | | |
| 9534 | | > show #!3.1 models |
| 9535 | | |
| 9536 | | > hide #!3.1 models |
| 9537 | | |
| 9538 | | > show #!3.2 models |
| 9539 | | |
| 9540 | | > hide #!3.2 models |
| 9541 | | |
| 9542 | | > show #!3.2 models |
| 9543 | | |
| 9544 | | > select #3.2/A:90 |
| 9545 | | |
| 9546 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 9547 | | |
| 9548 | | > select add #3.2/A:83 |
| 9549 | | |
| 9550 | | 16 atoms, 14 bonds, 2 residues, 1 model selected |
| 9551 | | |
| 9552 | | > color #3.2/A:84-90 yellow green cartoons |
| 9553 | | |
| 9554 | | > select clear |
| 9555 | | |
| 9556 | | > hide #!3.2 models |
| 9557 | | |
| 9558 | | > show #!2.5 models |
| 9559 | | |
| 9560 | | > hide #!2.5 models |
| 9561 | | |
| 9562 | | > show #!3.1 models |
| 9563 | | |
| 9564 | | > hide #!3.1 models |
| 9565 | | |
| 9566 | | > show #!3.2 models |
| 9567 | | |
| 9568 | | Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with |
| 9569 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 9570 | | |
| 9571 | | Mismatch between Cocoa '\x0' and Carbon 'U' for virtual key 32 with |
| 9572 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 9573 | | |
| 9574 | | Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with |
| 9575 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 9576 | | |
| 9577 | | Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with |
| 9578 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 9579 | | |
| 9580 | | Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with |
| 9581 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 9582 | | |
| 9583 | | Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with |
| 9584 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 9585 | | |
| 9586 | | Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with |
| 9587 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 9588 | | |
| 9589 | | Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with |
| 9590 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 9591 | | |
| 9592 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 9593 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 9594 | | |
| 9595 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 9596 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 9597 | | |
| 9598 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 9599 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 9600 | | |
| 9601 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 9602 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 9603 | | |
| 9604 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 9605 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 9606 | | |
| 9607 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 9608 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 9609 | | |
| 9610 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 9611 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 9612 | | |
| 9613 | | Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with |
| 9614 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 9615 | | |
| 9616 | | > undo |
| 9617 | | |
| 9618 | | [Repeated 1 time(s)] |
| 9619 | | |
| 9620 | | > hide #!3.1 models |
| 9621 | | |
| 9622 | | > show #!3.3 models |
| 9623 | | |
| 9624 | | > hide #!3.3 models |
| 9625 | | |
| 9626 | | > show #!3.2 models |
| 9627 | | |
| 9628 | | > select #3.2/B:135 |
| 9629 | | |
| 9630 | | 6 atoms, 5 bonds, 1 residue, 1 model selected |
| 9631 | | |
| 9632 | | > select #3.2/A:90 |
| 9633 | | |
| 9634 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 9635 | | |
| 9636 | | > select add #3.2/A:84 |
| 9637 | | |
| 9638 | | 16 atoms, 14 bonds, 2 residues, 1 model selected |
| 9639 | | |
| 9640 | | > color #3.2/A:84-90 #FFB381 cartoons |
| 9641 | | |
| 9642 | | > select clear |
| 9643 | | |
| 9644 | | > hide #!3.2 models |
| 9645 | | |
| 9646 | | > show #!3.1 models |
| 9647 | | |
| 9648 | | > hide #!3.1 models |
| 9649 | | |
| 9650 | | > show #!3.2 models |
| 9651 | | |
| 9652 | | > select #3.2/A:117 |
| 9653 | | |
| 9654 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 9655 | | |
| 9656 | | > select add #3.2/A:116 |
| 9657 | | |
| 9658 | | 17 atoms, 15 bonds, 2 residues, 1 model selected |
| 9659 | | |
| 9660 | | > select add #3.2/A:115 |
| 9661 | | |
| 9662 | | 25 atoms, 22 bonds, 3 residues, 1 model selected |
| 9663 | | |
| 9664 | | > color sel yellow green cartoons |
| 9665 | | |
| 9666 | | > select clear |
| 9667 | | |
| 9668 | | > hide #!3.2 models |
| 9669 | | |
| 9670 | | > show #!3.3 models |
| 9671 | | |
| 9672 | | > hide #!3.3 models |
| 9673 | | |
| 9674 | | > show #!3.4 models |
| 9675 | | |
| 9676 | | > hide #!3.4 models |
| 9677 | | |
| 9678 | | > show #!3.5 models |
| 9679 | | |
| 9680 | | > hide #!3.5 models |
| 9681 | | |
| 9682 | | > show #!3.3 models |
| 9683 | | |
| 9684 | | > hide #!3.3 models |
| 9685 | | |
| 9686 | | > show #!3.2 models |
| 9687 | | |
| 9688 | | > hide #!3.2 models |
| 9689 | | |
| 9690 | | > show #!3.3 models |
| 9691 | | |
| 9692 | | > hide #!3.3 models |
| 9693 | | |
| 9694 | | > show #!3.4 models |
| 9695 | | |
| 9696 | | > hide #!3.4 models |
| 9697 | | |
| 9698 | | > show #!3.5 models |
| 9699 | | |
| 9700 | | > select #3.5/I-J |
| 9701 | | |
| 9702 | | 855 atoms, 955 bonds, 26 pseudobonds, 42 residues, 2 models selected |
| 9703 | | |
| 9704 | | > show sel atoms |
| 9705 | | |
| 9706 | | > nucleotides sel stubs |
| 9707 | | |
| 9708 | | > color #3.5/I medium orchid target ca |
| 9709 | | |
| 9710 | | > color #3.5/I medium orchid |
| 9711 | | |
| 9712 | | > color #3.5/J light sky blue |
| 9713 | | |
| 9714 | | > select clear |
| 9715 | | |
| 9716 | | > hide #!3.5 models |
| 9717 | | |
| 9718 | | > show #!3.6 models |
| 9719 | | |
| 9720 | | > show #3.6/t,p |
| 9721 | | |
| 9722 | | > nucleotides #3.6/t,p slubs |
| 9723 | | |
| 9724 | | Missing or invalid "representation" argument: Should be one of 'atoms', |
| 9725 | | 'fill', 'ladder', 'slab', 'stubs', or 'tube/slab' |
| 9726 | | |
| 9727 | | > nucleotides #3.6/t,p stubs |
| 9728 | | |
| 9729 | | > color #3.6/t plum |
| 9730 | | |
| 9731 | | > color #3.6/p light blue |
| 9732 | | |
| 9733 | | > select clear |
| 9734 | | |
| 9735 | | > select #3.6/A:225-245 |
| 9736 | | |
| 9737 | | 132 atoms, 134 bonds, 1 pseudobond, 16 residues, 2 models selected |
| 9738 | | |
| 9739 | | > select #3.6/A:225-244 |
| 9740 | | |
| 9741 | | 126 atoms, 128 bonds, 1 pseudobond, 15 residues, 2 models selected |
| 9742 | | |
| 9743 | | > color sel yellow green cartoons |
| 9744 | | |
| 9745 | | > select clear |
| 9746 | | |
| 9747 | | > view v3 |
| 9748 | | |
| 9749 | | > hide #!3.6 models |
| 9750 | | |
| 9751 | | > show #!3.1 models |
| 9752 | | |
| 9753 | | > hide #!3.1 models |
| 9754 | | |
| 9755 | | > show #!3.6 models |
| 9756 | | |
| 9757 | | Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with |
| 9758 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 9759 | | |
| 9760 | | Mismatch between Cocoa '\x0' and Carbon 'T' for virtual key 17 with |
| 9761 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 9762 | | |
| 9763 | | Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with |
| 9764 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 9765 | | |
| 9766 | | Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with |
| 9767 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 9768 | | |
| 9769 | | Mismatch between Cocoa '\x0' and Carbon '\u2020' for virtual key 17 with |
| 9770 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 9771 | | |
| 9772 | | Mismatch between Cocoa '\x0' and Carbon '\u02c7' for virtual key 17 with |
| 9773 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 9774 | | |
| 9775 | | Mismatch between Cocoa '\x0' and Carbon '\u2020' for virtual key 17 with |
| 9776 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 9777 | | |
| 9778 | | Mismatch between Cocoa '\x0' and Carbon '\u02c7' for virtual key 17 with |
| 9779 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 9780 | | |
| 9781 | | Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with |
| 9782 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 9783 | | |
| 9784 | | Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with |
| 9785 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 9786 | | |
| 9787 | | Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with |
| 9788 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 9789 | | |
| 9790 | | Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with |
| 9791 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 9792 | | |
| 9793 | | Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with |
| 9794 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 9795 | | |
| 9796 | | Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with |
| 9797 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 9798 | | |
| 9799 | | Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with |
| 9800 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 9801 | | |
| 9802 | | Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with |
| 9803 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 9804 | | |
| 9805 | | > color #3.6/t thistle |
| 9806 | | |
| 9807 | | > hide #!3.6 models |
| 9808 | | |
| 9809 | | > show #!3.2 models |
| 9810 | | |
| 9811 | | > hide #!3.2 models |
| 9812 | | |
| 9813 | | > show #!3.1 models |
| 9814 | | |
| 9815 | | > color #3.1/k thistle |
| 9816 | | |
| 9817 | | > view v3 |
| 9818 | | |
| 9819 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 9820 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v15-Models-Compare.cxs" |
| 9821 | | |
| 9822 | | > hide #!3.1 models |
| 9823 | | |
| 9824 | | > show #!3.2 models |
| 9825 | | |
| 9826 | | > hide #!3.2 models |
| 9827 | | |
| 9828 | | > show #!3.4 models |
| 9829 | | |
| 9830 | | > hide #!3.4 models |
| 9831 | | |
| 9832 | | > show #!3.5 models |
| 9833 | | |
| 9834 | | > hide #!3.5 models |
| 9835 | | |
| 9836 | | > show #!3.2 models |
| 9837 | | |
| 9838 | | > hide #!3.2 models |
| 9839 | | |
| 9840 | | > show #!3.2 models |
| 9841 | | |
| 9842 | | > show #!2.5 models |
| 9843 | | |
| 9844 | | > view v3 |
| 9845 | | |
| 9846 | | [Repeated 1 time(s)] |
| 9847 | | |
| 9848 | | > hide #!3 models |
| 9849 | | |
| 9850 | | > show #!3 models |
| 9851 | | |
| 9852 | | > hide #!3 models |
| 9853 | | |
| 9854 | | > view v3 |
| 9855 | | |
| 9856 | | > hide #!2 models |
| 9857 | | |
| 9858 | | > show #!2 models |
| 9859 | | |
| 9860 | | > hide #!2.5 models |
| 9861 | | |
| 9862 | | > show #!2.1 models |
| 9863 | | |
| 9864 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 9865 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/SI-5-multi-comparison.cxs" |
| 9866 | | |
| 9867 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 9868 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S5/SI5-Stat1.jpg" width |
| 9869 | | > 1100 height 609 supersample 3 |
| 9870 | | |
| 9871 | | > hide #!2.1 models |
| 9872 | | |
| 9873 | | > show #!3 models |
| 9874 | | |
| 9875 | | > hide #!3.2 models |
| 9876 | | |
| 9877 | | > open 3U60 |
| 9878 | | |
| 9879 | | Summary of feedback from opening 3U60 fetched from pdb |
| 9880 | | --- |
| 9881 | | note | Fetching compressed mmCIF 3u60 from |
| 9882 | | http://files.rcsb.org/download/3u60.cif |
| 9883 | | |
| 9884 | | 3u60 title: |
| 9885 | | Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP |
| 9886 | | Analog [more info...] |
| 9887 | | |
| 9888 | | Chain information for 3u60 #4 |
| 9889 | | --- |
| 9890 | | Chain | Description | UniProt |
| 9891 | | A | DNA polymerase accessory protein 62 | DPA62_BPT4 |
| 9892 | | B C D E | DNA polymerase accessory protein 44 | DPA44_BPT4 |
| 9893 | | F G H | DNA polymerase processivity component | DPA5_BPT4 |
| 9894 | | I | Template DNA strand | |
| 9895 | | J | Primer DNA strand | |
| 9896 | | |
| 9897 | | Non-standard residues in 3u60 #4 |
| 9898 | | --- |
| 9899 | | 08T — |
| 9900 | | [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy- |
| 9901 | | oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium |
| 9902 | | ADP — adenosine-5'-diphosphate |
| 9903 | | MG — magnesium ion |
| 9904 | | |
| 9905 | | |
| 9906 | | > mmaker #4 to #2.4 |
| 9907 | | |
| 9908 | | Parameters |
| 9909 | | --- |
| 9910 | | Chain pairing | bb |
| 9911 | | Alignment algorithm | Needleman-Wunsch |
| 9912 | | Similarity matrix | BLOSUM-62 |
| 9913 | | SS fraction | 0.3 |
| 9914 | | Gap open (HH/SS/other) | 18/18/6 |
| 9915 | | Gap extend | 1 |
| 9916 | | SS matrix | | | H | S | O |
| 9917 | | ---|---|---|--- |
| 9918 | | H | 6 | -9 | -6 |
| 9919 | | S | | 6 | -6 |
| 9920 | | O | | | 4 |
| 9921 | | Iteration cutoff | 2 |
| 9922 | | |
| 9923 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with 3u60, chain C (#4), |
| 9924 | | sequence alignment score = 474.3 |
| 9925 | | RMSD between 146 pruned atom pairs is 1.106 angstroms; (across all 299 pairs: |
| 9926 | | 8.323) |
| 9927 | | |
| 9928 | | |
| 9929 | | > hide #4 |
| 9930 | | |
| 9931 | | > show #4 cartoons |
| 9932 | | |
| 9933 | | > cartoon style nucleic xsection oval width 2.5 thickness 2.5 |
| 9934 | | |
| 9935 | | > cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true |
| 9936 | | > xsection oval width 2.75 thickness 1 arrowScale 1.5 |
| 9937 | | |
| 9938 | | > color #4/A #FFB381 |
| 9939 | | |
| 9940 | | > color #4/B #D7819F |
| 9941 | | |
| 9942 | | > color #4/C #B48FE3 |
| 9943 | | |
| 9944 | | > color #4/D #D7CD85 |
| 9945 | | |
| 9946 | | > color #/E salmon |
| 9947 | | |
| 9948 | | Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', |
| 9949 | | 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' |
| 9950 | | or a keyword |
| 9951 | | |
| 9952 | | > color #4/E salmon |
| 9953 | | |
| 9954 | | > color #4/F navajo white |
| 9955 | | |
| 9956 | | > setattr #4/F c chain_id X |
| 9957 | | |
| 9958 | | Assigning chain_id attribute to 1 item |
| 9959 | | |
| 9960 | | > setattr #4/H c chain_id F |
| 9961 | | |
| 9962 | | Assigning chain_id attribute to 1 item |
| 9963 | | |
| 9964 | | > setattr #4/X c chain_id H |
| 9965 | | |
| 9966 | | Assigning chain_id attribute to 1 item |
| 9967 | | |
| 9968 | | > color /F navajo white |
| 9969 | | |
| 9970 | | > color /G #CAC6FD |
| 9971 | | |
| 9972 | | > color /H plum |
| 9973 | | |
| 9974 | | > select #4/I-J |
| 9975 | | |
| 9976 | | 897 atoms, 1003 bonds, 38 pseudobonds, 44 residues, 2 models selected |
| 9977 | | |
| 9978 | | > show sel |
| 9979 | | |
| 9980 | | > nucleotides sel stubs |
| 9981 | | |
| 9982 | | > color #4/I medium orchid |
| 9983 | | |
| 9984 | | > color #4/J light sky blue |
| 9985 | | |
| 9986 | | > select clear |
| 9987 | | |
| 9988 | | > rename #4 T4-partially-closed-3U60 id #3.7 |
| 9989 | | |
| 9990 | | > mmaker #3.7/A-H to #2.4/A-H pair ss |
| 9991 | | |
| 9992 | | Parameters |
| 9993 | | --- |
| 9994 | | Chain pairing | ss |
| 9995 | | Alignment algorithm | Needleman-Wunsch |
| 9996 | | Similarity matrix | BLOSUM-62 |
| 9997 | | SS fraction | 0.3 |
| 9998 | | Gap open (HH/SS/other) | 18/18/6 |
| 9999 | | Gap extend | 1 |
| 10000 | | SS matrix | | | H | S | O |
| 10001 | | ---|---|---|--- |
| 10002 | | H | 6 | -9 | -6 |
| 10003 | | S | | 6 | -6 |
| 10004 | | O | | | 4 |
| 10005 | | Iteration cutoff | 2 |
| 10006 | | |
| 10007 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain A (#2.4) with T4-partially-closed-3U60, |
| 10008 | | chain B (#3.7), sequence alignment score = 249.7 |
| 10009 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with T4-partially-closed-3U60, |
| 10010 | | chain C (#3.7), sequence alignment score = 474.3 |
| 10011 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain C (#2.4) with T4-partially-closed-3U60, |
| 10012 | | chain D (#3.7), sequence alignment score = 446.7 |
| 10013 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with T4-partially-closed-3U60, |
| 10014 | | chain E (#3.7), sequence alignment score = 411.7 |
| 10015 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain E (#2.4) with T4-partially-closed-3U60, |
| 10016 | | chain A (#3.7), sequence alignment score = 121.1 |
| 10017 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain F (#2.4) with T4-partially-closed-3U60, |
| 10018 | | chain G (#3.7), sequence alignment score = 106.8 |
| 10019 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain G (#2.4) with T4-partially-closed-3U60, |
| 10020 | | chain F (#3.7), sequence alignment score = 104.3 |
| 10021 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain H (#2.4) with T4-partially-closed-3U60, |
| 10022 | | chain H (#3.7), sequence alignment score = 115.5 |
| 10023 | | RMSD between 394 pruned atom pairs is 1.188 angstroms; (across all 2000 pairs: |
| 10024 | | 31.824) |
| 10025 | | |
| 10026 | | |
| 10027 | | > show #!2.4 models |
| 10028 | | |
| 10029 | | > mmaker #3.7/B-H to #2.4/B-H pair ss |
| 10030 | | |
| 10031 | | Parameters |
| 10032 | | --- |
| 10033 | | Chain pairing | ss |
| 10034 | | Alignment algorithm | Needleman-Wunsch |
| 10035 | | Similarity matrix | BLOSUM-62 |
| 10036 | | SS fraction | 0.3 |
| 10037 | | Gap open (HH/SS/other) | 18/18/6 |
| 10038 | | Gap extend | 1 |
| 10039 | | SS matrix | | | H | S | O |
| 10040 | | ---|---|---|--- |
| 10041 | | H | 6 | -9 | -6 |
| 10042 | | S | | 6 | -6 |
| 10043 | | O | | | 4 |
| 10044 | | Iteration cutoff | 2 |
| 10045 | | |
| 10046 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with T4-partially-closed-3U60, |
| 10047 | | chain B (#3.7), sequence alignment score = 469.2 |
| 10048 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain C (#2.4) with T4-partially-closed-3U60, |
| 10049 | | chain C (#3.7), sequence alignment score = 453.9 |
| 10050 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with T4-partially-closed-3U60, |
| 10051 | | chain D (#3.7), sequence alignment score = 406.4 |
| 10052 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain E (#2.4) with T4-partially-closed-3U60, |
| 10053 | | chain E (#3.7), sequence alignment score = 375.1 |
| 10054 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain F (#2.4) with T4-partially-closed-3U60, |
| 10055 | | chain G (#3.7), sequence alignment score = 106.8 |
| 10056 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain G (#2.4) with T4-partially-closed-3U60, |
| 10057 | | chain F (#3.7), sequence alignment score = 104.3 |
| 10058 | | Matchmaker Stat4-Ref80-Ct6.pdb, chain H (#2.4) with T4-partially-closed-3U60, |
| 10059 | | chain H (#3.7), sequence alignment score = 115.5 |
| 10060 | | RMSD between 424 pruned atom pairs is 1.235 angstroms; (across all 1810 pairs: |
| 10061 | | 28.258) |
| 10062 | | |
| 10063 | | |
| 10064 | | > hide #!3 models |
| 10065 | | |
| 10066 | | > show #!3 models |
| 10067 | | |
| 10068 | | > hide #!3 models |
| 10069 | | |
| 10070 | | > view v3 |
| 10071 | | |
| 10072 | | > hide #!2 models |
| 10073 | | |
| 10074 | | > show #!3 models |
| 10075 | | |
| 10076 | | > show #!3.4 models |
| 10077 | | |
| 10078 | | > hide #!3.7 models |
| 10079 | | |
| 10080 | | > hide #!3.4 models |
| 10081 | | |
| 10082 | | > show #!3.3 models |
| 10083 | | |
| 10084 | | > select #3.7/A:63 |
| 10085 | | |
| 10086 | | 11 atoms, 11 bonds, 1 residue, 1 model selected |
| 10087 | | |
| 10088 | | > show #!3.7 models |
| 10089 | | |
| 10090 | | > hide #!3.3 models |
| 10091 | | |
| 10092 | | > show sel atoms |
| 10093 | | |
| 10094 | | > style sel stick |
| 10095 | | |
| 10096 | | Changed 11 atom styles |
| 10097 | | |
| 10098 | | > color sel lime atoms |
| 10099 | | |
| 10100 | | > color sel byhetero |
| 10101 | | |
| 10102 | | > select clear |
| 10103 | | |
| 10104 | | > view v3 |
| 10105 | | |
| 10106 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 10107 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S5/Si5-multi- |
| 10108 | | > comparison-v2.cxs" |
| 10109 | | |
| 10110 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 10111 | | > Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S5/SI-5-multi- |
| 10112 | | > comparison-v2.cxs" |
| 10113 | | |
| 10114 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 10115 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v15-Models-Compare.cxs" |
| 10116 | | |
| 10117 | | ——— End of log from Tue Jul 5 16:32:16 2022 ——— |
| 10118 | | |
| 10119 | | opened ChimeraX session |
| 10120 | | |
| 10121 | | > hide #!3 models |
| 10122 | | |
| 10123 | | > hide #!2.4 models |
| 10124 | | |
| 10125 | | > show #!2.5 models |
| 10126 | | |
| 10127 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 10128 | | > Institute/Documents/Draft/3_ScRR91-10nt/0_MM/polish_5ntGap_P43_J266_sharp.mrc" |
| 10129 | | |
| 10130 | | Opened polish_5ntGap_P43_J266_sharp.mrc as #4, grid size 420,420,420, pixel |
| 10131 | | 0.828, shown at level 0.0553, step 2, values float32 |
| 10132 | | |
| 10133 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 10134 | | > Institute/Documents/Draft/3_ScRR91-10nt/0_MM/5ntGap-Rsr132-Ct1.pdb" |
| 10135 | | |
| 10136 | | Chain information for 5ntGap-Rsr132-Ct1.pdb #5 |
| 10137 | | --- |
| 10138 | | Chain | Description |
| 10139 | | A | No description available |
| 10140 | | B | No description available |
| 10141 | | C | No description available |
| 10142 | | D | No description available |
| 10143 | | E | No description available |
| 10144 | | F | No description available |
| 10145 | | G | No description available |
| 10146 | | H | No description available |
| 10147 | | I | No description available |
| 10148 | | J | No description available |
| 10149 | | K | No description available |
| 10150 | | |
| 10151 | | |
| 10152 | | > surface dust #5 size 10 |
| 10153 | | |
| 10154 | | No surfaces specified |
| 10155 | | |
| 10156 | | > surface dust #5 size 10 |
| 10157 | | |
| 10158 | | No surfaces specified |
| 10159 | | |
| 10160 | | > surface dust #5 size 10 |
| 10161 | | |
| 10162 | | No surfaces specified |
| 10163 | | |
| 10164 | | > hide #!5 models |
| 10165 | | |
| 10166 | | > show #!5 models |
| 10167 | | |
| 10168 | | > surface dust #4 size 10 |
| 10169 | | |
| 10170 | | > hide #5 |
| 10171 | | |
| 10172 | | > show #5 cartoons |
| 10173 | | |
| 10174 | | > show ligand & #5 |
| 10175 | | |
| 10176 | | > hide #!2 models |
| 10177 | | |
| 10178 | | > show #!2 models |
| 10179 | | |
| 10180 | | > hide #!4 models |
| 10181 | | |
| 10182 | | > hide #!2 models |
| 10183 | | |
| 10184 | | > show #!2 models |
| 10185 | | |
| 10186 | | > mmaker #5 #2.5 |
| 10187 | | |
| 10188 | | > matchmaker #5 #2.5 |
| 10189 | | |
| 10190 | | Missing required "to" argument |
| 10191 | | |
| 10192 | | > mmaker #5 to #2.5 |
| 10193 | | |
| 10194 | | Parameters |
| 10195 | | --- |
| 10196 | | Chain pairing | bb |
| 10197 | | Alignment algorithm | Needleman-Wunsch |
| 10198 | | Similarity matrix | BLOSUM-62 |
| 10199 | | SS fraction | 0.3 |
| 10200 | | Gap open (HH/SS/other) | 18/18/6 |
| 10201 | | Gap extend | 1 |
| 10202 | | SS matrix | | | H | S | O |
| 10203 | | ---|---|---|--- |
| 10204 | | H | 6 | -9 | -6 |
| 10205 | | S | | 6 | -6 |
| 10206 | | O | | | 4 |
| 10207 | | Iteration cutoff | 2 |
| 10208 | | |
| 10209 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 5ntGap-Rsr132-Ct1.pdb, |
| 10210 | | chain A (#5), sequence alignment score = 2053.5 |
| 10211 | | RMSD between 414 pruned atom pairs is 0.678 angstroms; (across all 426 pairs: |
| 10212 | | 0.922) |
| 10213 | | |
| 10214 | | |
| 10215 | | > mmaker #5/A-H to #2.5/A-H pair ss |
| 10216 | | |
| 10217 | | Parameters |
| 10218 | | --- |
| 10219 | | Chain pairing | ss |
| 10220 | | Alignment algorithm | Needleman-Wunsch |
| 10221 | | Similarity matrix | BLOSUM-62 |
| 10222 | | SS fraction | 0.3 |
| 10223 | | Gap open (HH/SS/other) | 18/18/6 |
| 10224 | | Gap extend | 1 |
| 10225 | | SS matrix | | | H | S | O |
| 10226 | | ---|---|---|--- |
| 10227 | | H | 6 | -9 | -6 |
| 10228 | | S | | 6 | -6 |
| 10229 | | O | | | 4 |
| 10230 | | Iteration cutoff | 2 |
| 10231 | | |
| 10232 | | Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 5ntGap-Rsr132-Ct1.pdb, |
| 10233 | | chain A (#5), sequence alignment score = 2053.5 |
| 10234 | | Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 5ntGap-Rsr132-Ct1.pdb, |
| 10235 | | chain B (#5), sequence alignment score = 1565.5 |
| 10236 | | Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 5ntGap-Rsr132-Ct1.pdb, |
| 10237 | | chain C (#5), sequence alignment score = 1613.7 |
| 10238 | | Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 5ntGap-Rsr132-Ct1.pdb, |
| 10239 | | chain D (#5), sequence alignment score = 1677.3 |
| 10240 | | Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 5ntGap-Rsr132-Ct1.pdb, |
| 10241 | | chain E (#5), sequence alignment score = 1627.1 |
| 10242 | | Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with 5ntGap-Rsr132-Ct1.pdb, |
| 10243 | | chain F (#5), sequence alignment score = 1258.7 |
| 10244 | | Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with 5ntGap-Rsr132-Ct1.pdb, |
| 10245 | | chain G (#5), sequence alignment score = 1329.4 |
| 10246 | | Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with 5ntGap-Rsr132-Ct1.pdb, |
| 10247 | | chain H (#5), sequence alignment score = 1376 |
| 10248 | | RMSD between 2539 pruned atom pairs is 0.887 angstroms; (across all 2572 |
| 10249 | | pairs: 0.979) |
| 10250 | | |
| 10251 | | |
| 10252 | | > hide #!2 models |
| 10253 | | |
| 10254 | | > show #!2 models |
| 10255 | | |
| 10256 | | > color /A #FFB381 |
| 10257 | | |
| 10258 | | > undo |
| 10259 | | |
| 10260 | | > color #4/A #FFB381 |
| 10261 | | |
| 10262 | | > color #4/A #FFB381 cartoons |
| 10263 | | |
| 10264 | | > color #5/A #FFB381 cartoons |
| 10265 | | |
| 10266 | | > color #5/A #D7819F cartoons |
| 10267 | | |
| 10268 | | > undo |
| 10269 | | |
| 10270 | | > color #5/B #D7819F cartoons |
| 10271 | | |
| 10272 | | > color #5/A #D7819F |
| 10273 | | |
| 10274 | | > color #5/B #D7819F |
| 10275 | | |
| 10276 | | > color #5/A #FFB381 |
| 10277 | | |
| 10278 | | > color #5/C #B48FE3 |
| 10279 | | |
| 10280 | | > color #5/C #D7CD85 |
| 10281 | | |
| 10282 | | > color #5/C #B48FE3 |
| 10283 | | |
| 10284 | | > color #5/D #D7CD85 |
| 10285 | | |
| 10286 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10287 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 10288 | | |
| 10289 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10290 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 10291 | | |
| 10292 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10293 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 10294 | | |
| 10295 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10296 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 10297 | | |
| 10298 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10299 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 10300 | | |
| 10301 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10302 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 10303 | | |
| 10304 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10305 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 10306 | | |
| 10307 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10308 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 10309 | | |
| 10310 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10311 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 10312 | | |
| 10313 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10314 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 10315 | | |
| 10316 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10317 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 10318 | | |
| 10319 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10320 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 10321 | | |
| 10322 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10323 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 10324 | | |
| 10325 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10326 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 10327 | | |
| 10328 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10329 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 10330 | | |
| 10331 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 10332 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 10333 | | |
| 10334 | | > color #5/E salmon |
| 10335 | | |
| 10336 | | > color #5/F navajo white |
| 10337 | | |
| 10338 | | > color #5/G #CAC6FD |
| 10339 | | |
| 10340 | | > color #5/H plum |
| 10341 | | |
| 10342 | | > color #5/I medium orchid |
| 10343 | | |
| 10344 | | > color #5/J light sky blue |
| 10345 | | |
| 10346 | | > color #5/K #E7F981 |
| 10347 | | |
| 10348 | | > select #5/A:225-245 |
| 10349 | | |
| 10350 | | 179 atoms, 183 bonds, 21 residues, 1 model selected |
| 10351 | | |
| 10352 | | > color sel yellow green |
| 10353 | | |
| 10354 | | > color #5 & ions green yellow |
| 10355 | | |
| 10356 | | > cartoon style nucleic xsection oval width 2.5 thickness 2.5 |
| 10357 | | |
| 10358 | | > cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true |
| 10359 | | > xsection oval width 2.75 thickness 1 arrowScale 1.5 |
| 10360 | | |
| 10361 | | [Repeated 1 time(s)] |
| 10362 | | |
| 10363 | | > hide #!2 models |
| 10364 | | |
| 10365 | | > show #!4 models |
| 10366 | | |
| 10367 | | > volume #4 level 0.2 |
| 10368 | | |
| 10369 | | > hide #!4 models |
| 10370 | | |
| 10371 | | > rename #4 id #1.6 |
| 10372 | | |
| 10373 | | > hide #!1.5 models |
| 10374 | | |
| 10375 | | > show #!1.6 models |
| 10376 | | |
| 10377 | | > hide #!1.6 models |
| 10378 | | |
| 10379 | | > rename #5 id #2.6 |
| 10380 | | |
| 10381 | | > show #!2 models |
| 10382 | | |
| 10383 | | > hide #!2.5 models |
| 10384 | | |
| 10385 | | > show #!2.5 models |
| 10386 | | |
| 10387 | | > hide #!2.5 models |
| 10388 | | |
| 10389 | | > show #!2.5 models |
| 10390 | | |
| 10391 | | > hide #!2.5 models |
| 10392 | | |
| 10393 | | > show #!2.5 models |
| 10394 | | |
| 10395 | | > hide #!2.5 models |
| 10396 | | |
| 10397 | | > show #!2.5 models |
| 10398 | | |
| 10399 | | > select /E:69-76,82-89 |
| 10400 | | |
| 10401 | | 1684 atoms, 1677 bonds, 1 pseudobond, 208 residues, 14 models selected |
| 10402 | | |
| 10403 | | > setattr sel res ss_type 2 |
| 10404 | | |
| 10405 | | Assigning ss_type attribute to 208 items |
| 10406 | | |
| 10407 | | > setattr sel res ss_id 88 |
| 10408 | | |
| 10409 | | Assigning ss_id attribute to 208 items |
| 10410 | | |
| 10411 | | > hide #!2.5 models |
| 10412 | | |
| 10413 | | > show #!2.5 models |
| 10414 | | |
| 10415 | | > hide #!2.5 models |
| 10416 | | |
| 10417 | | > select clear |
| 10418 | | |
| 10419 | | > show #!2.5 models |
| 10420 | | |
| 10421 | | > hide #!2.5 models |
| 10422 | | |
| 10423 | | > sho3 #2.6/I-K |
| 10424 | | |
| 10425 | | Unknown command: sho3 #2.6/I-K |
| 10426 | | |
| 10427 | | > show #2.6/I-K |
| 10428 | | |
| 10429 | | > nucleotides #!2.6 stubs |
| 10430 | | |
| 10431 | | > hide #!2.6 models |
| 10432 | | |
| 10433 | | > show #!2.5 models |
| 10434 | | |
| 10435 | | > hide #!2.5 models |
| 10436 | | |
| 10437 | | > show #!2.6 models |
| 10438 | | |
| 10439 | | > select ligands |
| 10440 | | |
| 10441 | | Expected an objects specifier or a keyword |
| 10442 | | |
| 10443 | | > select ligand |
| 10444 | | |
| 10445 | | 1898 atoms, 2011 bonds, 9 pseudobonds, 69 residues, 16 models selected |
| 10446 | | |
| 10447 | | > color sel & #!2.6 byhetero |
| 10448 | | |
| 10449 | | > show sel |
| 10450 | | |
| 10451 | | > hide #!2.6 models |
| 10452 | | |
| 10453 | | > show #!2.5 models |
| 10454 | | |
| 10455 | | > color sel by hetero |
| 10456 | | |
| 10457 | | Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', |
| 10458 | | 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' |
| 10459 | | or a keyword |
| 10460 | | |
| 10461 | | > color sel by hetero |
| 10462 | | |
| 10463 | | Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', |
| 10464 | | 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' |
| 10465 | | or a keyword |
| 10466 | | |
| 10467 | | > color sel by heter |
| 10468 | | |
| 10469 | | Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', |
| 10470 | | 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' |
| 10471 | | or a keyword |
| 10472 | | |
| 10473 | | > color sel byhetero |
| 10474 | | |
| 10475 | | > hide #!2.5 models |
| 10476 | | |
| 10477 | | > show #!2.4 models |
| 10478 | | |
| 10479 | | > show #!2.6 models |
| 10480 | | |
| 10481 | | > select clear |
| 10482 | | |
| 10483 | | > hide #!2.4 models |
| 10484 | | |
| 10485 | | > show #!2.5 models |
| 10486 | | |
| 10487 | | > hide #!2.5 models |
| 10488 | | |
| 10489 | | > select /E:69-76,82-89 |
| 10490 | | |
| 10491 | | 1684 atoms, 1677 bonds, 1 pseudobond, 208 residues, 14 models selected |
| 10492 | | |
| 10493 | | > select /F:2-7,68-72,79-84,91-94,118-124,262-266,281-286,406-410,462-467 |
| 10494 | | |
| 10495 | | 3470 atoms, 3444 bonds, 428 residues, 10 models selected |
| 10496 | | |
| 10497 | | > select /H:251-256,261-266,283-288,320-325 |
| 10498 | | |
| 10499 | | 1434 atoms, 1423 bonds, 2 pseudobonds, 182 residues, 12 models selected |
| 10500 | | |
| 10501 | | > setattr sel res ss_type 2 |
| 10502 | | |
| 10503 | | Assigning ss_type attribute to 182 items |
| 10504 | | |
| 10505 | | > setattr sel res ss_id 88 |
| 10506 | | |
| 10507 | | Assigning ss_id attribute to 182 items |
| 10508 | | |
| 10509 | | > select /F:2-7,68-72,79-84,91-94,118-124,262-266,281-286,406-410,462-467 |
| 10510 | | |
| 10511 | | 3470 atoms, 3444 bonds, 428 residues, 10 models selected |
| 10512 | | |
| 10513 | | > setattr sel res ss_type 2 |
| 10514 | | |
| 10515 | | Assigning ss_type attribute to 428 items |
| 10516 | | |
| 10517 | | > setattr sel res ss_id 88 |
| 10518 | | |
| 10519 | | Assigning ss_id attribute to 428 items |
| 10520 | | |
| 10521 | | > select /H:251-256,261-266,283-288,320-325 |
| 10522 | | |
| 10523 | | 1434 atoms, 1423 bonds, 2 pseudobonds, 182 residues, 12 models selected |
| 10524 | | |
| 10525 | | > setattr sel res ss_type 2 |
| 10526 | | |
| 10527 | | Assigning ss_type attribute to 182 items |
| 10528 | | |
| 10529 | | > setattr sel res ss_id 88 |
| 10530 | | |
| 10531 | | Assigning ss_id attribute to 182 items |
| 10532 | | |
| 10533 | | > select clear |
| 10534 | | |
| 10535 | | > select #8/A:542-551 |
| 10536 | | |
| 10537 | | Nothing selected |
| 10538 | | |
| 10539 | | > select #2.6/A:542-551 |
| 10540 | | |
| 10541 | | Nothing selected |
| 10542 | | |
| 10543 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 10544 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v16-Models-Compare.cxs" |
| 10545 | | |
| 10546 | | ——— End of log from Mon Nov 14 16:29:22 2022 ——— |
| 10547 | | |
| 10548 | | opened ChimeraX session |
| 10549 | | |
| 10550 | | > windowsize 1100 609 |
| 10551 | | |
| 10552 | | > show #!2.5 models |
| 10553 | | |
| 10554 | | > hide #!2.5 models |
| 10555 | | |
| 10556 | | > show #!2.5 models |
| 10557 | | |
| 10558 | | > hide #!2.5 models |
| 10559 | | |
| 10560 | | > scene a |
| 10561 | | |
| 10562 | | Unknown command: scene a |
| 10563 | | |
| 10564 | | > scene |
| 10565 | | |
| 10566 | | Unknown command: scene |
| 10567 | | |
| 10568 | | > view name a |
| 10569 | | |
| 10570 | | > view a |
| 10571 | | |
| 10572 | | > hide #!2 models |
| 10573 | | |
| 10574 | | > show #!1.5 models |
| 10575 | | |
| 10576 | | > show #!1.6 models |
| 10577 | | |
| 10578 | | > select #1.6 |
| 10579 | | |
| 10580 | | 2 models selected |
| 10581 | | |
| 10582 | | > ui mousemode right "rotate selected models" |
| 10583 | | |
| 10584 | | > view matrix models |
| 10585 | | > #1.6,-0.22141,-0.65568,-0.72185,456.14,0.65793,0.44593,-0.60685,79.739,0.71979,-0.60929,0.33266,88.355 |
| 10586 | | |
| 10587 | | > view matrix models |
| 10588 | | > #1.6,-0.82155,0.31994,-0.47191,354.07,0.54784,0.21373,-0.80882,173.93,-0.15792,-0.92302,-0.35086,417.05 |
| 10589 | | |
| 10590 | | > view matrix models |
| 10591 | | > #1.6,0.2326,0.87708,-0.42028,59.036,0.72056,-0.44564,-0.53122,209.05,-0.65321,-0.17928,-0.73564,443.87 |
| 10592 | | |
| 10593 | | > view matrix models |
| 10594 | | > #1.6,0.70108,0.12899,-0.70132,150.99,0.22706,-0.97269,0.048074,290.41,-0.67597,-0.19295,-0.71122,446.18 |
| 10595 | | |
| 10596 | | > view matrix models |
| 10597 | | > #1.6,0.60047,-0.51721,-0.60985,264.85,-0.16538,-0.82649,0.53811,252.8,-0.78236,-0.22226,-0.58182,448.44 |
| 10598 | | |
| 10599 | | > view matrix models |
| 10600 | | > #1.6,0.57011,-0.73495,-0.36719,266.56,-0.36389,-0.62659,0.68918,228.56,-0.73659,-0.25929,-0.62467,453.83 |
| 10601 | | |
| 10602 | | > view matrix models |
| 10603 | | > #1.6,0.94044,-0.052853,-0.33581,76.94,0.08167,-0.92378,0.37411,252.82,-0.32999,-0.37925,-0.86445,441.82 |
| 10604 | | |
| 10605 | | > view matrix models |
| 10606 | | > #1.6,0.85393,-0.51064,0.10029,97.231,-0.50456,-0.76526,0.39974,327.03,-0.12737,-0.39195,-0.91113,415.36 |
| 10607 | | |
| 10608 | | > view matrix models |
| 10609 | | > #1.6,0.58674,-0.80823,-0.049953,222.25,-0.71053,-0.54344,0.447,318.01,-0.38843,-0.22678,-0.89314,431.01 |
| 10610 | | |
| 10611 | | > view matrix models |
| 10612 | | > #1.6,0.90943,-0.40959,-0.071959,99.096,-0.37535,-0.88295,0.28196,343.98,-0.17902,-0.22941,-0.95672,404.46 |
| 10613 | | |
| 10614 | | > view matrix models |
| 10615 | | > #1.6,0.90303,-0.42331,-0.073067,102.8,-0.38805,-0.87682,0.28392,344.89,-0.18425,-0.22803,-0.95606,405.05 |
| 10616 | | |
| 10617 | | > ui mousemode right "translate selected models" |
| 10618 | | |
| 10619 | | > view matrix models |
| 10620 | | > #1.6,0.90303,-0.42331,-0.073067,102.34,-0.38805,-0.87682,0.28392,342.46,-0.18425,-0.22803,-0.95606,409.64 |
| 10621 | | |
| 10622 | | Drag select of 1.5 polish-stat5-cs_P24_J261_sharp.mrc , 1.6 |
| 10623 | | polish_5ntGap_P43_J266_sharp.mrc |
| 10624 | | |
| 10625 | | > fitmap #1.6 into #1.5 |
| 10626 | | |
| 10627 | | Expected a keyword |
| 10628 | | |
| 10629 | | > fitmap #1.6 inMap #1.5 |
| 10630 | | |
| 10631 | | Fit map polish_5ntGap_P43_J266_sharp.mrc in map polish- |
| 10632 | | stat5-cs_P24_J261_sharp.mrc using 18449 points |
| 10633 | | correlation = 0.3556, correlation about mean = 0.09213, overlap = 778.8 |
| 10634 | | steps = 124, shift = 4.9, angle = 6.7 degrees |
| 10635 | | |
| 10636 | | Position of polish_5ntGap_P43_J266_sharp.mrc (#1.6) relative to polish- |
| 10637 | | stat5-cs_P24_J261_sharp.mrc (#1.5) coordinates: |
| 10638 | | Matrix rotation and translation |
| 10639 | | 0.87352274 -0.45623470 -0.16972896 125.07705210 |
| 10640 | | -0.41255062 -0.87892728 0.23935084 354.13160520 |
| 10641 | | -0.25837957 -0.13905661 -0.95598287 408.84027559 |
| 10642 | | Axis -0.96754585 0.22666977 0.11169533 |
| 10643 | | Axis point 0.00000000 212.54782761 193.62884215 |
| 10644 | | Rotation angle (degrees) 168.72313703 |
| 10645 | | Shift along axis 4.91869518 |
| 10646 | | |
| 10647 | | |
| 10648 | | > hide #!1.5 models |
| 10649 | | |
| 10650 | | > show #!1.5 models |
| 10651 | | |
| 10652 | | > hide #!1.5 models |
| 10653 | | |
| 10654 | | > show #!1.5 models |
| 10655 | | |
| 10656 | | > hide #!1.5 models |
| 10657 | | |
| 10658 | | > show #!1.5 models |
| 10659 | | |
| 10660 | | > select #1.6 |
| 10661 | | |
| 10662 | | 2 models selected |
| 10663 | | |
| 10664 | | > view matrix models |
| 10665 | | > #1.6,0.87352,-0.45623,-0.16973,125.95,-0.41255,-0.87893,0.23935,358.3,-0.25838,-0.13906,-0.95598,410.76 |
| 10666 | | |
| 10667 | | > fitmap #1.6 inMap #1.5 |
| 10668 | | |
| 10669 | | Fit map polish_5ntGap_P43_J266_sharp.mrc in map polish- |
| 10670 | | stat5-cs_P24_J261_sharp.mrc using 18449 points |
| 10671 | | correlation = 0.8771, correlation about mean = 0.5704, overlap = 3014 |
| 10672 | | steps = 52, shift = 1.94, angle = 0.441 degrees |
| 10673 | | |
| 10674 | | Position of polish_5ntGap_P43_J266_sharp.mrc (#1.6) relative to polish- |
| 10675 | | stat5-cs_P24_J261_sharp.mrc (#1.5) coordinates: |
| 10676 | | Matrix rotation and translation |
| 10677 | | 0.87170089 -0.46143907 -0.16495923 125.42444601 |
| 10678 | | -0.41755781 -0.87560736 0.24281108 358.94595186 |
| 10679 | | -0.25648204 -0.14277861 -0.95594520 409.63204578 |
| 10680 | | Axis -0.96705741 0.22953883 0.11005401 |
| 10681 | | Axis point 0.00000000 215.64863841 193.33966149 |
| 10682 | | Rotation angle (degrees) 168.50032611 |
| 10683 | | Shift along axis 6.18104297 |
| 10684 | | |
| 10685 | | |
| 10686 | | > select clear |
| 10687 | | |
| 10688 | | > hide #!1.5 models |
| 10689 | | |
| 10690 | | > show #!1.5 models |
| 10691 | | |
| 10692 | | > hide #!1.5 models |
| 10693 | | |
| 10694 | | > show #!1.5 models |
| 10695 | | |
| 10696 | | > view a |
| 10697 | | |
| 10698 | | > undo |
| 10699 | | |
| 10700 | | > fitmap #1.6 inMap #1.5 |
| 10701 | | |
| 10702 | | Fit map polish_5ntGap_P43_J266_sharp.mrc in map polish- |
| 10703 | | stat5-cs_P24_J261_sharp.mrc using 18449 points |
| 10704 | | correlation = 0.8772, correlation about mean = 0.5706, overlap = 3014 |
| 10705 | | steps = 44, shift = 0.0164, angle = 0.00928 degrees |
| 10706 | | |
| 10707 | | Position of polish_5ntGap_P43_J266_sharp.mrc (#1.6) relative to polish- |
| 10708 | | stat5-cs_P24_J261_sharp.mrc (#1.5) coordinates: |
| 10709 | | Matrix rotation and translation |
| 10710 | | 0.87176732 -0.46134892 -0.16486031 125.39301972 |
| 10711 | | -0.41746972 -0.87563656 0.24285724 358.93687422 |
| 10712 | | -0.25639964 -0.14289082 -0.95595054 409.64287180 |
| 10713 | | Axis -0.96707449 0.22949008 0.11000561 |
| 10714 | | Axis point 0.00000000 215.64574697 193.33322266 |
| 10715 | | Rotation angle (degrees) 168.49574430 |
| 10716 | | Shift along axis 6.17107225 |
| 10717 | | |
| 10718 | | |
| 10719 | | > hide #!1 models |
| 10720 | | |
| 10721 | | > show #!2 models |
| 10722 | | |
| 10723 | | > show #!1 models |
| 10724 | | |
| 10725 | | > hide #!2 models |
| 10726 | | |
| 10727 | | > hide #!1.5 models |
| 10728 | | |
| 10729 | | > volume #1.6 level 0.15 |
| 10730 | | |
| 10731 | | > show #!1.5 models |
| 10732 | | |
| 10733 | | > hide #!1.5 models |
| 10734 | | |
| 10735 | | > view name b |
| 10736 | | |
| 10737 | | > volume #1.6 level 0.125 |
| 10738 | | |
| 10739 | | > volume #1.6 level 0.1 |
| 10740 | | |
| 10741 | | > volume #1.6 level 0.09 |
| 10742 | | |
| 10743 | | > fitmap #1.6 inMap #1.5 |
| 10744 | | |
| 10745 | | Fit map polish_5ntGap_P43_J266_sharp.mrc in map polish- |
| 10746 | | stat5-cs_P24_J261_sharp.mrc using 43198 points |
| 10747 | | correlation = 0.8254, correlation about mean = 0.6664, overlap = 3446 |
| 10748 | | steps = 36, shift = 0.0184, angle = 0.0274 degrees |
| 10749 | | |
| 10750 | | Position of polish_5ntGap_P43_J266_sharp.mrc (#1.6) relative to polish- |
| 10751 | | stat5-cs_P24_J261_sharp.mrc (#1.5) coordinates: |
| 10752 | | Matrix rotation and translation |
| 10753 | | 0.87164345 -0.46144439 -0.16524759 125.49552069 |
| 10754 | | -0.41744562 -0.87558413 0.24308762 358.88898373 |
| 10755 | | -0.25685959 -0.14290385 -0.95582511 409.68868322 |
| 10756 | | Axis -0.96704169 0.22951963 0.11023209 |
| 10757 | | Axis point 0.00000000 215.65386308 193.36616354 |
| 10758 | | Rotation angle (degrees) 168.48799029 |
| 10759 | | Shift along axis 6.17350609 |
| 10760 | | |
| 10761 | | |
| 10762 | | > show #!1.5 models |
| 10763 | | |
| 10764 | | > hide #!1.5 models |
| 10765 | | |
| 10766 | | > show #!1.5 models |
| 10767 | | |
| 10768 | | > hide #!1.5 models |
| 10769 | | |
| 10770 | | > view b |
| 10771 | | |
| 10772 | | > hide #!1.6 models |
| 10773 | | |
| 10774 | | > show #!2 models |
| 10775 | | |
| 10776 | | > show #!1.6 models |
| 10777 | | |
| 10778 | | > hide #!1.6 models |
| 10779 | | |
| 10780 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 10781 | | > Institute/Documents/Draft/3_ScRR91-10nt/Overall-v17-Models-Compare.cxs" |
| 10782 | | |
| 10783 | | [Repeated 1 time(s)] |
| 10784 | | |
| 10785 | | ——— End of log from Mon Nov 14 16:55:53 2022 ——— |
| 10786 | | |
| 10787 | | opened ChimeraX session |
| 10788 | | |
| 10789 | | > hide #!2 models |
| 10790 | | |
| 10791 | | > show #!3 models |
| 10792 | | |
| 10793 | | > hide #!3.7 models |
| 10794 | | |
| 10795 | | > show #!3.6 models |
| 10796 | | |
| 10797 | | > show #!3.5 models |
| 10798 | | |
| 10799 | | > hide #!3.6 models |
| 10800 | | |
| 10801 | | > hide #!3.5 models |
| 10802 | | |
| 10803 | | > show #!3.4 models |
| 10804 | | |
| 10805 | | > hide #!3.4 models |
| 10806 | | |
| 10807 | | > show #!3.3 models |
| 10808 | | |
| 10809 | | > hide #!3.3 models |
| 10810 | | |
| 10811 | | > show #!3.2 models |
| 10812 | | |
| 10813 | | > hide #!3.2 models |
| 10814 | | |
| 10815 | | > show #!3.1 models |
| 10816 | | |
| 10817 | | > show #!2.5 models |
| 10818 | | |
| 10819 | | > hide #!2.6 models |
| 10820 | | |
| 10821 | | > hide #!3 models |
| 10822 | | |
| 10823 | | > show #!3 models |
| 10824 | | |
| 10825 | | > hide #!2.5 models |
| 10826 | | |
| 10827 | | > hide #!3 models |
| 10828 | | |
| 10829 | | > show #!2.5 models |
| 10830 | | |
| 10831 | | > open /Users/fengwei.zheng/Documents/Phenix/4_Elg1_RFC- |
| 10832 | | > PCNA/2_Coot/0-Apo/Elg1-RFC-AF5-v2_Rsr02-Ct1.pdb |
| 10833 | | |
| 10834 | | Chain information for Elg1-RFC-AF5-v2_Rsr02-Ct1.pdb #4 |
| 10835 | | --- |
| 10836 | | Chain | Description |
| 10837 | | A | No description available |
| 10838 | | B | No description available |
| 10839 | | C | No description available |
| 10840 | | D | No description available |
| 10841 | | E | No description available |
| 10842 | | |
| 10843 | | |
| 10844 | | > open /Users/fengwei.zheng/Documents/Phenix/4_Elg1_RFC- |
| 10845 | | > PCNA/2_Coot/1-Cmplx/Elg1_RFC-PCNA-v3_rsr04.pdb |
| 10846 | | |
| 10847 | | Chain information for Elg1_RFC-PCNA-v3_rsr04.pdb #5 |
| 10848 | | --- |
| 10849 | | Chain | Description |
| 10850 | | A | No description available |
| 10851 | | B | No description available |
| 10852 | | C | No description available |
| 10853 | | D | No description available |
| 10854 | | E | No description available |
| 10855 | | F | No description available |
| 10856 | | G | No description available |
| 10857 | | H | No description available |
| 10858 | | |
| 10859 | | |
| 10860 | | > hide #!2 models |
| 10861 | | |
| 10862 | | > show #!3 models |
| 10863 | | |
| 10864 | | > rename #4-5 id #4 Elg1_RFC |
| 10865 | | |
| 10866 | | Expected '.' or a keyword |
| 10867 | | |
| 10868 | | > rename #4-5 id #4 |
| 10869 | | |
| 10870 | | > rename #4 Elg1_RFC |
| 10871 | | |
| 10872 | | > hide #4 |
| 10873 | | |
| 10874 | | > show #4 cartoons |
| 10875 | | |
| 10876 | | > hide #4.2 models |
| 10877 | | |
| 10878 | | > hide #4.1 models |
| 10879 | | |
| 10880 | | > show #4.2 models |
| 10881 | | |
| 10882 | | > mmaker #4.2 to #3.1 |
| 10883 | | |
| 10884 | | Parameters |
| 10885 | | --- |
| 10886 | | Chain pairing | bb |
| 10887 | | Alignment algorithm | Needleman-Wunsch |
| 10888 | | Similarity matrix | BLOSUM-62 |
| 10889 | | SS fraction | 0.3 |
| 10890 | | Gap open (HH/SS/other) | 18/18/6 |
| 10891 | | Gap extend | 1 |
| 10892 | | SS matrix | | | H | S | O |
| 10893 | | ---|---|---|--- |
| 10894 | | H | 6 | -9 | -6 |
| 10895 | | S | | 6 | -6 |
| 10896 | | O | | | 4 |
| 10897 | | Iteration cutoff | 2 |
| 10898 | | |
| 10899 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with Elg1_RFC- |
| 10900 | | PCNA-v3_rsr04.pdb, chain E (#4.2), sequence alignment score = 1645.8 |
| 10901 | | RMSD between 290 pruned atom pairs is 0.912 angstroms; (across all 341 pairs: |
| 10902 | | 1.436) |
| 10903 | | |
| 10904 | | |
| 10905 | | > hide #4.2 models |
| 10906 | | |
| 10907 | | > show #4.2 models |
| 10908 | | |
| 10909 | | > hide #4.2 models |
| 10910 | | |
| 10911 | | > show #4.2 models |
| 10912 | | |
| 10913 | | > hide #!3 models |
| 10914 | | |
| 10915 | | > show #!3 models |
| 10916 | | |
| 10917 | | > mmaker #4.2/A-H to #3.1/A-H pair ss |
| 10918 | | |
| 10919 | | Parameters |
| 10920 | | --- |
| 10921 | | Chain pairing | ss |
| 10922 | | Alignment algorithm | Needleman-Wunsch |
| 10923 | | Similarity matrix | BLOSUM-62 |
| 10924 | | SS fraction | 0.3 |
| 10925 | | Gap open (HH/SS/other) | 18/18/6 |
| 10926 | | Gap extend | 1 |
| 10927 | | SS matrix | | | H | S | O |
| 10928 | | ---|---|---|--- |
| 10929 | | H | 6 | -9 | -6 |
| 10930 | | S | | 6 | -6 |
| 10931 | | O | | | 4 |
| 10932 | | Iteration cutoff | 2 |
| 10933 | | |
| 10934 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with Elg1_RFC- |
| 10935 | | PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 7.2 |
| 10936 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain B (#3.1) with Elg1_RFC- |
| 10937 | | PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 9.5 |
| 10938 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain C (#3.1) with Elg1_RFC- |
| 10939 | | PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 4.3 |
| 10940 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain D (#3.1) with Elg1_RFC- |
| 10941 | | PCNA-v3_rsr04.pdb, chain A (#4.2), sequence alignment score = 228.1 |
| 10942 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with Elg1_RFC- |
| 10943 | | PCNA-v3_rsr04.pdb, chain B (#4.2), sequence alignment score = 483.9 |
| 10944 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC- |
| 10945 | | PCNA-v3_rsr04.pdb, chain C (#4.2), sequence alignment score = 1.9 |
| 10946 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC- |
| 10947 | | PCNA-v3_rsr04.pdb, chain D (#4.2), sequence alignment score = 8.5 |
| 10948 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC- |
| 10949 | | PCNA-v3_rsr04.pdb, chain E (#4.2), sequence alignment score = 13.7 |
| 10950 | | RMSD between 179 pruned atom pairs is 1.291 angstroms; (across all 861 pairs: |
| 10951 | | 44.247) |
| 10952 | | |
| 10953 | | |
| 10954 | | > mmaker #4.2/F-H to #3.1/F-H pair ss |
| 10955 | | |
| 10956 | | Parameters |
| 10957 | | --- |
| 10958 | | Chain pairing | ss |
| 10959 | | Alignment algorithm | Needleman-Wunsch |
| 10960 | | Similarity matrix | BLOSUM-62 |
| 10961 | | SS fraction | 0.3 |
| 10962 | | Gap open (HH/SS/other) | 18/18/6 |
| 10963 | | Gap extend | 1 |
| 10964 | | SS matrix | | | H | S | O |
| 10965 | | ---|---|---|--- |
| 10966 | | H | 6 | -9 | -6 |
| 10967 | | S | | 6 | -6 |
| 10968 | | O | | | 4 |
| 10969 | | Iteration cutoff | 2 |
| 10970 | | |
| 10971 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC- |
| 10972 | | PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1242.4 |
| 10973 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC- |
| 10974 | | PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1237.2 |
| 10975 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC- |
| 10976 | | PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1161.4 |
| 10977 | | RMSD between 403 pruned atom pairs is 1.252 angstroms; (across all 767 pairs: |
| 10978 | | 3.172) |
| 10979 | | |
| 10980 | | |
| 10981 | | > mmaker #4.1 to #4.2 |
| 10982 | | |
| 10983 | | Parameters |
| 10984 | | --- |
| 10985 | | Chain pairing | bb |
| 10986 | | Alignment algorithm | Needleman-Wunsch |
| 10987 | | Similarity matrix | BLOSUM-62 |
| 10988 | | SS fraction | 0.3 |
| 10989 | | Gap open (HH/SS/other) | 18/18/6 |
| 10990 | | Gap extend | 1 |
| 10991 | | SS matrix | | | H | S | O |
| 10992 | | ---|---|---|--- |
| 10993 | | H | 6 | -9 | -6 |
| 10994 | | S | | 6 | -6 |
| 10995 | | O | | | 4 |
| 10996 | | Iteration cutoff | 2 |
| 10997 | | |
| 10998 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Elg1-RFC- |
| 10999 | | AF5-v2_Rsr02-Ct1.pdb, chain A (#4.1), sequence alignment score = 3064.9 |
| 11000 | | RMSD between 606 pruned atom pairs is 0.297 angstroms; (across all 606 pairs: |
| 11001 | | 0.297) |
| 11002 | | |
| 11003 | | |
| 11004 | | > hide #!3 models |
| 11005 | | |
| 11006 | | > show #4.1 models |
| 11007 | | |
| 11008 | | > mmaker #4.1/A-E to #4.2/A-E pair ss |
| 11009 | | |
| 11010 | | Parameters |
| 11011 | | --- |
| 11012 | | Chain pairing | ss |
| 11013 | | Alignment algorithm | Needleman-Wunsch |
| 11014 | | Similarity matrix | BLOSUM-62 |
| 11015 | | SS fraction | 0.3 |
| 11016 | | Gap open (HH/SS/other) | 18/18/6 |
| 11017 | | Gap extend | 1 |
| 11018 | | SS matrix | | | H | S | O |
| 11019 | | ---|---|---|--- |
| 11020 | | H | 6 | -9 | -6 |
| 11021 | | S | | 6 | -6 |
| 11022 | | O | | | 4 |
| 11023 | | Iteration cutoff | 2 |
| 11024 | | |
| 11025 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Elg1-RFC- |
| 11026 | | AF5-v2_Rsr02-Ct1.pdb, chain A (#4.1), sequence alignment score = 3064.9 |
| 11027 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Elg1-RFC- |
| 11028 | | AF5-v2_Rsr02-Ct1.pdb, chain B (#4.1), sequence alignment score = 1641.2 |
| 11029 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Elg1-RFC- |
| 11030 | | AF5-v2_Rsr02-Ct1.pdb, chain C (#4.1), sequence alignment score = 1739.6 |
| 11031 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Elg1-RFC- |
| 11032 | | AF5-v2_Rsr02-Ct1.pdb, chain D (#4.1), sequence alignment score = 1806.3 |
| 11033 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Elg1-RFC- |
| 11034 | | AF5-v2_Rsr02-Ct1.pdb, chain E (#4.1), sequence alignment score = 1802.2 |
| 11035 | | RMSD between 1976 pruned atom pairs is 0.355 angstroms; (across all 1976 |
| 11036 | | pairs: 0.355) |
| 11037 | | |
| 11038 | | |
| 11039 | | > hide #4.1 models |
| 11040 | | |
| 11041 | | > show #!3 models |
| 11042 | | |
| 11043 | | > hide #!1 models |
| 11044 | | |
| 11045 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 11046 | | > Institute/Documents/Structures/RR911/templates/ystRFC-PCNA_1sxj.pdb" |
| 11047 | | |
| 11048 | | ystRFC-PCNA_1sxj.pdb title: |
| 11049 | | Crystal structure of the eukaryotic clamp loader (replication factor C, RFC) |
| 11050 | | bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA) |
| 11051 | | [more info...] |
| 11052 | | |
| 11053 | | Chain information for ystRFC-PCNA_1sxj.pdb #5 |
| 11054 | | --- |
| 11055 | | Chain | Description | UniProt |
| 11056 | | A | activator 1 95 kda subunit | RFC1_YEAST |
| 11057 | | B | activator 1 37 kda subunit | RFC4_YEAST |
| 11058 | | C | activator 1 40 kda subunit | RFC3_YEAST |
| 11059 | | D | activator 1 41 kda subunit | RFC2_YEAST |
| 11060 | | E | activator 1 40 kda subunit | RFC5_YEAST |
| 11061 | | F | PCNA | PCNA_YEAST |
| 11062 | | G | PCNA | PCNA_YEAST |
| 11063 | | H | PCNA | PCNA_YEAST |
| 11064 | | |
| 11065 | | Non-standard residues in ystRFC-PCNA_1sxj.pdb #5 |
| 11066 | | --- |
| 11067 | | ADP — adenosine-5'-diphosphate |
| 11068 | | AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine |
| 11069 | | 5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate); |
| 11070 | | adenosine-5'-diphosphate monothiophosphate) |
| 11071 | | MG — magnesium ion |
| 11072 | | |
| 11073 | | |
| 11074 | | > rename #5 id #4.3 |
| 11075 | | |
| 11076 | | > close #4.3 |
| 11077 | | |
| 11078 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 11079 | | > Institute/Documents/Structures/RR911/templates/ystRFC-PCNA_1sxj.pdb" |
| 11080 | | |
| 11081 | | ystRFC-PCNA_1sxj.pdb title: |
| 11082 | | Crystal structure of the eukaryotic clamp loader (replication factor C, RFC) |
| 11083 | | bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA) |
| 11084 | | [more info...] |
| 11085 | | |
| 11086 | | Chain information for ystRFC-PCNA_1sxj.pdb #5 |
| 11087 | | --- |
| 11088 | | Chain | Description | UniProt |
| 11089 | | A | activator 1 95 kda subunit | RFC1_YEAST |
| 11090 | | B | activator 1 37 kda subunit | RFC4_YEAST |
| 11091 | | C | activator 1 40 kda subunit | RFC3_YEAST |
| 11092 | | D | activator 1 41 kda subunit | RFC2_YEAST |
| 11093 | | E | activator 1 40 kda subunit | RFC5_YEAST |
| 11094 | | F | PCNA | PCNA_YEAST |
| 11095 | | G | PCNA | PCNA_YEAST |
| 11096 | | H | PCNA | PCNA_YEAST |
| 11097 | | |
| 11098 | | Non-standard residues in ystRFC-PCNA_1sxj.pdb #5 |
| 11099 | | --- |
| 11100 | | ADP — adenosine-5'-diphosphate |
| 11101 | | AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine |
| 11102 | | 5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate); |
| 11103 | | adenosine-5'-diphosphate monothiophosphate) |
| 11104 | | MG — magnesium ion |
| 11105 | | |
| 11106 | | |
| 11107 | | > rename #5 id #4 |
| 11108 | | |
| 11109 | | > hide #4.2 models |
| 11110 | | |
| 11111 | | > mmaker #4.3/A-H to #3.1/A-H pair ss |
| 11112 | | |
| 11113 | | Parameters |
| 11114 | | --- |
| 11115 | | Chain pairing | ss |
| 11116 | | Alignment algorithm | Needleman-Wunsch |
| 11117 | | Similarity matrix | BLOSUM-62 |
| 11118 | | SS fraction | 0.3 |
| 11119 | | Gap open (HH/SS/other) | 18/18/6 |
| 11120 | | Gap extend | 1 |
| 11121 | | SS matrix | | | H | S | O |
| 11122 | | ---|---|---|--- |
| 11123 | | H | 6 | -9 | -6 |
| 11124 | | S | | 6 | -6 |
| 11125 | | O | | | 4 |
| 11126 | | Iteration cutoff | 2 |
| 11127 | | |
| 11128 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11129 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 11130 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain B (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11131 | | chain B (#4.3), sequence alignment score = 1541.7 |
| 11132 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain C (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11133 | | chain C (#4.3), sequence alignment score = 1606.5 |
| 11134 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain D (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11135 | | chain D (#4.3), sequence alignment score = 1617.1 |
| 11136 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11137 | | chain E (#4.3), sequence alignment score = 1471.9 |
| 11138 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11139 | | chain F (#4.3), sequence alignment score = 1241.2 |
| 11140 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11141 | | chain G (#4.3), sequence alignment score = 1219.8 |
| 11142 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11143 | | chain H (#4.3), sequence alignment score = 1142.2 |
| 11144 | | RMSD between 606 pruned atom pairs is 0.928 angstroms; (across all 2490 pairs: |
| 11145 | | 35.810) |
| 11146 | | |
| 11147 | | |
| 11148 | | > hide #4.3 |
| 11149 | | |
| 11150 | | > show #4.3 cartoons |
| 11151 | | |
| 11152 | | > mmaker #4.3/A to #3.1/A pair ss |
| 11153 | | |
| 11154 | | Parameters |
| 11155 | | --- |
| 11156 | | Chain pairing | ss |
| 11157 | | Alignment algorithm | Needleman-Wunsch |
| 11158 | | Similarity matrix | BLOSUM-62 |
| 11159 | | SS fraction | 0.3 |
| 11160 | | Gap open (HH/SS/other) | 18/18/6 |
| 11161 | | Gap extend | 1 |
| 11162 | | SS matrix | | | H | S | O |
| 11163 | | ---|---|---|--- |
| 11164 | | H | 6 | -9 | -6 |
| 11165 | | S | | 6 | -6 |
| 11166 | | O | | | 4 |
| 11167 | | Iteration cutoff | 2 |
| 11168 | | |
| 11169 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11170 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 11171 | | RMSD between 204 pruned atom pairs is 0.730 angstroms; (across all 441 pairs: |
| 11172 | | 18.453) |
| 11173 | | |
| 11174 | | |
| 11175 | | > mmaker #4.3/A,F-H to #3.1/A,F-H pair ss |
| 11176 | | |
| 11177 | | Parameters |
| 11178 | | --- |
| 11179 | | Chain pairing | ss |
| 11180 | | Alignment algorithm | Needleman-Wunsch |
| 11181 | | Similarity matrix | BLOSUM-62 |
| 11182 | | SS fraction | 0.3 |
| 11183 | | Gap open (HH/SS/other) | 18/18/6 |
| 11184 | | Gap extend | 1 |
| 11185 | | SS matrix | | | H | S | O |
| 11186 | | ---|---|---|--- |
| 11187 | | H | 6 | -9 | -6 |
| 11188 | | S | | 6 | -6 |
| 11189 | | O | | | 4 |
| 11190 | | Iteration cutoff | 2 |
| 11191 | | |
| 11192 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11193 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 11194 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11195 | | chain F (#4.3), sequence alignment score = 1241.2 |
| 11196 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11197 | | chain G (#4.3), sequence alignment score = 1219.8 |
| 11198 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11199 | | chain H (#4.3), sequence alignment score = 1142.2 |
| 11200 | | RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 1208 pairs: |
| 11201 | | 33.241) |
| 11202 | | |
| 11203 | | |
| 11204 | | > scene name a |
| 11205 | | |
| 11206 | | Unknown command: scene name a |
| 11207 | | |
| 11208 | | > view name elg1a |
| 11209 | | |
| 11210 | | > mmaker #4.3/A to #3.1/A pair ss |
| 11211 | | |
| 11212 | | Parameters |
| 11213 | | --- |
| 11214 | | Chain pairing | ss |
| 11215 | | Alignment algorithm | Needleman-Wunsch |
| 11216 | | Similarity matrix | BLOSUM-62 |
| 11217 | | SS fraction | 0.3 |
| 11218 | | Gap open (HH/SS/other) | 18/18/6 |
| 11219 | | Gap extend | 1 |
| 11220 | | SS matrix | | | H | S | O |
| 11221 | | ---|---|---|--- |
| 11222 | | H | 6 | -9 | -6 |
| 11223 | | S | | 6 | -6 |
| 11224 | | O | | | 4 |
| 11225 | | Iteration cutoff | 2 |
| 11226 | | |
| 11227 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11228 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 11229 | | RMSD between 204 pruned atom pairs is 0.730 angstroms; (across all 441 pairs: |
| 11230 | | 18.453) |
| 11231 | | |
| 11232 | | |
| 11233 | | > hide #!3 models |
| 11234 | | |
| 11235 | | > setattr #4.3/H c chain_id X |
| 11236 | | |
| 11237 | | Assigning chain_id attribute to 1 item |
| 11238 | | |
| 11239 | | > setattr #4.3/F c chain_id G |
| 11240 | | |
| 11241 | | Assigning chain_id attribute to 1 item |
| 11242 | | |
| 11243 | | > undo |
| 11244 | | |
| 11245 | | > hide #!3 models |
| 11246 | | |
| 11247 | | > undo |
| 11248 | | |
| 11249 | | > view elg1a |
| 11250 | | |
| 11251 | | > hide #!3 models |
| 11252 | | |
| 11253 | | > close #4.3 |
| 11254 | | |
| 11255 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 11256 | | > Institute/Documents/Structures/RR911/templates/ystRFC-PCNA_1sxj.pdb" |
| 11257 | | |
| 11258 | | ystRFC-PCNA_1sxj.pdb title: |
| 11259 | | Crystal structure of the eukaryotic clamp loader (replication factor C, RFC) |
| 11260 | | bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA) |
| 11261 | | [more info...] |
| 11262 | | |
| 11263 | | Chain information for ystRFC-PCNA_1sxj.pdb #5 |
| 11264 | | --- |
| 11265 | | Chain | Description | UniProt |
| 11266 | | A | activator 1 95 kda subunit | RFC1_YEAST |
| 11267 | | B | activator 1 37 kda subunit | RFC4_YEAST |
| 11268 | | C | activator 1 40 kda subunit | RFC3_YEAST |
| 11269 | | D | activator 1 41 kda subunit | RFC2_YEAST |
| 11270 | | E | activator 1 40 kda subunit | RFC5_YEAST |
| 11271 | | F | PCNA | PCNA_YEAST |
| 11272 | | G | PCNA | PCNA_YEAST |
| 11273 | | H | PCNA | PCNA_YEAST |
| 11274 | | |
| 11275 | | Non-standard residues in ystRFC-PCNA_1sxj.pdb #5 |
| 11276 | | --- |
| 11277 | | ADP — adenosine-5'-diphosphate |
| 11278 | | AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine |
| 11279 | | 5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate); |
| 11280 | | adenosine-5'-diphosphate monothiophosphate) |
| 11281 | | MG — magnesium ion |
| 11282 | | |
| 11283 | | |
| 11284 | | > rename #5 id #4 |
| 11285 | | |
| 11286 | | > show #!3 models |
| 11287 | | |
| 11288 | | > hide #4.3 |
| 11289 | | |
| 11290 | | > show #4.3 cartoons |
| 11291 | | |
| 11292 | | > mmaker #4.3/A to #3.1/A pair ss |
| 11293 | | |
| 11294 | | Parameters |
| 11295 | | --- |
| 11296 | | Chain pairing | ss |
| 11297 | | Alignment algorithm | Needleman-Wunsch |
| 11298 | | Similarity matrix | BLOSUM-62 |
| 11299 | | SS fraction | 0.3 |
| 11300 | | Gap open (HH/SS/other) | 18/18/6 |
| 11301 | | Gap extend | 1 |
| 11302 | | SS matrix | | | H | S | O |
| 11303 | | ---|---|---|--- |
| 11304 | | H | 6 | -9 | -6 |
| 11305 | | S | | 6 | -6 |
| 11306 | | O | | | 4 |
| 11307 | | Iteration cutoff | 2 |
| 11308 | | |
| 11309 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11310 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 11311 | | RMSD between 204 pruned atom pairs is 0.730 angstroms; (across all 441 pairs: |
| 11312 | | 18.453) |
| 11313 | | |
| 11314 | | |
| 11315 | | > hide #!3 models |
| 11316 | | |
| 11317 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 11318 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC- |
| 11319 | | > PCNA_v1.cxs" |
| 11320 | | |
| 11321 | | > view name a |
| 11322 | | |
| 11323 | | > show #!3 models |
| 11324 | | |
| 11325 | | > hide #!3 models |
| 11326 | | |
| 11327 | | > setattr #4.3/H c chain_id X |
| 11328 | | |
| 11329 | | Assigning chain_id attribute to 1 item |
| 11330 | | |
| 11331 | | > setattr #4.3/G c chain_id H |
| 11332 | | |
| 11333 | | Assigning chain_id attribute to 1 item |
| 11334 | | |
| 11335 | | > setattr #4.3/F c chain_id G |
| 11336 | | |
| 11337 | | Assigning chain_id attribute to 1 item |
| 11338 | | |
| 11339 | | > setattr #4.3/X c chain_id F |
| 11340 | | |
| 11341 | | Assigning chain_id attribute to 1 item |
| 11342 | | |
| 11343 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 11344 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC- |
| 11345 | | > PCNA_v2.cxs" |
| 11346 | | |
| 11347 | | > show #!3 models |
| 11348 | | |
| 11349 | | > mmaker #4.3/A,F-H to #3.1/A,F-H pair ss |
| 11350 | | |
| 11351 | | Parameters |
| 11352 | | --- |
| 11353 | | Chain pairing | ss |
| 11354 | | Alignment algorithm | Needleman-Wunsch |
| 11355 | | Similarity matrix | BLOSUM-62 |
| 11356 | | SS fraction | 0.3 |
| 11357 | | Gap open (HH/SS/other) | 18/18/6 |
| 11358 | | Gap extend | 1 |
| 11359 | | SS matrix | | | H | S | O |
| 11360 | | ---|---|---|--- |
| 11361 | | H | 6 | -9 | -6 |
| 11362 | | S | | 6 | -6 |
| 11363 | | O | | | 4 |
| 11364 | | Iteration cutoff | 2 |
| 11365 | | |
| 11366 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11367 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 11368 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11369 | | chain G (#4.3), sequence alignment score = 1241.2 |
| 11370 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11371 | | chain H (#4.3), sequence alignment score = 1219.8 |
| 11372 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11373 | | chain F (#4.3), sequence alignment score = 1142.2 |
| 11374 | | RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 1208 pairs: |
| 11375 | | 33.241) |
| 11376 | | |
| 11377 | | |
| 11378 | | > hide #!3 models |
| 11379 | | |
| 11380 | | > show #!3 models |
| 11381 | | |
| 11382 | | > hide #!4.3 models |
| 11383 | | |
| 11384 | | > hide #!3 models |
| 11385 | | |
| 11386 | | > show #!4.3 models |
| 11387 | | |
| 11388 | | > mmaker #4.3/F-H to #3.1/F-H pair ss |
| 11389 | | |
| 11390 | | Parameters |
| 11391 | | --- |
| 11392 | | Chain pairing | ss |
| 11393 | | Alignment algorithm | Needleman-Wunsch |
| 11394 | | Similarity matrix | BLOSUM-62 |
| 11395 | | SS fraction | 0.3 |
| 11396 | | Gap open (HH/SS/other) | 18/18/6 |
| 11397 | | Gap extend | 1 |
| 11398 | | SS matrix | | | H | S | O |
| 11399 | | ---|---|---|--- |
| 11400 | | H | 6 | -9 | -6 |
| 11401 | | S | | 6 | -6 |
| 11402 | | O | | | 4 |
| 11403 | | Iteration cutoff | 2 |
| 11404 | | |
| 11405 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11406 | | chain G (#4.3), sequence alignment score = 1241.2 |
| 11407 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11408 | | chain H (#4.3), sequence alignment score = 1219.8 |
| 11409 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11410 | | chain F (#4.3), sequence alignment score = 1142.2 |
| 11411 | | RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 767 pairs: |
| 11412 | | 2.686) |
| 11413 | | |
| 11414 | | |
| 11415 | | > mmaker #4.3/F to #3.1/F pair ss |
| 11416 | | |
| 11417 | | Parameters |
| 11418 | | --- |
| 11419 | | Chain pairing | ss |
| 11420 | | Alignment algorithm | Needleman-Wunsch |
| 11421 | | Similarity matrix | BLOSUM-62 |
| 11422 | | SS fraction | 0.3 |
| 11423 | | Gap open (HH/SS/other) | 18/18/6 |
| 11424 | | Gap extend | 1 |
| 11425 | | SS matrix | | | H | S | O |
| 11426 | | ---|---|---|--- |
| 11427 | | H | 6 | -9 | -6 |
| 11428 | | S | | 6 | -6 |
| 11429 | | O | | | 4 |
| 11430 | | Iteration cutoff | 2 |
| 11431 | | |
| 11432 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11433 | | chain F (#4.3), sequence alignment score = 1172.8 |
| 11434 | | RMSD between 239 pruned atom pairs is 0.861 angstroms; (across all 254 pairs: |
| 11435 | | 1.184) |
| 11436 | | |
| 11437 | | |
| 11438 | | > hide #!4.3 models |
| 11439 | | |
| 11440 | | > show #!3 models |
| 11441 | | |
| 11442 | | > show #!4.3 models |
| 11443 | | |
| 11444 | | > mmaker #4.3/F-H to #3.1/F-H pair ss |
| 11445 | | |
| 11446 | | Parameters |
| 11447 | | --- |
| 11448 | | Chain pairing | ss |
| 11449 | | Alignment algorithm | Needleman-Wunsch |
| 11450 | | Similarity matrix | BLOSUM-62 |
| 11451 | | SS fraction | 0.3 |
| 11452 | | Gap open (HH/SS/other) | 18/18/6 |
| 11453 | | Gap extend | 1 |
| 11454 | | SS matrix | | | H | S | O |
| 11455 | | ---|---|---|--- |
| 11456 | | H | 6 | -9 | -6 |
| 11457 | | S | | 6 | -6 |
| 11458 | | O | | | 4 |
| 11459 | | Iteration cutoff | 2 |
| 11460 | | |
| 11461 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11462 | | chain G (#4.3), sequence alignment score = 1241.2 |
| 11463 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11464 | | chain H (#4.3), sequence alignment score = 1219.8 |
| 11465 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ystRFC-PCNA_1sxj.pdb, |
| 11466 | | chain F (#4.3), sequence alignment score = 1142.2 |
| 11467 | | RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 767 pairs: |
| 11468 | | 2.686) |
| 11469 | | |
| 11470 | | |
| 11471 | | > hide #!4.3 models |
| 11472 | | |
| 11473 | | > show #!4.3 models |
| 11474 | | |
| 11475 | | > hide #!3 models |
| 11476 | | |
| 11477 | | Populating font family aliases took 332 ms. Replace uses of missing font |
| 11478 | | family ".AppleSystemUIFont" with one that exists to avoid this cost. |
| 11479 | | |
| 11480 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 11481 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/ScRFC-PCNA_1SXJ.pdb" models |
| 11482 | | > #4.3 relModel #3.1 |
| 11483 | | |
| 11484 | | > close #4.3 |
| 11485 | | |
| 11486 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 11487 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/ScRFC-PCNA_1SXJ.pdb" |
| 11488 | | |
| 11489 | | ScRFC-PCNA_1SXJ.pdb title: |
| 11490 | | Crystal structure of the eukaryotic clamp loader (replication factor C, RFC) |
| 11491 | | bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA) |
| 11492 | | [more info...] |
| 11493 | | |
| 11494 | | Chain information for ScRFC-PCNA_1SXJ.pdb #5 |
| 11495 | | --- |
| 11496 | | Chain | Description | UniProt |
| 11497 | | A | activator 1 95 kda subunit | RFC1_YEAST |
| 11498 | | B | activator 1 37 kda subunit | RFC4_YEAST |
| 11499 | | C | activator 1 40 kda subunit | RFC3_YEAST |
| 11500 | | D | activator 1 41 kda subunit | RFC2_YEAST |
| 11501 | | E | activator 1 40 kda subunit | RFC5_YEAST |
| 11502 | | F | PCNA | PCNA_YEAST |
| 11503 | | G | PCNA | PCNA_YEAST |
| 11504 | | H | PCNA | PCNA_YEAST |
| 11505 | | |
| 11506 | | Non-standard residues in ScRFC-PCNA_1SXJ.pdb #5 |
| 11507 | | --- |
| 11508 | | ADP — adenosine-5'-diphosphate |
| 11509 | | AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine |
| 11510 | | 5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate); |
| 11511 | | adenosine-5'-diphosphate monothiophosphate) |
| 11512 | | MG — magnesium ion |
| 11513 | | |
| 11514 | | |
| 11515 | | > rename #5 id #4 |
| 11516 | | |
| 11517 | | > hide #4.3 |
| 11518 | | |
| 11519 | | > show #4.3 cartoons |
| 11520 | | |
| 11521 | | > mmaker #4.3/F-H to #3.1/F-H pair ss |
| 11522 | | |
| 11523 | | Parameters |
| 11524 | | --- |
| 11525 | | Chain pairing | ss |
| 11526 | | Alignment algorithm | Needleman-Wunsch |
| 11527 | | Similarity matrix | BLOSUM-62 |
| 11528 | | SS fraction | 0.3 |
| 11529 | | Gap open (HH/SS/other) | 18/18/6 |
| 11530 | | Gap extend | 1 |
| 11531 | | SS matrix | | | H | S | O |
| 11532 | | ---|---|---|--- |
| 11533 | | H | 6 | -9 | -6 |
| 11534 | | S | | 6 | -6 |
| 11535 | | O | | | 4 |
| 11536 | | Iteration cutoff | 2 |
| 11537 | | |
| 11538 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11539 | | chain G (#4.3), sequence alignment score = 1241.2 |
| 11540 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11541 | | chain H (#4.3), sequence alignment score = 1219.8 |
| 11542 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11543 | | chain F (#4.3), sequence alignment score = 1142.2 |
| 11544 | | RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 767 pairs: |
| 11545 | | 2.686) |
| 11546 | | |
| 11547 | | |
| 11548 | | > show #!3 models |
| 11549 | | |
| 11550 | | > hide #!3 models |
| 11551 | | |
| 11552 | | > close #4.3 |
| 11553 | | |
| 11554 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 11555 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/ScRFC-PCNA_1SXJ.pdb" |
| 11556 | | |
| 11557 | | Summary of feedback from opening /Users/fengwei.zheng/OneDrive - Van Andel |
| 11558 | | Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/ScRFC-PCNA_1SXJ.pdb |
| 11559 | | --- |
| 11560 | | warnings | Cannot find LINK/SSBOND residue MSE (-2 ) |
| 11561 | | Cannot find LINK/SSBOND residue HIS (-3 ) |
| 11562 | | |
| 11563 | | ScRFC-PCNA_1SXJ.pdb title: |
| 11564 | | Crystal structure of the eukaryotic clamp loader (replication factor C, RFC) |
| 11565 | | bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA) |
| 11566 | | [more info...] |
| 11567 | | |
| 11568 | | Chain information for ScRFC-PCNA_1SXJ.pdb #5 |
| 11569 | | --- |
| 11570 | | Chain | Description | UniProt |
| 11571 | | A | activator 1 95 kda subunit | RFC1_YEAST |
| 11572 | | B | activator 1 37 kda subunit | RFC4_YEAST |
| 11573 | | C | activator 1 40 kda subunit | RFC3_YEAST |
| 11574 | | D | activator 1 41 kda subunit | RFC2_YEAST |
| 11575 | | E | activator 1 40 kda subunit | RFC5_YEAST |
| 11576 | | F | PCNA | PCNA_YEAST |
| 11577 | | G | PCNA | PCNA_YEAST |
| 11578 | | H | PCNA | PCNA_YEAST |
| 11579 | | |
| 11580 | | Non-standard residues in ScRFC-PCNA_1SXJ.pdb #5 |
| 11581 | | --- |
| 11582 | | ADP — adenosine-5'-diphosphate |
| 11583 | | AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine |
| 11584 | | 5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate); |
| 11585 | | adenosine-5'-diphosphate monothiophosphate) |
| 11586 | | MG — magnesium ion |
| 11587 | | |
| 11588 | | |
| 11589 | | > rename #5 id #4 |
| 11590 | | |
| 11591 | | > hide #4.3 |
| 11592 | | |
| 11593 | | > show #4.3 cartoons |
| 11594 | | |
| 11595 | | > mmaker #4.3/F-H to #3.1/F-H pair ss |
| 11596 | | |
| 11597 | | Parameters |
| 11598 | | --- |
| 11599 | | Chain pairing | ss |
| 11600 | | Alignment algorithm | Needleman-Wunsch |
| 11601 | | Similarity matrix | BLOSUM-62 |
| 11602 | | SS fraction | 0.3 |
| 11603 | | Gap open (HH/SS/other) | 18/18/6 |
| 11604 | | Gap extend | 1 |
| 11605 | | SS matrix | | | H | S | O |
| 11606 | | ---|---|---|--- |
| 11607 | | H | 6 | -9 | -6 |
| 11608 | | S | | 6 | -6 |
| 11609 | | O | | | 4 |
| 11610 | | Iteration cutoff | 2 |
| 11611 | | |
| 11612 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11613 | | chain G (#4.3), sequence alignment score = 1241.2 |
| 11614 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11615 | | chain H (#4.3), sequence alignment score = 1219.8 |
| 11616 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11617 | | chain F (#4.3), sequence alignment score = 1142.2 |
| 11618 | | RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 767 pairs: |
| 11619 | | 2.686) |
| 11620 | | |
| 11621 | | |
| 11622 | | > lighting soft |
| 11623 | | |
| 11624 | | > hide #!4.3 models |
| 11625 | | |
| 11626 | | > show #!3 models |
| 11627 | | |
| 11628 | | > mmaker #4.3/F,G,H to #3.1/F,G,H pair ss |
| 11629 | | |
| 11630 | | Parameters |
| 11631 | | --- |
| 11632 | | Chain pairing | ss |
| 11633 | | Alignment algorithm | Needleman-Wunsch |
| 11634 | | Similarity matrix | BLOSUM-62 |
| 11635 | | SS fraction | 0.3 |
| 11636 | | Gap open (HH/SS/other) | 18/18/6 |
| 11637 | | Gap extend | 1 |
| 11638 | | SS matrix | | | H | S | O |
| 11639 | | ---|---|---|--- |
| 11640 | | H | 6 | -9 | -6 |
| 11641 | | S | | 6 | -6 |
| 11642 | | O | | | 4 |
| 11643 | | Iteration cutoff | 2 |
| 11644 | | |
| 11645 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11646 | | chain F (#4.3), sequence alignment score = 1172.8 |
| 11647 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11648 | | chain G (#4.3), sequence alignment score = 1216.2 |
| 11649 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11650 | | chain H (#4.3), sequence alignment score = 1124.2 |
| 11651 | | RMSD between 547 pruned atom pairs is 0.967 angstroms; (across all 765 pairs: |
| 11652 | | 2.525) |
| 11653 | | |
| 11654 | | |
| 11655 | | > show #!4.3 models |
| 11656 | | |
| 11657 | | > hide #!3 models |
| 11658 | | |
| 11659 | | > mmaker #4.3/A,F,G,H to #3.1/A,F,G,H pair ss |
| 11660 | | |
| 11661 | | Parameters |
| 11662 | | --- |
| 11663 | | Chain pairing | ss |
| 11664 | | Alignment algorithm | Needleman-Wunsch |
| 11665 | | Similarity matrix | BLOSUM-62 |
| 11666 | | SS fraction | 0.3 |
| 11667 | | Gap open (HH/SS/other) | 18/18/6 |
| 11668 | | Gap extend | 1 |
| 11669 | | SS matrix | | | H | S | O |
| 11670 | | ---|---|---|--- |
| 11671 | | H | 6 | -9 | -6 |
| 11672 | | S | | 6 | -6 |
| 11673 | | O | | | 4 |
| 11674 | | Iteration cutoff | 2 |
| 11675 | | |
| 11676 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11677 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 11678 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11679 | | chain F (#4.3), sequence alignment score = 1172.8 |
| 11680 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11681 | | chain G (#4.3), sequence alignment score = 1216.2 |
| 11682 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11683 | | chain H (#4.3), sequence alignment score = 1124.2 |
| 11684 | | RMSD between 580 pruned atom pairs is 1.006 angstroms; (across all 1206 pairs: |
| 11685 | | 13.225) |
| 11686 | | |
| 11687 | | |
| 11688 | | > mmaker #4.3/A,F-H to #3.1/A,F-H pair ss |
| 11689 | | |
| 11690 | | Parameters |
| 11691 | | --- |
| 11692 | | Chain pairing | ss |
| 11693 | | Alignment algorithm | Needleman-Wunsch |
| 11694 | | Similarity matrix | BLOSUM-62 |
| 11695 | | SS fraction | 0.3 |
| 11696 | | Gap open (HH/SS/other) | 18/18/6 |
| 11697 | | Gap extend | 1 |
| 11698 | | SS matrix | | | H | S | O |
| 11699 | | ---|---|---|--- |
| 11700 | | H | 6 | -9 | -6 |
| 11701 | | S | | 6 | -6 |
| 11702 | | O | | | 4 |
| 11703 | | Iteration cutoff | 2 |
| 11704 | | |
| 11705 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11706 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 11707 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11708 | | chain G (#4.3), sequence alignment score = 1241.2 |
| 11709 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11710 | | chain H (#4.3), sequence alignment score = 1219.8 |
| 11711 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11712 | | chain F (#4.3), sequence alignment score = 1142.2 |
| 11713 | | RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 1208 pairs: |
| 11714 | | 33.241) |
| 11715 | | |
| 11716 | | |
| 11717 | | > mmaker #4.3/A,F,G,H to #3.1/A,F,G,H pair ss |
| 11718 | | |
| 11719 | | Parameters |
| 11720 | | --- |
| 11721 | | Chain pairing | ss |
| 11722 | | Alignment algorithm | Needleman-Wunsch |
| 11723 | | Similarity matrix | BLOSUM-62 |
| 11724 | | SS fraction | 0.3 |
| 11725 | | Gap open (HH/SS/other) | 18/18/6 |
| 11726 | | Gap extend | 1 |
| 11727 | | SS matrix | | | H | S | O |
| 11728 | | ---|---|---|--- |
| 11729 | | H | 6 | -9 | -6 |
| 11730 | | S | | 6 | -6 |
| 11731 | | O | | | 4 |
| 11732 | | Iteration cutoff | 2 |
| 11733 | | |
| 11734 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11735 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 11736 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11737 | | chain F (#4.3), sequence alignment score = 1172.8 |
| 11738 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11739 | | chain G (#4.3), sequence alignment score = 1216.2 |
| 11740 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11741 | | chain H (#4.3), sequence alignment score = 1124.2 |
| 11742 | | RMSD between 580 pruned atom pairs is 1.006 angstroms; (across all 1206 pairs: |
| 11743 | | 13.225) |
| 11744 | | |
| 11745 | | |
| 11746 | | > hide #!4.3 models |
| 11747 | | |
| 11748 | | > show #4.2 models |
| 11749 | | |
| 11750 | | > show #!3 models |
| 11751 | | |
| 11752 | | > mmaker #4.2/A,F,G,H to #3.1/A,F,G,H pair ss |
| 11753 | | |
| 11754 | | Parameters |
| 11755 | | --- |
| 11756 | | Chain pairing | ss |
| 11757 | | Alignment algorithm | Needleman-Wunsch |
| 11758 | | Similarity matrix | BLOSUM-62 |
| 11759 | | SS fraction | 0.3 |
| 11760 | | Gap open (HH/SS/other) | 18/18/6 |
| 11761 | | Gap extend | 1 |
| 11762 | | SS matrix | | | H | S | O |
| 11763 | | ---|---|---|--- |
| 11764 | | H | 6 | -9 | -6 |
| 11765 | | S | | 6 | -6 |
| 11766 | | O | | | 4 |
| 11767 | | Iteration cutoff | 2 |
| 11768 | | |
| 11769 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with Elg1_RFC- |
| 11770 | | PCNA-v3_rsr04.pdb, chain A (#4.2), sequence alignment score = 349.3 |
| 11771 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC- |
| 11772 | | PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1178.8 |
| 11773 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC- |
| 11774 | | PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1237.2 |
| 11775 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC- |
| 11776 | | PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1154.8 |
| 11777 | | RMSD between 567 pruned atom pairs is 1.192 angstroms; (across all 1307 pairs: |
| 11778 | | 25.309) |
| 11779 | | |
| 11780 | | |
| 11781 | | > hide #!3 models |
| 11782 | | |
| 11783 | | > hide #4.2 models |
| 11784 | | |
| 11785 | | > show #4.1 models |
| 11786 | | |
| 11787 | | > mmaker #4.1/A-E to #4.2/A-E pair ss |
| 11788 | | |
| 11789 | | Parameters |
| 11790 | | --- |
| 11791 | | Chain pairing | ss |
| 11792 | | Alignment algorithm | Needleman-Wunsch |
| 11793 | | Similarity matrix | BLOSUM-62 |
| 11794 | | SS fraction | 0.3 |
| 11795 | | Gap open (HH/SS/other) | 18/18/6 |
| 11796 | | Gap extend | 1 |
| 11797 | | SS matrix | | | H | S | O |
| 11798 | | ---|---|---|--- |
| 11799 | | H | 6 | -9 | -6 |
| 11800 | | S | | 6 | -6 |
| 11801 | | O | | | 4 |
| 11802 | | Iteration cutoff | 2 |
| 11803 | | |
| 11804 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Elg1-RFC- |
| 11805 | | AF5-v2_Rsr02-Ct1.pdb, chain A (#4.1), sequence alignment score = 3064.9 |
| 11806 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Elg1-RFC- |
| 11807 | | AF5-v2_Rsr02-Ct1.pdb, chain B (#4.1), sequence alignment score = 1641.2 |
| 11808 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Elg1-RFC- |
| 11809 | | AF5-v2_Rsr02-Ct1.pdb, chain C (#4.1), sequence alignment score = 1739.6 |
| 11810 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Elg1-RFC- |
| 11811 | | AF5-v2_Rsr02-Ct1.pdb, chain D (#4.1), sequence alignment score = 1806.3 |
| 11812 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Elg1-RFC- |
| 11813 | | AF5-v2_Rsr02-Ct1.pdb, chain E (#4.1), sequence alignment score = 1802.2 |
| 11814 | | RMSD between 1976 pruned atom pairs is 0.355 angstroms; (across all 1976 |
| 11815 | | pairs: 0.355) |
| 11816 | | |
| 11817 | | |
| 11818 | | > show #4.2 models |
| 11819 | | |
| 11820 | | > hide #4.2 models |
| 11821 | | |
| 11822 | | > hide #4.1 models |
| 11823 | | |
| 11824 | | > show #!4.3 models |
| 11825 | | |
| 11826 | | > show #!3 models |
| 11827 | | |
| 11828 | | > mmaker #4.2/A,B,C,D,E,F,G,H to #3.1/A,B,C,D,E,F,G,H pair ss |
| 11829 | | |
| 11830 | | Parameters |
| 11831 | | --- |
| 11832 | | Chain pairing | ss |
| 11833 | | Alignment algorithm | Needleman-Wunsch |
| 11834 | | Similarity matrix | BLOSUM-62 |
| 11835 | | SS fraction | 0.3 |
| 11836 | | Gap open (HH/SS/other) | 18/18/6 |
| 11837 | | Gap extend | 1 |
| 11838 | | SS matrix | | | H | S | O |
| 11839 | | ---|---|---|--- |
| 11840 | | H | 6 | -9 | -6 |
| 11841 | | S | | 6 | -6 |
| 11842 | | O | | | 4 |
| 11843 | | Iteration cutoff | 2 |
| 11844 | | |
| 11845 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with Elg1_RFC- |
| 11846 | | PCNA-v3_rsr04.pdb, chain A (#4.2), sequence alignment score = 349.3 |
| 11847 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain B (#3.1) with Elg1_RFC- |
| 11848 | | PCNA-v3_rsr04.pdb, chain B (#4.2), sequence alignment score = 1567.2 |
| 11849 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain C (#3.1) with Elg1_RFC- |
| 11850 | | PCNA-v3_rsr04.pdb, chain C (#4.2), sequence alignment score = 1634.8 |
| 11851 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain D (#3.1) with Elg1_RFC- |
| 11852 | | PCNA-v3_rsr04.pdb, chain D (#4.2), sequence alignment score = 1643.5 |
| 11853 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with Elg1_RFC- |
| 11854 | | PCNA-v3_rsr04.pdb, chain E (#4.2), sequence alignment score = 1645.8 |
| 11855 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC- |
| 11856 | | PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1178.8 |
| 11857 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC- |
| 11858 | | PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1237.2 |
| 11859 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC- |
| 11860 | | PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1154.8 |
| 11861 | | RMSD between 291 pruned atom pairs is 0.986 angstroms; (across all 2629 pairs: |
| 11862 | | 21.565) |
| 11863 | | |
| 11864 | | |
| 11865 | | > show #4.2 models |
| 11866 | | |
| 11867 | | > hide #!4.3 models |
| 11868 | | |
| 11869 | | > mmaker #4.2/A,F,G,H to #3.1/A,F,G,H pair ss |
| 11870 | | |
| 11871 | | Parameters |
| 11872 | | --- |
| 11873 | | Chain pairing | ss |
| 11874 | | Alignment algorithm | Needleman-Wunsch |
| 11875 | | Similarity matrix | BLOSUM-62 |
| 11876 | | SS fraction | 0.3 |
| 11877 | | Gap open (HH/SS/other) | 18/18/6 |
| 11878 | | Gap extend | 1 |
| 11879 | | SS matrix | | | H | S | O |
| 11880 | | ---|---|---|--- |
| 11881 | | H | 6 | -9 | -6 |
| 11882 | | S | | 6 | -6 |
| 11883 | | O | | | 4 |
| 11884 | | Iteration cutoff | 2 |
| 11885 | | |
| 11886 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with Elg1_RFC- |
| 11887 | | PCNA-v3_rsr04.pdb, chain A (#4.2), sequence alignment score = 349.3 |
| 11888 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC- |
| 11889 | | PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1178.8 |
| 11890 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC- |
| 11891 | | PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1237.2 |
| 11892 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC- |
| 11893 | | PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1154.8 |
| 11894 | | RMSD between 567 pruned atom pairs is 1.192 angstroms; (across all 1307 pairs: |
| 11895 | | 25.309) |
| 11896 | | |
| 11897 | | |
| 11898 | | > hide #4.2 models |
| 11899 | | |
| 11900 | | > show #!4.3 models |
| 11901 | | |
| 11902 | | > mmaker #4.3/A,B,C,D,E,F,G,H to #3.1/A,B,C,D,E,F,G,H pair ss |
| 11903 | | |
| 11904 | | Parameters |
| 11905 | | --- |
| 11906 | | Chain pairing | ss |
| 11907 | | Alignment algorithm | Needleman-Wunsch |
| 11908 | | Similarity matrix | BLOSUM-62 |
| 11909 | | SS fraction | 0.3 |
| 11910 | | Gap open (HH/SS/other) | 18/18/6 |
| 11911 | | Gap extend | 1 |
| 11912 | | SS matrix | | | H | S | O |
| 11913 | | ---|---|---|--- |
| 11914 | | H | 6 | -9 | -6 |
| 11915 | | S | | 6 | -6 |
| 11916 | | O | | | 4 |
| 11917 | | Iteration cutoff | 2 |
| 11918 | | |
| 11919 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11920 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 11921 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain B (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11922 | | chain B (#4.3), sequence alignment score = 1541.7 |
| 11923 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain C (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11924 | | chain C (#4.3), sequence alignment score = 1606.5 |
| 11925 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain D (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11926 | | chain D (#4.3), sequence alignment score = 1617.1 |
| 11927 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11928 | | chain E (#4.3), sequence alignment score = 1471.9 |
| 11929 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11930 | | chain F (#4.3), sequence alignment score = 1172.8 |
| 11931 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11932 | | chain G (#4.3), sequence alignment score = 1216.2 |
| 11933 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11934 | | chain H (#4.3), sequence alignment score = 1124.2 |
| 11935 | | RMSD between 531 pruned atom pairs is 1.127 angstroms; (across all 2488 pairs: |
| 11936 | | 14.043) |
| 11937 | | |
| 11938 | | |
| 11939 | | > mmaker #4.2/F,G,H to #3.1/F,G,H pair ss |
| 11940 | | |
| 11941 | | Parameters |
| 11942 | | --- |
| 11943 | | Chain pairing | ss |
| 11944 | | Alignment algorithm | Needleman-Wunsch |
| 11945 | | Similarity matrix | BLOSUM-62 |
| 11946 | | SS fraction | 0.3 |
| 11947 | | Gap open (HH/SS/other) | 18/18/6 |
| 11948 | | Gap extend | 1 |
| 11949 | | SS matrix | | | H | S | O |
| 11950 | | ---|---|---|--- |
| 11951 | | H | 6 | -9 | -6 |
| 11952 | | S | | 6 | -6 |
| 11953 | | O | | | 4 |
| 11954 | | Iteration cutoff | 2 |
| 11955 | | |
| 11956 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC- |
| 11957 | | PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1178.8 |
| 11958 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC- |
| 11959 | | PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1237.2 |
| 11960 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC- |
| 11961 | | PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1154.8 |
| 11962 | | RMSD between 569 pruned atom pairs is 1.194 angstroms; (across all 765 pairs: |
| 11963 | | 1.944) |
| 11964 | | |
| 11965 | | |
| 11966 | | > mmaker #4.3/F,G,H to #3.1/F,G,H pair ss |
| 11967 | | |
| 11968 | | Parameters |
| 11969 | | --- |
| 11970 | | Chain pairing | ss |
| 11971 | | Alignment algorithm | Needleman-Wunsch |
| 11972 | | Similarity matrix | BLOSUM-62 |
| 11973 | | SS fraction | 0.3 |
| 11974 | | Gap open (HH/SS/other) | 18/18/6 |
| 11975 | | Gap extend | 1 |
| 11976 | | SS matrix | | | H | S | O |
| 11977 | | ---|---|---|--- |
| 11978 | | H | 6 | -9 | -6 |
| 11979 | | S | | 6 | -6 |
| 11980 | | O | | | 4 |
| 11981 | | Iteration cutoff | 2 |
| 11982 | | |
| 11983 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11984 | | chain F (#4.3), sequence alignment score = 1172.8 |
| 11985 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11986 | | chain G (#4.3), sequence alignment score = 1216.2 |
| 11987 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 11988 | | chain H (#4.3), sequence alignment score = 1124.2 |
| 11989 | | RMSD between 547 pruned atom pairs is 0.967 angstroms; (across all 765 pairs: |
| 11990 | | 2.525) |
| 11991 | | |
| 11992 | | |
| 11993 | | > mmaker #4.3/A,F,G,H to #3.1/A,F,G,H pair ss |
| 11994 | | |
| 11995 | | Parameters |
| 11996 | | --- |
| 11997 | | Chain pairing | ss |
| 11998 | | Alignment algorithm | Needleman-Wunsch |
| 11999 | | Similarity matrix | BLOSUM-62 |
| 12000 | | SS fraction | 0.3 |
| 12001 | | Gap open (HH/SS/other) | 18/18/6 |
| 12002 | | Gap extend | 1 |
| 12003 | | SS matrix | | | H | S | O |
| 12004 | | ---|---|---|--- |
| 12005 | | H | 6 | -9 | -6 |
| 12006 | | S | | 6 | -6 |
| 12007 | | O | | | 4 |
| 12008 | | Iteration cutoff | 2 |
| 12009 | | |
| 12010 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 12011 | | chain A (#4.3), sequence alignment score = 1956.8 |
| 12012 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 12013 | | chain F (#4.3), sequence alignment score = 1172.8 |
| 12014 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 12015 | | chain G (#4.3), sequence alignment score = 1216.2 |
| 12016 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 12017 | | chain H (#4.3), sequence alignment score = 1124.2 |
| 12018 | | RMSD between 580 pruned atom pairs is 1.006 angstroms; (across all 1206 pairs: |
| 12019 | | 13.225) |
| 12020 | | |
| 12021 | | |
| 12022 | | > hide #!4.3 models |
| 12023 | | |
| 12024 | | > show #4.2 models |
| 12025 | | |
| 12026 | | > mmaker #4.2/F,G,H to #3.1/F,G,H pair ss |
| 12027 | | |
| 12028 | | Parameters |
| 12029 | | --- |
| 12030 | | Chain pairing | ss |
| 12031 | | Alignment algorithm | Needleman-Wunsch |
| 12032 | | Similarity matrix | BLOSUM-62 |
| 12033 | | SS fraction | 0.3 |
| 12034 | | Gap open (HH/SS/other) | 18/18/6 |
| 12035 | | Gap extend | 1 |
| 12036 | | SS matrix | | | H | S | O |
| 12037 | | ---|---|---|--- |
| 12038 | | H | 6 | -9 | -6 |
| 12039 | | S | | 6 | -6 |
| 12040 | | O | | | 4 |
| 12041 | | Iteration cutoff | 2 |
| 12042 | | |
| 12043 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC- |
| 12044 | | PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1178.8 |
| 12045 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC- |
| 12046 | | PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1237.2 |
| 12047 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC- |
| 12048 | | PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1154.8 |
| 12049 | | RMSD between 569 pruned atom pairs is 1.194 angstroms; (across all 765 pairs: |
| 12050 | | 1.944) |
| 12051 | | |
| 12052 | | |
| 12053 | | > show #!4.3 models |
| 12054 | | |
| 12055 | | > hide #!4.3 models |
| 12056 | | |
| 12057 | | > hide #4.2 models |
| 12058 | | |
| 12059 | | > show #4.1 models |
| 12060 | | |
| 12061 | | > show #4.2 models |
| 12062 | | |
| 12063 | | > hide #!3 models |
| 12064 | | |
| 12065 | | > hide #4.1 models |
| 12066 | | |
| 12067 | | > show #4.1 models |
| 12068 | | |
| 12069 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12070 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC- |
| 12071 | | > PCNA_v3.cxs" |
| 12072 | | |
| 12073 | | > cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true |
| 12074 | | > xsection oval width 2.75 thickness 1 arrowScale 1.5 |
| 12075 | | |
| 12076 | | > color /A #FFB381 |
| 12077 | | |
| 12078 | | > color /B #D7819F |
| 12079 | | |
| 12080 | | > color /C #B48FE3 |
| 12081 | | |
| 12082 | | > color /D #D7CD85 |
| 12083 | | |
| 12084 | | > color /E salmon |
| 12085 | | |
| 12086 | | > color /F navajo white |
| 12087 | | |
| 12088 | | > color /G #CAC6FD |
| 12089 | | |
| 12090 | | > color /H plum |
| 12091 | | |
| 12092 | | > show #!4.3 models |
| 12093 | | |
| 12094 | | > hide #4.2 models |
| 12095 | | |
| 12096 | | > hide #4.1 models |
| 12097 | | |
| 12098 | | > show #!3 models |
| 12099 | | |
| 12100 | | > hide #!3 models |
| 12101 | | |
| 12102 | | > show #!3 models |
| 12103 | | |
| 12104 | | > hide #!3 models |
| 12105 | | |
| 12106 | | > show #!3 models |
| 12107 | | |
| 12108 | | > hide #!4.3 models |
| 12109 | | |
| 12110 | | > hide #!3 models |
| 12111 | | |
| 12112 | | > show #4.1 models |
| 12113 | | |
| 12114 | | > show #!3 models |
| 12115 | | |
| 12116 | | > hide #!4 models |
| 12117 | | |
| 12118 | | > show #!4 models |
| 12119 | | |
| 12120 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12121 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC- |
| 12122 | | > PCNA_v4.cxs" |
| 12123 | | |
| 12124 | | ——— End of log from Tue Dec 6 11:47:28 2022 ——— |
| 12125 | | |
| 12126 | | opened ChimeraX session |
| 12127 | | |
| 12128 | | > hide #!3 models |
| 12129 | | |
| 12130 | | > show #!3 models |
| 12131 | | |
| 12132 | | > hide #4.1 models |
| 12133 | | |
| 12134 | | > show #4.2 models |
| 12135 | | |
| 12136 | | > hide #4.2 models |
| 12137 | | |
| 12138 | | > show #4.2 models |
| 12139 | | |
| 12140 | | > view name a |
| 12141 | | |
| 12142 | | > hide #!3 models |
| 12143 | | |
| 12144 | | > show #4.1 models |
| 12145 | | |
| 12146 | | > select #4.1-2/A:278-329 |
| 12147 | | |
| 12148 | | 838 atoms, 848 bonds, 104 residues, 2 models selected |
| 12149 | | |
| 12150 | | > delete sel |
| 12151 | | |
| 12152 | | > show #!4.3 models |
| 12153 | | |
| 12154 | | > hide #!4.3 models |
| 12155 | | |
| 12156 | | > select #4.1-2/B:1-8 |
| 12157 | | |
| 12158 | | 122 atoms, 120 bonds, 16 residues, 2 models selected |
| 12159 | | |
| 12160 | | > delete sel |
| 12161 | | |
| 12162 | | > select #4.1-2/C:1-9 |
| 12163 | | |
| 12164 | | 138 atoms, 136 bonds, 18 residues, 2 models selected |
| 12165 | | |
| 12166 | | > show #!4.3 models |
| 12167 | | |
| 12168 | | > hide #!4.3 models |
| 12169 | | |
| 12170 | | > delete sel |
| 12171 | | |
| 12172 | | > show #!4.3 models |
| 12173 | | |
| 12174 | | > hide #!4.2 models |
| 12175 | | |
| 12176 | | > hide #!4.1 models |
| 12177 | | |
| 12178 | | > show #!4.2 models |
| 12179 | | |
| 12180 | | > show #!4.1 models |
| 12181 | | |
| 12182 | | > hide #!4.3 models |
| 12183 | | |
| 12184 | | > select #4.1-2/D:1-23 |
| 12185 | | |
| 12186 | | 356 atoms, 360 bonds, 46 residues, 2 models selected |
| 12187 | | |
| 12188 | | > show #!4.3 models |
| 12189 | | |
| 12190 | | > hide #!4.3 models |
| 12191 | | |
| 12192 | | > delete sel |
| 12193 | | |
| 12194 | | > show #!4.3 models |
| 12195 | | |
| 12196 | | > hide #!4.2 models |
| 12197 | | |
| 12198 | | > hide #!4.1 models |
| 12199 | | |
| 12200 | | > show #!4.1 models |
| 12201 | | |
| 12202 | | > hide #!4.1 models |
| 12203 | | |
| 12204 | | > show #!4.1 models |
| 12205 | | |
| 12206 | | > hide #!4.3 models |
| 12207 | | |
| 12208 | | > show #!4.3 models |
| 12209 | | |
| 12210 | | > hide #!4.1 models |
| 12211 | | |
| 12212 | | > show #!4.1 models |
| 12213 | | |
| 12214 | | > hide #!4.3 models |
| 12215 | | |
| 12216 | | > show #!4.2 models |
| 12217 | | |
| 12218 | | > select #4.1-2/A:663-696 |
| 12219 | | |
| 12220 | | 570 atoms, 578 bonds, 68 residues, 2 models selected |
| 12221 | | |
| 12222 | | > delete sel |
| 12223 | | |
| 12224 | | > select #4.1-2/A:734-765 |
| 12225 | | |
| 12226 | | 546 atoms, 552 bonds, 64 residues, 2 models selected |
| 12227 | | |
| 12228 | | > delete sel |
| 12229 | | |
| 12230 | | > select #4.1-2/A:734-791 |
| 12231 | | |
| 12232 | | 440 atoms, 456 bonds, 52 residues, 2 models selected |
| 12233 | | |
| 12234 | | > delete sel |
| 12235 | | |
| 12236 | | > view a |
| 12237 | | |
| 12238 | | > show #!3 models |
| 12239 | | |
| 12240 | | > hide #!4.2 models |
| 12241 | | |
| 12242 | | > hide #!4.1 models |
| 12243 | | |
| 12244 | | > show #!4.1 models |
| 12245 | | |
| 12246 | | > show #!4.2 models |
| 12247 | | |
| 12248 | | > hide #!4.1 models |
| 12249 | | |
| 12250 | | > hide #!3 models |
| 12251 | | |
| 12252 | | > show #!3 models |
| 12253 | | |
| 12254 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12255 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC- |
| 12256 | | > PCNA_v5.cxs" |
| 12257 | | |
| 12258 | | > hide #!3 models |
| 12259 | | |
| 12260 | | > color #4.1-2/A:557-616 magenta |
| 12261 | | |
| 12262 | | > select #4.1-2/A:515-532 |
| 12263 | | |
| 12264 | | 272 atoms, 272 bonds, 36 residues, 2 models selected |
| 12265 | | |
| 12266 | | > select #4.1-2/A:515-533 |
| 12267 | | |
| 12268 | | 280 atoms, 280 bonds, 38 residues, 2 models selected |
| 12269 | | |
| 12270 | | > select #4.1-2/A:515-534 |
| 12271 | | |
| 12272 | | 292 atoms, 292 bonds, 40 residues, 2 models selected |
| 12273 | | |
| 12274 | | > select #4.1-2/A:515-535 |
| 12275 | | |
| 12276 | | 304 atoms, 304 bonds, 42 residues, 2 models selected |
| 12277 | | |
| 12278 | | > select #4.1-2/A:213-231 |
| 12279 | | |
| 12280 | | 280 atoms, 284 bonds, 38 residues, 2 models selected |
| 12281 | | |
| 12282 | | > select #4.1-2/A:213-232 |
| 12283 | | |
| 12284 | | 296 atoms, 300 bonds, 40 residues, 2 models selected |
| 12285 | | |
| 12286 | | > select #4.1-2/A:213-231 |
| 12287 | | |
| 12288 | | 280 atoms, 284 bonds, 38 residues, 2 models selected |
| 12289 | | |
| 12290 | | > select #4.1-2/A:212-231 |
| 12291 | | |
| 12292 | | 296 atoms, 300 bonds, 40 residues, 2 models selected |
| 12293 | | |
| 12294 | | > select #4.1-2/A:212-231,515-535 |
| 12295 | | |
| 12296 | | 600 atoms, 604 bonds, 82 residues, 2 models selected |
| 12297 | | |
| 12298 | | > show #!4.1 models |
| 12299 | | |
| 12300 | | > hide #!4.2 models |
| 12301 | | |
| 12302 | | > show #!4.2 models |
| 12303 | | |
| 12304 | | > color sel blue cartoons |
| 12305 | | |
| 12306 | | > view a |
| 12307 | | |
| 12308 | | > select clear |
| 12309 | | |
| 12310 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12311 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC- |
| 12312 | | > PCNA_v6.cxs" |
| 12313 | | |
| 12314 | | > hide #!4.1 models |
| 12315 | | |
| 12316 | | > show #!4.1 models |
| 12317 | | |
| 12318 | | > hide #!4.1 models |
| 12319 | | |
| 12320 | | > show #!4.1 models |
| 12321 | | |
| 12322 | | > hide #!4.1 models |
| 12323 | | |
| 12324 | | > show #!4.1 models |
| 12325 | | |
| 12326 | | > hide #!4.2 models |
| 12327 | | |
| 12328 | | > show #!4.2 models |
| 12329 | | |
| 12330 | | > select #4.1-2/A:1-231,515-535 |
| 12331 | | |
| 12332 | | 1028 atoms, 1050 bonds, 134 residues, 2 models selected |
| 12333 | | |
| 12334 | | > color sel blue cartoons |
| 12335 | | |
| 12336 | | > hide #!4.2 models |
| 12337 | | |
| 12338 | | > show #!4.2 models |
| 12339 | | |
| 12340 | | > view a |
| 12341 | | |
| 12342 | | > select clear |
| 12343 | | |
| 12344 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12345 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC- |
| 12346 | | > PCNA_v6.cxs" |
| 12347 | | |
| 12348 | | > hide #!4.2 models |
| 12349 | | |
| 12350 | | > show #!4.2 models |
| 12351 | | |
| 12352 | | > hide #!4.2 models |
| 12353 | | |
| 12354 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12355 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Elg1_RFC-v1.jpg" width 1100 |
| 12356 | | > height 609 supersample 3 |
| 12357 | | |
| 12358 | | > hide #!4.1 models |
| 12359 | | |
| 12360 | | > show #!4.2 models |
| 12361 | | |
| 12362 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12363 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Elg1_RFC-PCNA_v1.jpg" width |
| 12364 | | > 1100 height 609 supersample 3 |
| 12365 | | |
| 12366 | | > hide #!4.2 models |
| 12367 | | |
| 12368 | | > hide #!4 models |
| 12369 | | |
| 12370 | | > show #!4.3 models |
| 12371 | | |
| 12372 | | > show #!4.2 models |
| 12373 | | |
| 12374 | | > hide #!4.2 models |
| 12375 | | |
| 12376 | | > show #!4.2 models |
| 12377 | | |
| 12378 | | > hide #!4.2 models |
| 12379 | | |
| 12380 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12381 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/RFC-PCNA_v1.jpg" width 1100 |
| 12382 | | > height 609 supersample 3 |
| 12383 | | |
| 12384 | | > hide #!4.3 models |
| 12385 | | |
| 12386 | | > hide #!4 models |
| 12387 | | |
| 12388 | | > show #!3 models |
| 12389 | | |
| 12390 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12391 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Elg1_RFC-PCNA-2DNA_v1.jpg" |
| 12392 | | > width 1100 height 609 supersample 3 |
| 12393 | | |
| 12394 | | > hide #!3 models |
| 12395 | | |
| 12396 | | > show #!2 models |
| 12397 | | |
| 12398 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12399 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Rad24_RFC- |
| 12400 | | > PCNA-10nt_gap_DNA_v1.jpg" width 1100 height 609 supersample 3 |
| 12401 | | |
| 12402 | | > hide #!2 models |
| 12403 | | |
| 12404 | | > show #!4 models |
| 12405 | | |
| 12406 | | > show #!4.2 models |
| 12407 | | |
| 12408 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12409 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC- |
| 12410 | | > PCNA_v7.cxs" |
| 12411 | | |
| 12412 | | ——— End of log from Tue Dec 6 12:15:53 2022 ——— |
| 12413 | | |
| 12414 | | opened ChimeraX session |
| 12415 | | |
| 12416 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12417 | | > Institute/Downloads/12-Elg1_RFC/0-map/0-CS/Local/0-Elg1RFC/cryosparc_P29_J632_004_volume_map_sharp.mrc" |
| 12418 | | |
| 12419 | | Opened cryosparc_P29_J632_004_volume_map_sharp.mrc as #5, grid size |
| 12420 | | 420,420,420, pixel 0.828, shown at level 0.1, step 2, values float32 |
| 12421 | | |
| 12422 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12423 | | > Institute/Downloads/12-Elg1_RFC/0-map/0-CS/Local/1-Elg1RFC- |
| 12424 | | > PCNA/cryosparc_P29_J677_003_volume_map_sharp.mrc" |
| 12425 | | |
| 12426 | | Opened cryosparc_P29_J677_003_volume_map_sharp.mrc as #6, grid size |
| 12427 | | 420,420,420, pixel 0.828, shown at level 0.0613, step 2, values float32 |
| 12428 | | |
| 12429 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12430 | | > Institute/Downloads/12-Elg1_RFC/0-map/0-CS/Local/1-Elg1RFC- |
| 12431 | | > PCNA/Open/cryosparc_P29_J701_004_volume_map_sharp.mrc" |
| 12432 | | |
| 12433 | | Opened cryosparc_P29_J701_004_volume_map_sharp.mrc as #7, grid size |
| 12434 | | 420,420,420, pixel 0.828, shown at level 0.0759, step 2, values float32 |
| 12435 | | |
| 12436 | | > surface dust #0-9 size 10 |
| 12437 | | |
| 12438 | | > volume #5-7 step 1 level 0.15 |
| 12439 | | |
| 12440 | | > hide #!4 models |
| 12441 | | |
| 12442 | | > show #!4 models |
| 12443 | | |
| 12444 | | > select add #5 |
| 12445 | | |
| 12446 | | 2 models selected |
| 12447 | | |
| 12448 | | > select subtract #5 |
| 12449 | | |
| 12450 | | Nothing selected |
| 12451 | | |
| 12452 | | > select add #5 |
| 12453 | | |
| 12454 | | 2 models selected |
| 12455 | | |
| 12456 | | > select add #6 |
| 12457 | | |
| 12458 | | 4 models selected |
| 12459 | | |
| 12460 | | > ui mousemode right "rotate selected models" |
| 12461 | | |
| 12462 | | > view matrix models |
| 12463 | | > #5,-0.36561,0.14267,-0.91977,377.08,0.71938,0.67036,-0.18197,-33.129,0.59061,-0.72819,-0.34773,269.16,#6,-0.36561,0.14267,-0.91977,377.08,0.71938,0.67036,-0.18197,-33.129,0.59061,-0.72819,-0.34773,269.16 |
| 12464 | | |
| 12465 | | > view matrix models |
| 12466 | | > #5,0.38251,0.71444,0.58589,-123.87,0.90722,-0.41055,-0.091667,108.33,0.17504,0.56659,-0.80519,195.32,#6,0.38251,0.71444,0.58589,-123.87,0.90722,-0.41055,-0.091667,108.33,0.17504,0.56659,-0.80519,195.32 |
| 12467 | | |
| 12468 | | > view matrix models |
| 12469 | | > #5,0.88522,0.1504,0.44019,-84.089,0.39058,-0.75428,-0.52774,336.56,0.25266,0.63909,-0.72645,154.9,#6,0.88522,0.1504,0.44019,-84.089,0.39058,-0.75428,-0.52774,336.56,0.25266,0.63909,-0.72645,154.9 |
| 12470 | | |
| 12471 | | > view matrix models |
| 12472 | | > #5,0.89431,0.22573,0.38634,-89.043,0.44658,-0.3965,-0.8021,314.2,-0.027878,0.88985,-0.4554,109.97,#6,0.89431,0.22573,0.38634,-89.043,0.44658,-0.3965,-0.8021,314.2,-0.027878,0.88985,-0.4554,109.97 |
| 12473 | | |
| 12474 | | > view matrix models |
| 12475 | | > #5,0.90632,0.21245,0.36532,-84.98,0.42181,-0.40187,-0.81276,321.38,-0.025859,0.89071,-0.45383,109.18,#6,0.90632,0.21245,0.36532,-84.98,0.42181,-0.40187,-0.81276,321.38,-0.025859,0.89071,-0.45383,109.18 |
| 12476 | | |
| 12477 | | > select add #7 |
| 12478 | | |
| 12479 | | 6 models selected |
| 12480 | | |
| 12481 | | > view matrix models |
| 12482 | | > #5,0.90662,0.20218,0.37036,-84.14,0.42188,-0.45113,-0.78645,325.27,0.0080759,0.86925,-0.4943,114.4,#6,0.90662,0.20218,0.37036,-84.14,0.42188,-0.45113,-0.78645,325.27,0.0080759,0.86925,-0.4943,114.4,#7,0.99993,0.00015236,-0.011438,2.0352,-0.00079073,0.99844,-0.055827,10.423,0.011412,0.055833,0.99837,-11.573 |
| 12483 | | |
| 12484 | | > hide #!7 models |
| 12485 | | |
| 12486 | | > hide #!5 models |
| 12487 | | |
| 12488 | | > select subtract #7 |
| 12489 | | |
| 12490 | | 4 models selected |
| 12491 | | |
| 12492 | | > view matrix models |
| 12493 | | > #5,-0.025136,0.96689,0.25395,-29.878,0.9987,0.013002,0.04935,-5.9153,0.044414,0.25486,-0.96596,297.84,#6,-0.025136,0.96689,0.25395,-29.878,0.9987,0.013002,0.04935,-5.9153,0.044414,0.25486,-0.96596,297.84 |
| 12494 | | |
| 12495 | | > view matrix models |
| 12496 | | > #5,0.83634,-0.074993,-0.54306,139.79,-0.058915,-0.99716,0.04697,353.6,-0.54504,-0.0072879,-0.83838,423.6,#6,0.83634,-0.074993,-0.54306,139.79,-0.058915,-0.99716,0.04697,353.6,-0.54504,-0.0072879,-0.83838,423.6 |
| 12497 | | |
| 12498 | | > view matrix models |
| 12499 | | > #5,0.040608,-0.99887,0.024519,336,-0.58373,-0.0038,0.81194,138.69,-0.81093,-0.047284,-0.58322,431.43,#6,0.040608,-0.99887,0.024519,336,-0.58373,-0.0038,0.81194,138.69,-0.81093,-0.047284,-0.58322,431.43 |
| 12500 | | |
| 12501 | | > view matrix models |
| 12502 | | > #5,-0.34757,-0.41118,0.84269,156.84,-0.32076,0.89664,0.3052,29.408,-0.88109,-0.16422,-0.44353,438.68,#6,-0.34757,-0.41118,0.84269,156.84,-0.32076,0.89664,0.3052,29.408,-0.88109,-0.16422,-0.44353,438.68 |
| 12503 | | |
| 12504 | | > view matrix models |
| 12505 | | > #5,-0.72128,-0.40442,-0.56231,473.99,-0.6819,0.27219,0.67892,132.68,-0.12151,0.87313,-0.4721,132.58,#6,-0.72128,-0.40442,-0.56231,473.99,-0.6819,0.27219,0.67892,132.68,-0.12151,0.87313,-0.4721,132.58 |
| 12506 | | |
| 12507 | | > view matrix models |
| 12508 | | > #5,0.63823,-0.66341,-0.39057,247.93,-0.76761,-0.50984,-0.38836,473.33,0.058516,0.54767,-0.83464,221.68,#6,0.63823,-0.66341,-0.39057,247.93,-0.76761,-0.50984,-0.38836,473.33,0.058516,0.54767,-0.83464,221.68 |
| 12509 | | |
| 12510 | | > view matrix models |
| 12511 | | > #5,0.73227,-0.63751,-0.23951,199.79,-0.66536,-0.59476,-0.45117,481.12,0.14518,0.48974,-0.8597,220.82,#6,0.73227,-0.63751,-0.23951,199.79,-0.66536,-0.59476,-0.45117,481.12,0.14518,0.48974,-0.8597,220.82 |
| 12512 | | |
| 12513 | | > view matrix models |
| 12514 | | > #5,0.56843,-0.71447,-0.40794,272.08,-0.81895,-0.4439,-0.3637,466.66,0.078766,0.54082,-0.83744,219.79,#6,0.56843,-0.71447,-0.40794,272.08,-0.81895,-0.4439,-0.3637,466.66,0.078766,0.54082,-0.83744,219.79 |
| 12515 | | |
| 12516 | | > view matrix models |
| 12517 | | > #5,0.76854,-0.57763,-0.2751,189.55,-0.63121,-0.61435,-0.47343,482.46,0.10446,0.5375,-0.83677,215.71,#6,0.76854,-0.57763,-0.2751,189.55,-0.63121,-0.61435,-0.47343,482.46,0.10446,0.5375,-0.83677,215.71 |
| 12518 | | |
| 12519 | | > view matrix models |
| 12520 | | > #5,0.72535,-0.61997,-0.29918,208.73,-0.67932,-0.57436,-0.45677,481.1,0.11135,0.53456,-0.83777,215.18,#6,0.72535,-0.61997,-0.29918,208.73,-0.67932,-0.57436,-0.45677,481.1,0.11135,0.53456,-0.83777,215.18 |
| 12521 | | |
| 12522 | | > select subtract #6 |
| 12523 | | |
| 12524 | | 2 models selected |
| 12525 | | |
| 12526 | | > show #!5 models |
| 12527 | | |
| 12528 | | > hide #!6 models |
| 12529 | | |
| 12530 | | > view matrix models |
| 12531 | | > #5,-0.80566,-0.57504,0.14226,369.37,-0.59084,0.76275,-0.26291,190.14,0.042677,-0.29587,-0.95428,397.4 |
| 12532 | | |
| 12533 | | > view matrix models |
| 12534 | | > #5,-0.92978,0.33001,0.16309,223.08,0.21293,0.84357,-0.493,86.718,-0.30027,-0.42365,-0.85461,458.03 |
| 12535 | | |
| 12536 | | > view matrix models |
| 12537 | | > #5,0.17164,0.86776,0.46641,-110.41,0.18657,0.43623,-0.88028,236.27,-0.96733,0.23811,-0.087023,305.61 |
| 12538 | | |
| 12539 | | > view matrix models |
| 12540 | | > #5,0.74719,-0.043762,0.66317,-77.351,0.3703,0.85601,-0.36073,34.117,-0.55189,0.5151,0.6558,49.671 |
| 12541 | | |
| 12542 | | > view matrix models |
| 12543 | | > #5,0.64687,-0.30179,-0.70034,238.94,0.41416,0.91015,-0.0096631,-48.062,0.64033,-0.2838,0.71374,-12.728 |
| 12544 | | |
| 12545 | | > view matrix models |
| 12546 | | > #5,-0.21312,0.41992,-0.88218,283.84,0.37224,0.86973,0.32406,-95.962,0.90334,-0.25932,-0.34167,135.98 |
| 12547 | | |
| 12548 | | > view matrix models |
| 12549 | | > #5,-0.21634,0.9726,-0.085136,36.819,0.6005,0.20131,0.77387,-96.775,0.7698,0.11629,-0.6276,143.46 |
| 12550 | | |
| 12551 | | > view matrix models |
| 12552 | | > #5,-0.15506,0.93711,-0.31269,75.462,0.94378,0.04698,-0.32721,79.427,-0.29195,-0.34585,-0.89172,449.57 |
| 12553 | | |
| 12554 | | > view matrix models |
| 12555 | | > #5,-0.063094,0.99767,-0.025884,-3.805,0.91806,0.047849,-0.39355,95.816,-0.39139,-0.048593,-0.91894,417.47 |
| 12556 | | |
| 12557 | | > volume #5 level 0.25 |
| 12558 | | |
| 12559 | | > volume #5 level 0.3 |
| 12560 | | |
| 12561 | | > view matrix models |
| 12562 | | > #5,0.92485,-0.32999,0.18913,33.246,0.054759,-0.37655,-0.92478,412.25,0.37638,0.86563,-0.33018,17.895 |
| 12563 | | |
| 12564 | | > view matrix models |
| 12565 | | > #5,0.84021,-0.40253,0.36333,28.01,0.19614,-0.39907,-0.8957,387.7,0.50554,0.82384,-0.25636,-9.4418 |
| 12566 | | |
| 12567 | | > view matrix models |
| 12568 | | > #5,0.79692,-0.41261,0.44122,22.54,0.26503,-0.41754,-0.86915,374.8,0.54285,0.80958,-0.22339,-19.095 |
| 12569 | | |
| 12570 | | > view matrix models |
| 12571 | | > #5,0.2021,0.27397,0.94026,-95.635,0.91547,-0.39395,-0.081984,118.21,0.34795,0.87735,-0.33043,20.499 |
| 12572 | | |
| 12573 | | > view matrix models |
| 12574 | | > #5,0.11026,0.78859,0.60496,-111.24,0.94572,-0.27046,0.18018,42.54,0.30571,0.55225,-0.7756,168.27 |
| 12575 | | |
| 12576 | | > volume #5 level 0.275 |
| 12577 | | |
| 12578 | | > volume #5 level 0.28 |
| 12579 | | |
| 12580 | | > show #!6 models |
| 12581 | | |
| 12582 | | > hide #!5 models |
| 12583 | | |
| 12584 | | > select add #6 |
| 12585 | | |
| 12586 | | 4 models selected |
| 12587 | | |
| 12588 | | > select subtract #5 |
| 12589 | | |
| 12590 | | 2 models selected |
| 12591 | | |
| 12592 | | > ui mousemode right "translate selected models" |
| 12593 | | |
| 12594 | | > show #!5 models |
| 12595 | | |
| 12596 | | > select add #5 |
| 12597 | | |
| 12598 | | 4 models selected |
| 12599 | | |
| 12600 | | > view matrix models |
| 12601 | | > #5,0.11026,0.78859,0.60496,-109.28,0.94572,-0.27046,0.18018,55.78,0.30571,0.55225,-0.7756,163.39,#6,0.72535,-0.61997,-0.29918,210.69,-0.67932,-0.57436,-0.45677,494.34,0.11135,0.53456,-0.83777,210.29 |
| 12602 | | |
| 12603 | | > hide #!5 models |
| 12604 | | |
| 12605 | | > ui mousemode right "rotate selected models" |
| 12606 | | |
| 12607 | | > view matrix models |
| 12608 | | > #5,-0.39939,0.71253,0.57688,-4.9893,0.88904,0.14739,0.43346,-64.783,0.22382,0.68598,-0.69234,134.9,#6,0.92605,-0.36358,0.1012,59.536,-0.24962,-0.79119,-0.5583,473.97,0.28306,0.49175,-0.82344,184.79 |
| 12609 | | |
| 12610 | | > view matrix models |
| 12611 | | > #5,-0.38473,0.7224,0.57456,-8.8713,0.91382,0.21039,0.34738,-64.426,0.13007,0.65869,-0.74108,165.09,#6,0.92584,-0.36846,0.084066,63.487,-0.23103,-0.72784,-0.64566,475.56,0.29908,0.57835,-0.75898,155.57 |
| 12612 | | |
| 12613 | | > ui mousemode right "translate selected models" |
| 12614 | | |
| 12615 | | > view matrix models |
| 12616 | | > #5,-0.38473,0.7224,0.57456,-8.5561,0.91382,0.21039,0.34738,-63.28,0.13007,0.65869,-0.74108,163.55,#6,0.92584,-0.36846,0.084066,63.802,-0.23103,-0.72784,-0.64566,476.71,0.29908,0.57835,-0.75898,154.03 |
| 12617 | | |
| 12618 | | Drag select of 11 residues, 6 cryosparc_P29_J677_003_volume_map_sharp.mrc |
| 12619 | | |
| 12620 | | > select clear |
| 12621 | | |
| 12622 | | > rename #5-7 id #5 |
| 12623 | | |
| 12624 | | > hide #!4 models |
| 12625 | | |
| 12626 | | > show #!5.1 models |
| 12627 | | |
| 12628 | | > select add #5.1 |
| 12629 | | |
| 12630 | | 2 models selected |
| 12631 | | |
| 12632 | | > view matrix models |
| 12633 | | > #5.1,-0.38473,0.7224,0.57456,-6.5595,0.91382,0.21039,0.34738,-39.937,0.13007,0.65869,-0.74108,166.22 |
| 12634 | | |
| 12635 | | > ui mousemode right "rotate selected models" |
| 12636 | | |
| 12637 | | > view matrix models |
| 12638 | | > #5.1,-0.34188,0.75883,0.55434,-16.39,0.91905,0.39308,0.028727,-14.468,-0.1961,0.51929,-0.8318,261.68 |
| 12639 | | |
| 12640 | | > ui mousemode right "translate selected models" |
| 12641 | | |
| 12642 | | > view matrix models |
| 12643 | | > #5.1,-0.34188,0.75883,0.55434,4.1369,0.91905,0.39308,0.028727,-20.715,-0.1961,0.51929,-0.8318,267.79 |
| 12644 | | |
| 12645 | | > ui mousemode right "rotate selected models" |
| 12646 | | |
| 12647 | | > view matrix models |
| 12648 | | > #5.1,-0.14347,0.87483,0.4627,-32.283,0.98009,0.060752,0.18903,-0.79165,0.13726,0.48061,-0.86612,226.35 |
| 12649 | | |
| 12650 | | > view matrix models |
| 12651 | | > #5.1,-0.080913,0.89876,0.43091,-40.956,0.99399,0.040798,0.10155,16.749,0.07369,0.43654,-0.89666,250.38 |
| 12652 | | |
| 12653 | | > fitmap #5.1 inMap #5.2 |
| 12654 | | |
| 12655 | | Fit map cryosparc_P29_J632_004_volume_map_sharp.mrc in map |
| 12656 | | cryosparc_P29_J677_003_volume_map_sharp.mrc using 158091 points |
| 12657 | | correlation = 0.9533, correlation about mean = 0.8198, overlap = 3.161e+04 |
| 12658 | | steps = 192, shift = 3.9, angle = 21.1 degrees |
| 12659 | | |
| 12660 | | Position of cryosparc_P29_J632_004_volume_map_sharp.mrc (#5.1) relative to |
| 12661 | | cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) coordinates: |
| 12662 | | Matrix rotation and translation |
| 12663 | | -0.53250380 0.84041401 -0.10071736 138.03273860 |
| 12664 | | -0.59424680 -0.45593109 -0.66256892 467.48309176 |
| 12665 | | -0.60275237 -0.29296951 0.74219838 181.20849958 |
| 12666 | | Axis 0.23627820 0.32094187 -0.91715262 |
| 12667 | | Axis point 213.77740768 230.20734826 0.00000000 |
| 12668 | | Rotation angle (degrees) 128.54420570 |
| 12669 | | Shift along axis 16.45317566 |
| 12670 | | |
| 12671 | | |
| 12672 | | > select clear |
| 12673 | | |
| 12674 | | > hide #!5.1 models |
| 12675 | | |
| 12676 | | > show #!5.3 models |
| 12677 | | |
| 12678 | | > select add #5.3 |
| 12679 | | |
| 12680 | | 2 models selected |
| 12681 | | |
| 12682 | | > view matrix models |
| 12683 | | > #5.3,0.31714,0.53441,-0.78347,170.13,-0.94116,0.075628,-0.32938,387.12,-0.11677,0.84184,0.52695,-40.035 |
| 12684 | | |
| 12685 | | > view matrix models |
| 12686 | | > #5.3,-0.11454,-0.59602,-0.79476,445.23,-0.58842,0.68529,-0.42912,236.69,0.8004,0.4185,-0.4292,44.446 |
| 12687 | | |
| 12688 | | > view matrix models |
| 12689 | | > #5.3,0.31906,-0.94748,0.021986,281.39,0.25949,0.065023,-0.96355,291.21,0.91152,0.31314,0.26661,-83.105 |
| 12690 | | |
| 12691 | | > view matrix models |
| 12692 | | > #5.3,0.8625,-0.31808,0.39361,8.2688,0.30282,-0.29877,-0.905,336.17,0.40546,0.89976,-0.16137,-17.822 |
| 12693 | | |
| 12694 | | > view matrix models |
| 12695 | | > #5.3,0.82719,-0.52666,-0.19591,157.7,-0.50038,-0.53175,-0.68327,478.8,0.25568,0.66322,-0.70339,148.14 |
| 12696 | | |
| 12697 | | > view matrix models |
| 12698 | | > #5.3,0.56647,-0.81097,0.14641,191.26,-0.26656,-0.34842,-0.89864,444.54,0.77978,0.47002,-0.41354,36.301 |
| 12699 | | |
| 12700 | | > view matrix models |
| 12701 | | > #5.3,0.92616,-0.37016,0.072179,64.333,-0.15623,-0.55078,-0.8199,445.9,0.34325,0.74808,-0.56794,93.305 |
| 12702 | | |
| 12703 | | > view matrix models |
| 12704 | | > #5.3,0.50968,-0.8593,-0.042875,244.05,-0.57304,-0.30187,-0.7619,465.96,0.64176,0.41289,-0.64627,112.9 |
| 12705 | | |
| 12706 | | > view matrix models |
| 12707 | | > #5.3,0.66291,-0.70836,0.24244,138.91,-0.16081,-0.45097,-0.87793,439.88,0.73122,0.543,-0.41286,32.092 |
| 12708 | | |
| 12709 | | > view matrix models |
| 12710 | | > #5.3,0.80243,-0.57884,0.14507,109.32,-0.22841,-0.52251,-0.82147,454.06,0.5513,0.62604,-0.55149,74.676 |
| 12711 | | |
| 12712 | | > view matrix models |
| 12713 | | > #5.3,0.67169,-0.73577,-0.086441,201.76,-0.5878,-0.45829,-0.66668,478.51,0.45091,0.49861,-0.74031,148.86 |
| 12714 | | |
| 12715 | | > view matrix models |
| 12716 | | > #5.3,0.80497,-0.59024,0.060255,126.24,-0.33294,-0.53344,-0.77756,466.52,0.49109,0.60585,-0.62592,102.35 |
| 12717 | | |
| 12718 | | > view matrix models |
| 12719 | | > #5.3,0.60624,-0.79158,0.076619,193.49,-0.45551,-0.42459,-0.78245,470.2,0.65191,0.43945,-0.61798,101.35 |
| 12720 | | |
| 12721 | | > view matrix models |
| 12722 | | > #5.3,0.84623,-0.52947,0.059717,108.46,-0.30283,-0.57014,-0.7637,465.05,0.4384,0.62818,-0.64281,110.87 |
| 12723 | | |
| 12724 | | > view matrix models |
| 12725 | | > #5.3,0.54906,-0.83423,0.05094,215.7,-0.52702,-0.39288,-0.75359,472.12,0.64867,0.38692,-0.65537,117.84 |
| 12726 | | |
| 12727 | | > view matrix models |
| 12728 | | > #5.3,0.55801,-0.81859,0.13614,195.94,-0.54037,-0.48295,-0.68902,478.44,0.62978,0.31091,-0.71184,144.64 |
| 12729 | | |
| 12730 | | > ui mousemode right "translate selected models" |
| 12731 | | |
| 12732 | | > view matrix models |
| 12733 | | > #5.3,0.55801,-0.81859,0.13614,207.98,-0.54037,-0.48295,-0.68902,495.07,0.62978,0.31091,-0.71184,141.49 |
| 12734 | | |
| 12735 | | > view matrix models |
| 12736 | | > #5.3,0.55801,-0.81859,0.13614,210.12,-0.54037,-0.48295,-0.68902,493.2,0.62978,0.31091,-0.71184,137.83 |
| 12737 | | |
| 12738 | | > ui mousemode right "rotate selected models" |
| 12739 | | |
| 12740 | | > view matrix models |
| 12741 | | > #5.3,0.78743,-0.6164,0.0020855,158.62,-0.462,-0.59243,-0.65999,493.08,0.40805,0.51873,-0.75127,148.14 |
| 12742 | | |
| 12743 | | > ui mousemode right "translate selected models" |
| 12744 | | |
| 12745 | | > view matrix models |
| 12746 | | > #5.3,0.78743,-0.6164,0.0020855,138.41,-0.462,-0.59243,-0.65999,498.92,0.40805,0.51873,-0.75127,139.79 |
| 12747 | | |
| 12748 | | > ui mousemode right "rotate selected models" |
| 12749 | | |
| 12750 | | > ui mousemode right "translate selected models" |
| 12751 | | |
| 12752 | | > view matrix models |
| 12753 | | > #5.3,0.78743,-0.6164,0.0020855,143.47,-0.462,-0.59243,-0.65999,505.73,0.40805,0.51873,-0.75127,139.27 |
| 12754 | | |
| 12755 | | > ui mousemode right "rotate selected models" |
| 12756 | | |
| 12757 | | > view matrix models |
| 12758 | | > #5.3,0.80165,-0.59211,0.0823,122.19,-0.34711,-0.57313,-0.74232,496.95,0.4867,0.56651,-0.66497,101.37 |
| 12759 | | |
| 12760 | | > fitmap #5.3 inMap #5.2 |
| 12761 | | |
| 12762 | | Fit map cryosparc_P29_J701_004_volume_map_sharp.mrc in map |
| 12763 | | cryosparc_P29_J677_003_volume_map_sharp.mrc using 347135 points |
| 12764 | | correlation = 0.8968, correlation about mean = 0.7925, overlap = 2.38e+04 |
| 12765 | | steps = 256, shift = 10.9, angle = 18.1 degrees |
| 12766 | | |
| 12767 | | Position of cryosparc_P29_J701_004_volume_map_sharp.mrc (#5.3) relative to |
| 12768 | | cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) coordinates: |
| 12769 | | Matrix rotation and translation |
| 12770 | | 0.99845364 0.05399836 0.01321052 -10.86198174 |
| 12771 | | -0.05443621 0.99788961 0.03539819 3.29465681 |
| 12772 | | -0.01127120 -0.03606258 0.99928597 7.38308998 |
| 12773 | | Axis -0.54074826 0.18525478 -0.82053153 |
| 12774 | | Axis point 51.38380777 198.36045742 0.00000000 |
| 12775 | | Rotation angle (degrees) 3.78862562 |
| 12776 | | Shift along axis 0.42589055 |
| 12777 | | |
| 12778 | | |
| 12779 | | > select clear |
| 12780 | | |
| 12781 | | > hide #!5.2 models |
| 12782 | | |
| 12783 | | > volume #5.3 level 0.175 |
| 12784 | | |
| 12785 | | > volume #5.3 level 0.2 |
| 12786 | | |
| 12787 | | > ui mousemode right select |
| 12788 | | |
| 12789 | | > hide #!5.1 models |
| 12790 | | |
| 12791 | | > show #!5.2 models |
| 12792 | | |
| 12793 | | > show #!4 models |
| 12794 | | |
| 12795 | | > fitmap #4.2 inMap #5.2 |
| 12796 | | |
| 12797 | | Fit molecule Elg1_RFC-PCNA-v3_rsr04.pdb (#4.2) to map |
| 12798 | | cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) using 20380 atoms |
| 12799 | | average map value = 0.05878, steps = 96 |
| 12800 | | shifted from previous position = 4.63 |
| 12801 | | rotated from previous position = 4.75 degrees |
| 12802 | | atoms outside contour = 16977, contour level = 0.15 |
| 12803 | | |
| 12804 | | Position of Elg1_RFC-PCNA-v3_rsr04.pdb (#4.2) relative to |
| 12805 | | cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) coordinates: |
| 12806 | | Matrix rotation and translation |
| 12807 | | 0.99758484 0.05159763 0.04649926 -22.87801885 |
| 12808 | | -0.05283491 0.99827034 0.02578373 10.04697680 |
| 12809 | | -0.04508845 -0.02817823 0.99858550 17.30051962 |
| 12810 | | Axis -0.36211712 0.61460848 -0.70080497 |
| 12811 | | Axis point 148.78669247 433.96861741 0.00000000 |
| 12812 | | Rotation angle (degrees) 4.27301044 |
| 12813 | | Shift along axis 2.33518917 |
| 12814 | | |
| 12815 | | |
| 12816 | | > ui mousemode right "translate selected models" |
| 12817 | | |
| 12818 | | > select add #4.2 |
| 12819 | | |
| 12820 | | 20380 atoms, 20704 bonds, 2 pseudobonds, 2575 residues, 2 models selected |
| 12821 | | |
| 12822 | | > view matrix models |
| 12823 | | > #4.2,0.93928,-0.32242,0.1175,45.368,-0.16291,-0.7203,-0.67426,471.11,0.30203,0.61417,-0.72909,143.34 |
| 12824 | | |
| 12825 | | > fitmap #4.2 inMap #5.2 |
| 12826 | | |
| 12827 | | Fit molecule Elg1_RFC-PCNA-v3_rsr04.pdb (#4.2) to map |
| 12828 | | cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) using 20380 atoms |
| 12829 | | average map value = 0.2398, steps = 116 |
| 12830 | | shifted from previous position = 3.53 |
| 12831 | | rotated from previous position = 4.23 degrees |
| 12832 | | atoms outside contour = 8754, contour level = 0.15 |
| 12833 | | |
| 12834 | | Position of Elg1_RFC-PCNA-v3_rsr04.pdb (#4.2) relative to |
| 12835 | | cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) coordinates: |
| 12836 | | Matrix rotation and translation |
| 12837 | | 0.99999878 0.00046628 0.00148852 -0.64945417 |
| 12838 | | -0.00046460 0.99999925 -0.00112811 0.37220285 |
| 12839 | | -0.00148904 0.00112742 0.99999825 0.01258259 |
| 12840 | | Axis 0.58590405 0.77346311 -0.24180832 |
| 12841 | | Axis point -7.55369589 0.00000000 398.64399382 |
| 12842 | | Rotation angle (degrees) 0.11028431 |
| 12843 | | Shift along axis -0.09567522 |
| 12844 | | |
| 12845 | | |
| 12846 | | > hide #!5 models |
| 12847 | | |
| 12848 | | > show #!4.1 models |
| 12849 | | |
| 12850 | | > mmaker #4.1 to #4.2 |
| 12851 | | |
| 12852 | | Parameters |
| 12853 | | --- |
| 12854 | | Chain pairing | bb |
| 12855 | | Alignment algorithm | Needleman-Wunsch |
| 12856 | | Similarity matrix | BLOSUM-62 |
| 12857 | | SS fraction | 0.3 |
| 12858 | | Gap open (HH/SS/other) | 18/18/6 |
| 12859 | | Gap extend | 1 |
| 12860 | | SS matrix | | | H | S | O |
| 12861 | | ---|---|---|--- |
| 12862 | | H | 6 | -9 | -6 |
| 12863 | | S | | 6 | -6 |
| 12864 | | O | | | 4 |
| 12865 | | Iteration cutoff | 2 |
| 12866 | | |
| 12867 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Elg1-RFC- |
| 12868 | | AF5-v2_Rsr02-Ct1.pdb, chain A (#4.1), sequence alignment score = 2856.7 |
| 12869 | | RMSD between 462 pruned atom pairs is 0.300 angstroms; (across all 462 pairs: |
| 12870 | | 0.300) |
| 12871 | | |
| 12872 | | |
| 12873 | | > hide #!4.1 models |
| 12874 | | |
| 12875 | | > show #!4.1 models |
| 12876 | | |
| 12877 | | > select clear |
| 12878 | | |
| 12879 | | > hide #!4.2 models |
| 12880 | | |
| 12881 | | > show #!5 models |
| 12882 | | |
| 12883 | | > show #!5.1 models |
| 12884 | | |
| 12885 | | > hide #!5.2 models |
| 12886 | | |
| 12887 | | > mmaker #4.1 to #5.1 |
| 12888 | | |
| 12889 | | No 'to' model specified |
| 12890 | | |
| 12891 | | > fitmap #4.1 inMap #5.1 |
| 12892 | | |
| 12893 | | Fit molecule Elg1-RFC-AF5-v2_Rsr02-Ct1.pdb (#4.1) to map |
| 12894 | | cryosparc_P29_J632_004_volume_map_sharp.mrc (#5.1) using 14258 atoms |
| 12895 | | average map value = 0.5589, steps = 64 |
| 12896 | | shifted from previous position = 0.245 |
| 12897 | | rotated from previous position = 0.684 degrees |
| 12898 | | atoms outside contour = 4131, contour level = 0.28 |
| 12899 | | |
| 12900 | | Position of Elg1-RFC-AF5-v2_Rsr02-Ct1.pdb (#4.1) relative to |
| 12901 | | cryosparc_P29_J632_004_volume_map_sharp.mrc (#5.1) coordinates: |
| 12902 | | Matrix rotation and translation |
| 12903 | | 1.00000000 -0.00001573 0.00012749 -0.01045293 |
| 12904 | | 0.00001571 0.99999999 0.00013730 -0.02133687 |
| 12905 | | -0.00012749 -0.00013730 0.99999998 0.05449296 |
| 12906 | | Axis -0.73023040 0.67806417 0.08362147 |
| 12907 | | Axis point 0.00000000 398.26212072 144.18039597 |
| 12908 | | Rotation angle (degrees) 0.01077290 |
| 12909 | | Shift along axis -0.00227793 |
| 12910 | | |
| 12911 | | |
| 12912 | | > color zone #5.1 near #4.1 distance 10 |
| 12913 | | |
| 12914 | | > hide #!4 models |
| 12915 | | |
| 12916 | | > show #!4 models |
| 12917 | | |
| 12918 | | > hide #!4.1 models |
| 12919 | | |
| 12920 | | > show #!4.2 models |
| 12921 | | |
| 12922 | | > hide #!5.1 models |
| 12923 | | |
| 12924 | | > show #!5.2 models |
| 12925 | | |
| 12926 | | > color zone #5.2 near #4.2 distance 10 |
| 12927 | | |
| 12928 | | > hide #!5.2 models |
| 12929 | | |
| 12930 | | > show #!5.3 models |
| 12931 | | |
| 12932 | | > color zone #5.3 near #4.2 distance 10 |
| 12933 | | |
| 12934 | | > hide #!4 models |
| 12935 | | |
| 12936 | | > show #!4.1 models |
| 12937 | | |
| 12938 | | > hide #!4.1 models |
| 12939 | | |
| 12940 | | > show #!4.1 models |
| 12941 | | |
| 12942 | | > hide #!4.1 models |
| 12943 | | |
| 12944 | | > hide #!4 models |
| 12945 | | |
| 12946 | | > hide #!5 models |
| 12947 | | |
| 12948 | | > show #!5.1 models |
| 12949 | | |
| 12950 | | > show #!5.2 models |
| 12951 | | |
| 12952 | | > hide #!5 models |
| 12953 | | |
| 12954 | | > show #!5 models |
| 12955 | | |
| 12956 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 12957 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC- |
| 12958 | | > PCNA_v8.cxs" |
| 12959 | | |
| 12960 | | ——— End of log from Thu Jan 12 10:32:45 2023 ——— |
| 12961 | | |
| 12962 | | opened ChimeraX session |
| 12963 | | |
| 12964 | | > hide #!5.1 models |
| 12965 | | |
| 12966 | | > hide #!5.2 models |
| 12967 | | |
| 12968 | | > hide #!4.2 models |
| 12969 | | |
| 12970 | | > show #!4.2 models |
| 12971 | | |
| 12972 | | > hide #!5 models |
| 12973 | | |
| 12974 | | > show #!5 models |
| 12975 | | |
| 12976 | | > open /Users/fengwei.zheng/Documents/Phenix/4_Elg1_RFC- |
| 12977 | | > PCNA/2_Coot/2-Open/Open-Rsr28.pdb |
| 12978 | | |
| 12979 | | Chain information for Open-Rsr28.pdb #6 |
| 12980 | | --- |
| 12981 | | Chain | Description |
| 12982 | | A | No description available |
| 12983 | | B | No description available |
| 12984 | | C | No description available |
| 12985 | | D | No description available |
| 12986 | | E | No description available |
| 12987 | | F | No description available |
| 12988 | | G | No description available |
| 12989 | | H | No description available |
| 12990 | | |
| 12991 | | |
| 12992 | | > hide #6 |
| 12993 | | |
| 12994 | | > undo |
| 12995 | | |
| 12996 | | > hide #6 & protein |
| 12997 | | |
| 12998 | | > show #6 cartoons |
| 12999 | | |
| 13000 | | > mmaker #6/A-H to #4.2/A-H pair ss |
| 13001 | | |
| 13002 | | Parameters |
| 13003 | | --- |
| 13004 | | Chain pairing | ss |
| 13005 | | Alignment algorithm | Needleman-Wunsch |
| 13006 | | Similarity matrix | BLOSUM-62 |
| 13007 | | SS fraction | 0.3 |
| 13008 | | Gap open (HH/SS/other) | 18/18/6 |
| 13009 | | Gap extend | 1 |
| 13010 | | SS matrix | | | H | S | O |
| 13011 | | ---|---|---|--- |
| 13012 | | H | 6 | -9 | -6 |
| 13013 | | S | | 6 | -6 |
| 13014 | | O | | | 4 |
| 13015 | | Iteration cutoff | 2 |
| 13016 | | |
| 13017 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb, |
| 13018 | | chain A (#6), sequence alignment score = 6.9 |
| 13019 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb, |
| 13020 | | chain B (#6), sequence alignment score = 3.9 |
| 13021 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain F (#4.2) with Open-Rsr28.pdb, |
| 13022 | | chain C (#6), sequence alignment score = 2.9 |
| 13023 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb, |
| 13024 | | chain D (#6), sequence alignment score = 172.4 |
| 13025 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb, |
| 13026 | | chain E (#6), sequence alignment score = 529.1 |
| 13027 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb, |
| 13028 | | chain F (#6), sequence alignment score = 5.5 |
| 13029 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb, |
| 13030 | | chain H (#6), sequence alignment score = 3.5 |
| 13031 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb, |
| 13032 | | chain G (#6), sequence alignment score = 16.9 |
| 13033 | | RMSD between 168 pruned atom pairs is 1.162 angstroms; (across all 685 pairs: |
| 13034 | | 34.822) |
| 13035 | | |
| 13036 | | |
| 13037 | | > hide #!5.3 models |
| 13038 | | |
| 13039 | | > hide #!6 models |
| 13040 | | |
| 13041 | | > hide #!4.2 models |
| 13042 | | |
| 13043 | | > show #!4.2 models |
| 13044 | | |
| 13045 | | > show #!6 models |
| 13046 | | |
| 13047 | | > hide #!4.2 models |
| 13048 | | |
| 13049 | | > show #!4.2 models |
| 13050 | | |
| 13051 | | > hide #!6 models |
| 13052 | | |
| 13053 | | > show #!6 models |
| 13054 | | |
| 13055 | | > hide #!5 models |
| 13056 | | |
| 13057 | | > hide #!4 models |
| 13058 | | |
| 13059 | | > mmaker #6/A-H to #4.2/A-H pair ss |
| 13060 | | |
| 13061 | | Parameters |
| 13062 | | --- |
| 13063 | | Chain pairing | ss |
| 13064 | | Alignment algorithm | Needleman-Wunsch |
| 13065 | | Similarity matrix | BLOSUM-62 |
| 13066 | | SS fraction | 0.3 |
| 13067 | | Gap open (HH/SS/other) | 18/18/6 |
| 13068 | | Gap extend | 1 |
| 13069 | | SS matrix | | | H | S | O |
| 13070 | | ---|---|---|--- |
| 13071 | | H | 6 | -9 | -6 |
| 13072 | | S | | 6 | -6 |
| 13073 | | O | | | 4 |
| 13074 | | Iteration cutoff | 2 |
| 13075 | | |
| 13076 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb, |
| 13077 | | chain A (#6), sequence alignment score = 6.9 |
| 13078 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb, |
| 13079 | | chain B (#6), sequence alignment score = 3.9 |
| 13080 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain F (#4.2) with Open-Rsr28.pdb, |
| 13081 | | chain C (#6), sequence alignment score = 2.9 |
| 13082 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb, |
| 13083 | | chain D (#6), sequence alignment score = 172.4 |
| 13084 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb, |
| 13085 | | chain E (#6), sequence alignment score = 529.1 |
| 13086 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb, |
| 13087 | | chain F (#6), sequence alignment score = 5.5 |
| 13088 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb, |
| 13089 | | chain H (#6), sequence alignment score = 3.5 |
| 13090 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb, |
| 13091 | | chain G (#6), sequence alignment score = 16.9 |
| 13092 | | RMSD between 168 pruned atom pairs is 1.162 angstroms; (across all 685 pairs: |
| 13093 | | 34.822) |
| 13094 | | |
| 13095 | | |
| 13096 | | > hide #!4.2 models |
| 13097 | | |
| 13098 | | > show #!4.2 models |
| 13099 | | |
| 13100 | | > view name a |
| 13101 | | |
| 13102 | | > hide #!6 models |
| 13103 | | |
| 13104 | | > show #!6 models |
| 13105 | | |
| 13106 | | > hide #!4 models |
| 13107 | | |
| 13108 | | > mmaker #6/A-H to #4.2/A-H |
| 13109 | | |
| 13110 | | Parameters |
| 13111 | | --- |
| 13112 | | Chain pairing | bb |
| 13113 | | Alignment algorithm | Needleman-Wunsch |
| 13114 | | Similarity matrix | BLOSUM-62 |
| 13115 | | SS fraction | 0.3 |
| 13116 | | Gap open (HH/SS/other) | 18/18/6 |
| 13117 | | Gap extend | 1 |
| 13118 | | SS matrix | | | H | S | O |
| 13119 | | ---|---|---|--- |
| 13120 | | H | 6 | -9 | -6 |
| 13121 | | S | | 6 | -6 |
| 13122 | | O | | | 4 |
| 13123 | | Iteration cutoff | 2 |
| 13124 | | |
| 13125 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb, |
| 13126 | | chain A (#6), sequence alignment score = 2124.7 |
| 13127 | | RMSD between 376 pruned atom pairs is 0.742 angstroms; (across all 454 pairs: |
| 13128 | | 1.890) |
| 13129 | | |
| 13130 | | |
| 13131 | | > show #!4 models |
| 13132 | | |
| 13133 | | > mmaker #6/A-H to #4.2/A-H pair ss |
| 13134 | | |
| 13135 | | Parameters |
| 13136 | | --- |
| 13137 | | Chain pairing | ss |
| 13138 | | Alignment algorithm | Needleman-Wunsch |
| 13139 | | Similarity matrix | BLOSUM-62 |
| 13140 | | SS fraction | 0.3 |
| 13141 | | Gap open (HH/SS/other) | 18/18/6 |
| 13142 | | Gap extend | 1 |
| 13143 | | SS matrix | | | H | S | O |
| 13144 | | ---|---|---|--- |
| 13145 | | H | 6 | -9 | -6 |
| 13146 | | S | | 6 | -6 |
| 13147 | | O | | | 4 |
| 13148 | | Iteration cutoff | 2 |
| 13149 | | |
| 13150 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb, |
| 13151 | | chain A (#6), sequence alignment score = 6.9 |
| 13152 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb, |
| 13153 | | chain B (#6), sequence alignment score = 3.9 |
| 13154 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain F (#4.2) with Open-Rsr28.pdb, |
| 13155 | | chain C (#6), sequence alignment score = 2.9 |
| 13156 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb, |
| 13157 | | chain D (#6), sequence alignment score = 172.4 |
| 13158 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb, |
| 13159 | | chain E (#6), sequence alignment score = 529.1 |
| 13160 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb, |
| 13161 | | chain F (#6), sequence alignment score = 5.5 |
| 13162 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb, |
| 13163 | | chain H (#6), sequence alignment score = 3.5 |
| 13164 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb, |
| 13165 | | chain G (#6), sequence alignment score = 16.9 |
| 13166 | | RMSD between 168 pruned atom pairs is 1.162 angstroms; (across all 685 pairs: |
| 13167 | | 34.822) |
| 13168 | | |
| 13169 | | |
| 13170 | | > mmaker #6/A-G to #4.2/A-G pair ss |
| 13171 | | |
| 13172 | | Parameters |
| 13173 | | --- |
| 13174 | | Chain pairing | ss |
| 13175 | | Alignment algorithm | Needleman-Wunsch |
| 13176 | | Similarity matrix | BLOSUM-62 |
| 13177 | | SS fraction | 0.3 |
| 13178 | | Gap open (HH/SS/other) | 18/18/6 |
| 13179 | | Gap extend | 1 |
| 13180 | | SS matrix | | | H | S | O |
| 13181 | | ---|---|---|--- |
| 13182 | | H | 6 | -9 | -6 |
| 13183 | | S | | 6 | -6 |
| 13184 | | O | | | 4 |
| 13185 | | Iteration cutoff | 2 |
| 13186 | | |
| 13187 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb, |
| 13188 | | chain A (#6), sequence alignment score = 6.9 |
| 13189 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain F (#4.2) with Open-Rsr28.pdb, |
| 13190 | | chain B (#6), sequence alignment score = 4.1 |
| 13191 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb, |
| 13192 | | chain C (#6), sequence alignment score = 229.3 |
| 13193 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb, |
| 13194 | | chain D (#6), sequence alignment score = 651.7 |
| 13195 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb, |
| 13196 | | chain E (#6), sequence alignment score = 521 |
| 13197 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb, |
| 13198 | | chain F (#6), sequence alignment score = 3.5 |
| 13199 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb, |
| 13200 | | chain G (#6), sequence alignment score = 16.9 |
| 13201 | | RMSD between 147 pruned atom pairs is 1.078 angstroms; (across all 1024 pairs: |
| 13202 | | 27.227) |
| 13203 | | |
| 13204 | | |
| 13205 | | > mmaker #6/A-H to #4.2/A-H |
| 13206 | | |
| 13207 | | Parameters |
| 13208 | | --- |
| 13209 | | Chain pairing | bb |
| 13210 | | Alignment algorithm | Needleman-Wunsch |
| 13211 | | Similarity matrix | BLOSUM-62 |
| 13212 | | SS fraction | 0.3 |
| 13213 | | Gap open (HH/SS/other) | 18/18/6 |
| 13214 | | Gap extend | 1 |
| 13215 | | SS matrix | | | H | S | O |
| 13216 | | ---|---|---|--- |
| 13217 | | H | 6 | -9 | -6 |
| 13218 | | S | | 6 | -6 |
| 13219 | | O | | | 4 |
| 13220 | | Iteration cutoff | 2 |
| 13221 | | |
| 13222 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb, |
| 13223 | | chain A (#6), sequence alignment score = 2124.7 |
| 13224 | | RMSD between 376 pruned atom pairs is 0.742 angstroms; (across all 454 pairs: |
| 13225 | | 1.890) |
| 13226 | | |
| 13227 | | |
| 13228 | | > mmaker #6/A-E,G,H to #4.2/A-E,G,H pair ss |
| 13229 | | |
| 13230 | | Parameters |
| 13231 | | --- |
| 13232 | | Chain pairing | ss |
| 13233 | | Alignment algorithm | Needleman-Wunsch |
| 13234 | | Similarity matrix | BLOSUM-62 |
| 13235 | | SS fraction | 0.3 |
| 13236 | | Gap open (HH/SS/other) | 18/18/6 |
| 13237 | | Gap extend | 1 |
| 13238 | | SS matrix | | | H | S | O |
| 13239 | | ---|---|---|--- |
| 13240 | | H | 6 | -9 | -6 |
| 13241 | | S | | 6 | -6 |
| 13242 | | O | | | 4 |
| 13243 | | Iteration cutoff | 2 |
| 13244 | | |
| 13245 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb, |
| 13246 | | chain A (#6), sequence alignment score = 2124.7 |
| 13247 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb, |
| 13248 | | chain B (#6), sequence alignment score = 1590.9 |
| 13249 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb, |
| 13250 | | chain C (#6), sequence alignment score = 1640.2 |
| 13251 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb, |
| 13252 | | chain D (#6), sequence alignment score = 1564.7 |
| 13253 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb, |
| 13254 | | chain E (#6), sequence alignment score = 1666.3 |
| 13255 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb, |
| 13256 | | chain G (#6), sequence alignment score = 1278.6 |
| 13257 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb, |
| 13258 | | chain H (#6), sequence alignment score = 1265.3 |
| 13259 | | RMSD between 1935 pruned atom pairs is 0.751 angstroms; (across all 2279 |
| 13260 | | pairs: 1.563) |
| 13261 | | |
| 13262 | | |
| 13263 | | > mmaker #6/A-E,G,H to #4.2/A-E,G,H pair ss |
| 13264 | | |
| 13265 | | Parameters |
| 13266 | | --- |
| 13267 | | Chain pairing | ss |
| 13268 | | Alignment algorithm | Needleman-Wunsch |
| 13269 | | Similarity matrix | BLOSUM-62 |
| 13270 | | SS fraction | 0.3 |
| 13271 | | Gap open (HH/SS/other) | 18/18/6 |
| 13272 | | Gap extend | 1 |
| 13273 | | SS matrix | | | H | S | O |
| 13274 | | ---|---|---|--- |
| 13275 | | H | 6 | -9 | -6 |
| 13276 | | S | | 6 | -6 |
| 13277 | | O | | | 4 |
| 13278 | | Iteration cutoff | 2 |
| 13279 | | |
| 13280 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb, |
| 13281 | | chain A (#6), sequence alignment score = 2124.7 |
| 13282 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb, |
| 13283 | | chain B (#6), sequence alignment score = 1590.9 |
| 13284 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb, |
| 13285 | | chain C (#6), sequence alignment score = 1640.2 |
| 13286 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb, |
| 13287 | | chain D (#6), sequence alignment score = 1564.7 |
| 13288 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb, |
| 13289 | | chain E (#6), sequence alignment score = 1666.3 |
| 13290 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb, |
| 13291 | | chain G (#6), sequence alignment score = 1278.6 |
| 13292 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb, |
| 13293 | | chain H (#6), sequence alignment score = 1265.3 |
| 13294 | | RMSD between 1935 pruned atom pairs is 0.751 angstroms; (across all 2279 |
| 13295 | | pairs: 1.563) |
| 13296 | | |
| 13297 | | |
| 13298 | | > view a |
| 13299 | | |
| 13300 | | > mmaker #6/A-E,G,H to #4.2/A-E,G,H pair ss |
| 13301 | | |
| 13302 | | Parameters |
| 13303 | | --- |
| 13304 | | Chain pairing | ss |
| 13305 | | Alignment algorithm | Needleman-Wunsch |
| 13306 | | Similarity matrix | BLOSUM-62 |
| 13307 | | SS fraction | 0.3 |
| 13308 | | Gap open (HH/SS/other) | 18/18/6 |
| 13309 | | Gap extend | 1 |
| 13310 | | SS matrix | | | H | S | O |
| 13311 | | ---|---|---|--- |
| 13312 | | H | 6 | -9 | -6 |
| 13313 | | S | | 6 | -6 |
| 13314 | | O | | | 4 |
| 13315 | | Iteration cutoff | 2 |
| 13316 | | |
| 13317 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb, |
| 13318 | | chain A (#6), sequence alignment score = 2124.7 |
| 13319 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb, |
| 13320 | | chain B (#6), sequence alignment score = 1590.9 |
| 13321 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb, |
| 13322 | | chain C (#6), sequence alignment score = 1640.2 |
| 13323 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb, |
| 13324 | | chain D (#6), sequence alignment score = 1564.7 |
| 13325 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb, |
| 13326 | | chain E (#6), sequence alignment score = 1666.3 |
| 13327 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb, |
| 13328 | | chain G (#6), sequence alignment score = 1278.6 |
| 13329 | | Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb, |
| 13330 | | chain H (#6), sequence alignment score = 1265.3 |
| 13331 | | RMSD between 1935 pruned atom pairs is 0.751 angstroms; (across all 2279 |
| 13332 | | pairs: 1.563) |
| 13333 | | |
| 13334 | | |
| 13335 | | > hide #!6 models |
| 13336 | | |
| 13337 | | > show #!6 models |
| 13338 | | |
| 13339 | | > cartoon style nucleic xsection oval width 2.5 thickness 2.5 |
| 13340 | | |
| 13341 | | > cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true |
| 13342 | | > xsection oval width 2.75 thickness 1 arrowScale |
| 13343 | | |
| 13344 | | Missing "arrowScale" keyword's argument |
| 13345 | | |
| 13346 | | > cartoon style nucleic xsection oval width 2.5 thickness 2.5 |
| 13347 | | |
| 13348 | | > cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true |
| 13349 | | > xsection oval width 2.75 thickness 1 arrowScale 1.5 |
| 13350 | | |
| 13351 | | > color /A #FFB381 |
| 13352 | | |
| 13353 | | > color /B #D7819F |
| 13354 | | |
| 13355 | | > color /C #B48FE3 |
| 13356 | | |
| 13357 | | > color /D #D7CD85 |
| 13358 | | |
| 13359 | | > color /E salmon |
| 13360 | | |
| 13361 | | > color /F navajo white |
| 13362 | | |
| 13363 | | > color /G #CAC6FD |
| 13364 | | |
| 13365 | | > color /H plum |
| 13366 | | |
| 13367 | | > hide #!4 models |
| 13368 | | |
| 13369 | | > show #!4 models |
| 13370 | | |
| 13371 | | > hide #!6 models |
| 13372 | | |
| 13373 | | > hide #!4 models |
| 13374 | | |
| 13375 | | > show #!6 models |
| 13376 | | |
| 13377 | | > hide #!6 models |
| 13378 | | |
| 13379 | | > show #!4.1 models |
| 13380 | | |
| 13381 | | > hide #!4.2 models |
| 13382 | | |
| 13383 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 13384 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/apo-4.jpg" width 1100 height |
| 13385 | | > 609 supersample 3 |
| 13386 | | |
| 13387 | | > hide #!4.1 models |
| 13388 | | |
| 13389 | | > show #!4.2 models |
| 13390 | | |
| 13391 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 13392 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/complex-4_closed.jpg" width |
| 13393 | | > 1100 height 609 supersample 3 |
| 13394 | | |
| 13395 | | > hide #!4.2 models |
| 13396 | | |
| 13397 | | > show #!6 models |
| 13398 | | |
| 13399 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 13400 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/complex-open-4.jpg" width |
| 13401 | | > 1100 height 609 supersample 3 |
| 13402 | | |
| 13403 | | > rename #6 id #4.4 |
| 13404 | | |
| 13405 | | > rename #4.3 id #4.5 |
| 13406 | | |
| 13407 | | > rename #4.4 id #4.3 |
| 13408 | | |
| 13409 | | > rename #4.5 id #4.4 |
| 13410 | | |
| 13411 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 13412 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC- |
| 13413 | | > PCNA_v9.cxs" |
| 13414 | | |
| 13415 | | ——— End of log from Thu Feb 2 14:25:37 2023 ——— |
| 13416 | | |
| 13417 | | opened ChimeraX session |
| 13418 | | |
| 13419 | | > close #1.1-6 |
| 13420 | | |
| 13421 | | > rename #5 id #1 |
| 13422 | | |
| 13423 | | > undo |
| 13424 | | |
| 13425 | | No undo action is available |
| 13426 | | |
| 13427 | | > undo |
| 13428 | | |
| 13429 | | No undo action is available |
| 13430 | | |
| 13431 | | > rename #1.1 id #1.9 |
| 13432 | | |
| 13433 | | > rename #1.1.1 id #1.1 |
| 13434 | | |
| 13435 | | > rename #1.9.1 id #1.1 |
| 13436 | | |
| 13437 | | > rename #1.9.2 id #1.2 |
| 13438 | | |
| 13439 | | > rename #1.9.3 id #1.3 |
| 13440 | | |
| 13441 | | > close #1.9 |
| 13442 | | |
| 13443 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13444 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 13445 | | |
| 13446 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13447 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 13448 | | |
| 13449 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13450 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 13451 | | |
| 13452 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13453 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 13454 | | |
| 13455 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13456 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 13457 | | |
| 13458 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13459 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 13460 | | |
| 13461 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13462 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 13463 | | |
| 13464 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13465 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 13466 | | |
| 13467 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13468 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 13469 | | |
| 13470 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13471 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 13472 | | |
| 13473 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13474 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 13475 | | |
| 13476 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13477 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 13478 | | |
| 13479 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13480 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 13481 | | |
| 13482 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13483 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 13484 | | |
| 13485 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13486 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 13487 | | |
| 13488 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with |
| 13489 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 13490 | | |
| 13491 | | > rename #2 id #5 |
| 13492 | | |
| 13493 | | > rename #4 id #2 |
| 13494 | | |
| 13495 | | > rename #5 id #3 |
| 13496 | | |
| 13497 | | > rename #3.8 id #4 |
| 13498 | | |
| 13499 | | > hide #!2 models |
| 13500 | | |
| 13501 | | > show #!3.7 models |
| 13502 | | |
| 13503 | | > hide #!3.1 models |
| 13504 | | |
| 13505 | | > hide #!3.7 models |
| 13506 | | |
| 13507 | | > show #!3.6 models |
| 13508 | | |
| 13509 | | > hide #!3.6 models |
| 13510 | | |
| 13511 | | > show #!3.5 models |
| 13512 | | |
| 13513 | | > show #!3.7 models |
| 13514 | | |
| 13515 | | > hide #!3.7 models |
| 13516 | | |
| 13517 | | > show #!3.7 models |
| 13518 | | |
| 13519 | | > hide #!3.7 models |
| 13520 | | |
| 13521 | | > show #!3.7 models |
| 13522 | | |
| 13523 | | > hide #!3.7 models |
| 13524 | | |
| 13525 | | > hide #!3.5 models |
| 13526 | | |
| 13527 | | > show #!3.3 models |
| 13528 | | |
| 13529 | | > show #!3.7 models |
| 13530 | | |
| 13531 | | > hide #!3.3 models |
| 13532 | | |
| 13533 | | > show #!3.3 models |
| 13534 | | |
| 13535 | | > hide #!3.3 models |
| 13536 | | |
| 13537 | | > show #!3.3 models |
| 13538 | | |
| 13539 | | > hide #!3.7 models |
| 13540 | | |
| 13541 | | > show #!3.7 models |
| 13542 | | |
| 13543 | | > hide #!3.7 models |
| 13544 | | |
| 13545 | | > show #!3.7 models |
| 13546 | | |
| 13547 | | Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with |
| 13548 | | QFlags<Qt::KeyboardModifier>(NoModifier) |
| 13549 | | |
| 13550 | | Mismatch between Cocoa '\x0' and Carbon 'M' for virtual key 46 with |
| 13551 | | QFlags<Qt::KeyboardModifier>(ShiftModifier) |
| 13552 | | |
| 13553 | | Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with |
| 13554 | | QFlags<Qt::KeyboardModifier>(ControlModifier) |
| 13555 | | |
| 13556 | | Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with |
| 13557 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) |
| 13558 | | |
| 13559 | | Mismatch between Cocoa '\x0' and Carbon '\u00b5' for virtual key 46 with |
| 13560 | | QFlags<Qt::KeyboardModifier>(AltModifier) |
| 13561 | | |
| 13562 | | Mismatch between Cocoa '\x0' and Carbon '\u00c2' for virtual key 46 with |
| 13563 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) |
| 13564 | | |
| 13565 | | Mismatch between Cocoa '\x0' and Carbon '\u00b5' for virtual key 46 with |
| 13566 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) |
| 13567 | | |
| 13568 | | Mismatch between Cocoa '\x0' and Carbon '\u00c2' for virtual key 46 with |
| 13569 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) |
| 13570 | | |
| 13571 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 13572 | | QFlags<Qt::KeyboardModifier>(MetaModifier) |
| 13573 | | |
| 13574 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 13575 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) |
| 13576 | | |
| 13577 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 13578 | | QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) |
| 13579 | | |
| 13580 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 13581 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) |
| 13582 | | |
| 13583 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 13584 | | QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) |
| 13585 | | |
| 13586 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 13587 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) |
| 13588 | | |
| 13589 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 13590 | | QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) |
| 13591 | | |
| 13592 | | Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with |
| 13593 | | QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) |
| 13594 | | |
| 13595 | | > hide #!3.7 models |
| 13596 | | |
| 13597 | | > hide #!3.3 models |
| 13598 | | |
| 13599 | | > show #!3.7 models |
| 13600 | | |
| 13601 | | > mmaker #3.7/A-H to #3.3/A-H pair ss |
| 13602 | | |
| 13603 | | Parameters |
| 13604 | | --- |
| 13605 | | Chain pairing | ss |
| 13606 | | Alignment algorithm | Needleman-Wunsch |
| 13607 | | Similarity matrix | BLOSUM-62 |
| 13608 | | SS fraction | 0.3 |
| 13609 | | Gap open (HH/SS/other) | 18/18/6 |
| 13610 | | Gap extend | 1 |
| 13611 | | SS matrix | | | H | S | O |
| 13612 | | ---|---|---|--- |
| 13613 | | H | 6 | -9 | -6 |
| 13614 | | S | | 6 | -6 |
| 13615 | | O | | | 4 |
| 13616 | | Iteration cutoff | 2 |
| 13617 | | |
| 13618 | | Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain B (#3.3) with T4-partially- |
| 13619 | | closed-3U60, chain B (#3.7), sequence alignment score = 1640.1 |
| 13620 | | Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain C (#3.3) with T4-partially- |
| 13621 | | closed-3U60, chain C (#3.7), sequence alignment score = 1670.1 |
| 13622 | | Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain D (#3.3) with T4-partially- |
| 13623 | | closed-3U60, chain D (#3.7), sequence alignment score = 1676.1 |
| 13624 | | Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain E (#3.3) with T4-partially- |
| 13625 | | closed-3U60, chain E (#3.7), sequence alignment score = 1595.7 |
| 13626 | | Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain A (#3.3) with T4-partially- |
| 13627 | | closed-3U60, chain A (#3.7), sequence alignment score = 970.8 |
| 13628 | | Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain G (#3.3) with T4-partially- |
| 13629 | | closed-3U60, chain G (#3.7), sequence alignment score = 1121.9 |
| 13630 | | Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain F (#3.3) with T4-partially- |
| 13631 | | closed-3U60, chain F (#3.7), sequence alignment score = 1072.1 |
| 13632 | | Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain H (#3.3) with T4-partially- |
| 13633 | | closed-3U60, chain H (#3.7), sequence alignment score = 1072.7 |
| 13634 | | RMSD between 1630 pruned atom pairs is 0.939 angstroms; (across all 2133 |
| 13635 | | pairs: 4.217) |
| 13636 | | |
| 13637 | | |
| 13638 | | > show #!3.3 models |
| 13639 | | |
| 13640 | | > hide #!3.7 models |
| 13641 | | |
| 13642 | | > show #!3.7 models |
| 13643 | | |
| 13644 | | > hide #!3.7 models |
| 13645 | | |
| 13646 | | > show #!3.7 models |
| 13647 | | |
| 13648 | | > hide #!3.7 models |
| 13649 | | |
| 13650 | | > show #!3.7 models |
| 13651 | | |
| 13652 | | > hide #!3.3 models |
| 13653 | | |
| 13654 | | > show #!3.3 models |
| 13655 | | |
| 13656 | | > hide #!3.3 models |
| 13657 | | |
| 13658 | | > show #!3.3 models |
| 13659 | | |
| 13660 | | > hide #!3 models |
| 13661 | | |
| 13662 | | > show #!4 models |
| 13663 | | |
| 13664 | | > hide #!4 models |
| 13665 | | |
| 13666 | | > show #!2 models |
| 13667 | | |
| 13668 | | > hide #!3.3 models |
| 13669 | | |
| 13670 | | > hide #!3.7 models |
| 13671 | | |
| 13672 | | > rename #2.4 id #3 |
| 13673 | | |
| 13674 | | > hide #!1.2 models |
| 13675 | | |
| 13676 | | > show #!1.2 models |
| 13677 | | |
| 13678 | | > hide #!1.2 models |
| 13679 | | |
| 13680 | | > show #!1.1 models |
| 13681 | | |
| 13682 | | > close #1.1-3 |
| 13683 | | |
| 13684 | | > undo |
| 13685 | | |
| 13686 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 13687 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Apo_P29_J632_004.mrc" |
| 13688 | | |
| 13689 | | Opened Apo_P29_J632_004.mrc as #5, grid size 420,420,420, pixel 0.828, shown |
| 13690 | | at level 0.1, step 2, values float32 |
| 13691 | | |
| 13692 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 13693 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Closed_P29_J651_004.mrc" |
| 13694 | | |
| 13695 | | Opened Closed_P29_J651_004.mrc as #6, grid size 420,420,420, pixel 0.828, |
| 13696 | | shown at level 0.112, step 2, values float32 |
| 13697 | | |
| 13698 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 13699 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Open_P29_J701_004.mrc" |
| 13700 | | |
| 13701 | | Opened Open_P29_J701_004.mrc as #7, grid size 420,420,420, pixel 0.828, shown |
| 13702 | | at level 0.0759, step 2, values float32 |
| 13703 | | |
| 13704 | | > surface dust #0-9 size 10 |
| 13705 | | |
| 13706 | | > volume #0-9 step 1 level 0.2 |
| 13707 | | |
| 13708 | | > rename #5-7 id #1 |
| 13709 | | |
| 13710 | | > close #2.1-3 |
| 13711 | | |
| 13712 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 13713 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Open_Rsr35-Ct2.pdb" |
| 13714 | | |
| 13715 | | Chain information for Open_Rsr35-Ct2.pdb #5 |
| 13716 | | --- |
| 13717 | | Chain | Description |
| 13718 | | A | No description available |
| 13719 | | B | No description available |
| 13720 | | C | No description available |
| 13721 | | D | No description available |
| 13722 | | E | No description available |
| 13723 | | F | No description available |
| 13724 | | G | No description available |
| 13725 | | H | No description available |
| 13726 | | |
| 13727 | | |
| 13728 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 13729 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Closed_Rsr21-Ct2.pdb" |
| 13730 | | |
| 13731 | | Chain information for Closed_Rsr21-Ct2.pdb #6 |
| 13732 | | --- |
| 13733 | | Chain | Description |
| 13734 | | A | No description available |
| 13735 | | B | No description available |
| 13736 | | C | No description available |
| 13737 | | D | No description available |
| 13738 | | E | No description available |
| 13739 | | F | No description available |
| 13740 | | G | No description available |
| 13741 | | H | No description available |
| 13742 | | |
| 13743 | | |
| 13744 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 13745 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Apo_Rsr13-Ct1.pdb" |
| 13746 | | |
| 13747 | | Chain information for Apo_Rsr13-Ct1.pdb #7 |
| 13748 | | --- |
| 13749 | | Chain | Description |
| 13750 | | A | No description available |
| 13751 | | B | No description available |
| 13752 | | C | No description available |
| 13753 | | D | No description available |
| 13754 | | E | No description available |
| 13755 | | |
| 13756 | | |
| 13757 | | > rename #5-7 id #2 |
| 13758 | | |
| 13759 | | > hide #!2 models |
| 13760 | | |
| 13761 | | > show #!2 models |
| 13762 | | |
| 13763 | | > hide #!2 models |
| 13764 | | |
| 13765 | | > show #!1.1 models |
| 13766 | | |
| 13767 | | > volume #1.1 level 0.2427 |
| 13768 | | |
| 13769 | | > volume #1.1 level 0.25 |
| 13770 | | |
| 13771 | | > volume #1.2 level 0.25 |
| 13772 | | |
| 13773 | | > show #!1.2 models |
| 13774 | | |
| 13775 | | > show #!1.1 models |
| 13776 | | |
| 13777 | | > hide #!1.1 models |
| 13778 | | |
| 13779 | | > fitmap #1.3 inMap #1.2 |
| 13780 | | |
| 13781 | | Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652 |
| 13782 | | points |
| 13783 | | correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04 |
| 13784 | | steps = 72, shift = 1.2, angle = 3.78 degrees |
| 13785 | | |
| 13786 | | Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc |
| 13787 | | (#1.2) coordinates: |
| 13788 | | Matrix rotation and translation |
| 13789 | | 0.99846800 0.05408100 0.01170019 -10.30909942 |
| 13790 | | -0.05446551 0.99788392 0.03551333 3.16581617 |
| 13791 | | -0.00975484 -0.03609618 0.99930071 7.19292834 |
| 13792 | | Axis -0.54332972 0.16278780 -0.82358542 |
| 13793 | | Axis point 50.16340237 190.10932176 0.00000000 |
| 13794 | | Rotation angle (degrees) 3.77845856 |
| 13795 | | Shift along axis 0.19260545 |
| 13796 | | |
| 13797 | | |
| 13798 | | > fitmap #1.3 inMap #1.2 |
| 13799 | | |
| 13800 | | Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652 |
| 13801 | | points |
| 13802 | | correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04 |
| 13803 | | steps = 44, shift = 0.0047, angle = 0.00319 degrees |
| 13804 | | |
| 13805 | | Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc |
| 13806 | | (#1.2) coordinates: |
| 13807 | | Matrix rotation and translation |
| 13808 | | 0.99846943 0.05406085 0.01167117 -10.30344284 |
| 13809 | | -0.05444475 0.99788351 0.03555654 3.15145256 |
| 13810 | | -0.00972425 -0.03613755 0.99929951 7.19271566 |
| 13811 | | Axis -0.54396073 0.16233238 -0.82325872 |
| 13812 | | Axis point 49.91498696 190.04300007 0.00000000 |
| 13813 | | Rotation angle (degrees) 3.77853341 |
| 13814 | | Shift along axis 0.19478517 |
| 13815 | | |
| 13816 | | |
| 13817 | | > hide #!1.3 models |
| 13818 | | |
| 13819 | | > show #!1.1 models |
| 13820 | | |
| 13821 | | > select add #1.1 |
| 13822 | | |
| 13823 | | 2 models selected |
| 13824 | | |
| 13825 | | > ui mousemode right "translate selected models" |
| 13826 | | |
| 13827 | | > view matrix models #1.1,1,0,0,20.005,0,1,0,-52.909,0,0,1,-5.5041 |
| 13828 | | |
| 13829 | | > ui mousemode right "rotate selected models" |
| 13830 | | |
| 13831 | | > view matrix models |
| 13832 | | > #1.1,0.96269,0.098534,0.25205,-38.349,0.098856,0.73896,-0.66646,101.45,-0.25192,0.66651,0.70164,-28.454 |
| 13833 | | |
| 13834 | | > view matrix models |
| 13835 | | > #1.1,0.53825,0.4119,0.73527,-114.61,-0.0030756,0.87339,-0.48702,60.74,-0.84278,0.25988,0.47137,184.39 |
| 13836 | | |
| 13837 | | > view matrix models |
| 13838 | | > #1.1,0.74584,0.42996,0.50878,-109.91,-0.55244,0.82603,0.11179,48.341,-0.3722,-0.36444,0.85361,148.27 |
| 13839 | | |
| 13840 | | > view matrix models |
| 13841 | | > #1.1,0.52749,0.25649,0.80992,-98.783,-0.6543,0.73073,0.19472,66.796,-0.54189,-0.63265,0.55328,280.07 |
| 13842 | | |
| 13843 | | > ui mousemode right "translate selected models" |
| 13844 | | |
| 13845 | | > view matrix models |
| 13846 | | > #1.1,0.52749,0.25649,0.80992,-106.74,-0.6543,0.73073,0.19472,87.853,-0.54189,-0.63265,0.55328,273.54 |
| 13847 | | |
| 13848 | | > ui mousemode right "rotate selected models" |
| 13849 | | |
| 13850 | | > view matrix models |
| 13851 | | > #1.1,0.098208,0.95952,0.26397,-61.158,-0.769,0.24153,-0.59186,340.57,-0.63165,-0.14487,0.7616,162 |
| 13852 | | |
| 13853 | | > ui mousemode right "translate selected models" |
| 13854 | | |
| 13855 | | > view matrix models |
| 13856 | | > #1.1,0.098208,0.95952,0.26397,-62.613,-0.769,0.24153,-0.59186,357.57,-0.63165,-0.14487,0.7616,153.86 |
| 13857 | | |
| 13858 | | > view matrix models |
| 13859 | | > #1.1,0.098208,0.95952,0.26397,-62.007,-0.769,0.24153,-0.59186,354.74,-0.63165,-0.14487,0.7616,153.58 |
| 13860 | | |
| 13861 | | > ui mousemode right "rotate selected models" |
| 13862 | | |
| 13863 | | > view matrix models |
| 13864 | | > #1.1,-0.37574,0.92601,-0.036368,77.617,-0.62871,-0.28355,-0.7241,450.56,-0.68084,-0.24921,0.68874,193.92 |
| 13865 | | |
| 13866 | | > ui mousemode right "move picked models" |
| 13867 | | |
| 13868 | | > view matrix models #1.2,1,0,0,0.60822,0,1,0,-1.1694,0,0,1,-1.7261 |
| 13869 | | |
| 13870 | | > ui mousemode right "move picked models" |
| 13871 | | |
| 13872 | | > ui mousemode right "translate selected models" |
| 13873 | | |
| 13874 | | > view matrix models |
| 13875 | | > #1.1,-0.37574,0.92601,-0.036368,77.411,-0.62871,-0.28355,-0.7241,451.31,-0.68084,-0.24921,0.68874,194.2 |
| 13876 | | |
| 13877 | | > view matrix models |
| 13878 | | > #1.1,-0.37574,0.92601,-0.036368,78.093,-0.62871,-0.28355,-0.7241,448.18,-0.68084,-0.24921,0.68874,193.83 |
| 13879 | | |
| 13880 | | > ui mousemode right "rotate selected models" |
| 13881 | | |
| 13882 | | > view matrix models |
| 13883 | | > #1.1,-0.47989,0.86818,0.12633,75.389,-0.66869,-0.26874,-0.69328,446.36,-0.56794,-0.41718,0.70951,201.6 |
| 13884 | | |
| 13885 | | > ui mousemode right "translate selected models" |
| 13886 | | |
| 13887 | | > view matrix models |
| 13888 | | > #1.1,-0.47989,0.86818,0.12633,74.505,-0.66869,-0.26874,-0.69328,449.25,-0.56794,-0.41718,0.70951,203.09 |
| 13889 | | |
| 13890 | | > fitmap #1.1 inMap #1.2 |
| 13891 | | |
| 13892 | | Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080 |
| 13893 | | points |
| 13894 | | correlation = 0.9554, correlation about mean = 0.8333, overlap = 6.544e+04 |
| 13895 | | steps = 136, shift = 10.4, angle = 13.8 degrees |
| 13896 | | |
| 13897 | | Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc |
| 13898 | | (#1.2) coordinates: |
| 13899 | | Matrix rotation and translation |
| 13900 | | -0.53167181 0.84082990 -0.10163741 138.30893277 |
| 13901 | | -0.59440769 -0.45592717 -0.66242729 467.36322207 |
| 13902 | | -0.60332793 -0.29177986 0.74219938 181.16060019 |
| 13903 | | Axis 0.23684727 0.32058507 -0.91713062 |
| 13904 | | Axis point 214.02322176 230.00862665 0.00000000 |
| 13905 | | Rotation angle (degrees) 128.51355729 |
| 13906 | | Shift along axis 16.43983009 |
| 13907 | | |
| 13908 | | |
| 13909 | | > select clear |
| 13910 | | |
| 13911 | | > fitmap #1.1 inMap #1.2 |
| 13912 | | |
| 13913 | | Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080 |
| 13914 | | points |
| 13915 | | correlation = 0.9554, correlation about mean = 0.8332, overlap = 6.544e+04 |
| 13916 | | steps = 40, shift = 0.02, angle = 0.0146 degrees |
| 13917 | | |
| 13918 | | Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc |
| 13919 | | (#1.2) coordinates: |
| 13920 | | Matrix rotation and translation |
| 13921 | | -0.53166894 0.84085996 -0.10140345 138.26555130 |
| 13922 | | -0.59444099 -0.45575618 -0.66251506 467.36512760 |
| 13923 | | -0.60329764 -0.29196031 0.74215304 181.21186663 |
| 13924 | | Axis 0.23677270 0.32069442 -0.91711165 |
| 13925 | | Axis point 214.01750894 230.03589560 0.00000000 |
| 13926 | | Rotation angle (degrees) 128.50888878 |
| 13927 | | Shift along axis 16.42738178 |
| 13928 | | |
| 13929 | | |
| 13930 | | > fitmap #1.1 inMap #1.2 |
| 13931 | | |
| 13932 | | Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080 |
| 13933 | | points |
| 13934 | | correlation = 0.9554, correlation about mean = 0.8332, overlap = 6.544e+04 |
| 13935 | | steps = 44, shift = 0.00271, angle = 0.0131 degrees |
| 13936 | | |
| 13937 | | Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc |
| 13938 | | (#1.2) coordinates: |
| 13939 | | Matrix rotation and translation |
| 13940 | | -0.53161955 0.84086495 -0.10162082 138.29770231 |
| 13941 | | -0.59440936 -0.45586428 -0.66246907 467.36981335 |
| 13942 | | -0.60337232 -0.29177714 0.74216436 181.19164725 |
| 13943 | | Axis 0.23686606 0.32061097 -0.91711672 |
| 13944 | | Axis point 214.03623238 230.01983811 0.00000000 |
| 13945 | | Rotation angle (degrees) 128.51062360 |
| 13946 | | Shift along axis 16.42803132 |
| 13947 | | |
| 13948 | | |
| 13949 | | > fitmap #1.1 inMap #1.2 |
| 13950 | | |
| 13951 | | Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080 |
| 13952 | | points |
| 13953 | | correlation = 0.9554, correlation about mean = 0.8333, overlap = 6.544e+04 |
| 13954 | | steps = 44, shift = 0.00547, angle = 0.00549 degrees |
| 13955 | | |
| 13956 | | Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc |
| 13957 | | (#1.2) coordinates: |
| 13958 | | Matrix rotation and translation |
| 13959 | | -0.53165206 0.84085176 -0.10155984 138.29032133 |
| 13960 | | -0.59445654 -0.45587056 -0.66242241 467.36761183 |
| 13961 | | -0.60329719 -0.29180533 0.74221436 181.17303227 |
| 13962 | | Axis 0.23681688 0.32060010 -0.91713322 |
| 13963 | | Axis point 214.02327529 230.01586551 0.00000000 |
| 13964 | | Rotation angle (degrees) 128.51021345 |
| 13965 | | Shift along axis 16.42778112 |
| 13966 | | |
| 13967 | | |
| 13968 | | > fitmap #1.1 inMap #1.2 |
| 13969 | | |
| 13970 | | Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080 |
| 13971 | | points |
| 13972 | | correlation = 0.9554, correlation about mean = 0.8332, overlap = 6.544e+04 |
| 13973 | | steps = 44, shift = 0.0043, angle = 0.00568 degrees |
| 13974 | | |
| 13975 | | Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc |
| 13976 | | (#1.2) coordinates: |
| 13977 | | Matrix rotation and translation |
| 13978 | | -0.53160795 0.84087318 -0.10161334 138.29147093 |
| 13979 | | -0.59441612 -0.45585042 -0.66247254 467.36956255 |
| 13980 | | -0.60337588 -0.29177506 0.74216229 181.19046957 |
| 13981 | | Axis 0.23686679 0.32061421 -0.91711540 |
| 13982 | | Axis point 214.03536942 230.02087432 0.00000000 |
| 13983 | | Rotation angle (degrees) 128.50976744 |
| 13984 | | Shift along axis 16.42941045 |
| 13985 | | |
| 13986 | | |
| 13987 | | > hide #!1.1 models |
| 13988 | | |
| 13989 | | > show #!1.3 models |
| 13990 | | |
| 13991 | | > fitmap #1.3 inMap #1.2 |
| 13992 | | |
| 13993 | | Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652 |
| 13994 | | points |
| 13995 | | correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04 |
| 13996 | | steps = 76, shift = 2.18, angle = 0.00673 degrees |
| 13997 | | |
| 13998 | | Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc |
| 13999 | | (#1.2) coordinates: |
| 14000 | | Matrix rotation and translation |
| 14001 | | 0.99847121 0.05403075 0.01165822 -10.30458864 |
| 14002 | | -0.05441530 0.99788108 0.03566953 3.12065853 |
| 14003 | | -0.00970627 -0.03624939 0.99929564 7.19549858 |
| 14004 | | Axis -0.54538334 0.16201351 -0.82237986 |
| 14005 | | Axis point 49.33029056 190.01227038 0.00000000 |
| 14006 | | Rotation angle (degrees) 3.78049874 |
| 14007 | | Shift along axis 0.20810677 |
| 14008 | | |
| 14009 | | |
| 14010 | | > fitmap #1.3 inMap #1.2 |
| 14011 | | |
| 14012 | | Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652 |
| 14013 | | points |
| 14014 | | correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04 |
| 14015 | | steps = 44, shift = 0.017, angle = 0.00916 degrees |
| 14016 | | |
| 14017 | | Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc |
| 14018 | | (#1.2) coordinates: |
| 14019 | | Matrix rotation and translation |
| 14020 | | 0.99847089 0.05401047 0.01177905 -10.31589801 |
| 14021 | | -0.05439840 0.99788567 0.03556701 3.14237342 |
| 14022 | | -0.00983316 -0.03615339 0.99929787 7.21475146 |
| 14023 | | Axis -0.54428386 0.16401441 -0.82271158 |
| 14024 | | Axis point 49.77722572 190.44719609 0.00000000 |
| 14025 | | Rotation angle (degrees) 3.77767482 |
| 14026 | | Shift along axis 0.19451174 |
| 14027 | | |
| 14028 | | |
| 14029 | | > fitmap #1.3 inMap #1.2 |
| 14030 | | |
| 14031 | | Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652 |
| 14032 | | points |
| 14033 | | correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04 |
| 14034 | | steps = 40, shift = 0.00249, angle = 0.00786 degrees |
| 14035 | | |
| 14036 | | Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc |
| 14037 | | (#1.2) coordinates: |
| 14038 | | Matrix rotation and translation |
| 14039 | | 0.99846855 0.05407941 0.01166090 -10.30495846 |
| 14040 | | -0.05446293 0.99788250 0.03555703 3.15432127 |
| 14041 | | -0.00971331 -0.03613766 0.99929962 7.19127314 |
| 14042 | | Axis -0.54385330 0.16213802 -0.82336799 |
| 14043 | | Axis point 49.94959949 190.00826391 0.00000000 |
| 14044 | | Rotation angle (degrees) 3.77931257 |
| 14045 | | Shift along axis 0.19475696 |
| 14046 | | |
| 14047 | | |
| 14048 | | > hide #!1.2 models |
| 14049 | | |
| 14050 | | > show #!1.2 models |
| 14051 | | |
| 14052 | | > hide #!1.3 models |
| 14053 | | |
| 14054 | | > show #!1.3 models |
| 14055 | | |
| 14056 | | > hide #!1.3 models |
| 14057 | | |
| 14058 | | > show #!2 models |
| 14059 | | |
| 14060 | | > hide #!2.1 models |
| 14061 | | |
| 14062 | | > hide #!2.3 models |
| 14063 | | |
| 14064 | | > hide #2 |
| 14065 | | |
| 14066 | | > show #2 cartoons |
| 14067 | | |
| 14068 | | > hide #!1.2 models |
| 14069 | | |
| 14070 | | > show #!2.1 models |
| 14071 | | |
| 14072 | | > hide #!2.1 models |
| 14073 | | |
| 14074 | | > show #!2.3 models |
| 14075 | | |
| 14076 | | > hide #!2.2 models |
| 14077 | | |
| 14078 | | > show #!2.2 models |
| 14079 | | |
| 14080 | | > hide #!2.3 models |
| 14081 | | |
| 14082 | | > show #!2.3 models |
| 14083 | | |
| 14084 | | > rename #2.1 id #2.4 |
| 14085 | | |
| 14086 | | > rename #2.3 id #2.1 |
| 14087 | | |
| 14088 | | > rename #2.4 id #2.3 |
| 14089 | | |
| 14090 | | > dssp #2.1 |
| 14091 | | |
| 14092 | | > hide #!2.2 models |
| 14093 | | |
| 14094 | | > show #!2.2 models |
| 14095 | | |
| 14096 | | > hide #!2.1 models |
| 14097 | | |
| 14098 | | > show #!2.1 models |
| 14099 | | |
| 14100 | | > hide #!2.1 models |
| 14101 | | |
| 14102 | | > show #!2.1 models |
| 14103 | | |
| 14104 | | > hide #!2.1 models |
| 14105 | | |
| 14106 | | > show #!2.3 models |
| 14107 | | |
| 14108 | | > hide #!2.3 models |
| 14109 | | |
| 14110 | | > show #!2.3 models |
| 14111 | | |
| 14112 | | > hide #!2.3 models |
| 14113 | | |
| 14114 | | > show #!1.2 models |
| 14115 | | |
| 14116 | | > fitmap #2.2 into #1.2 |
| 14117 | | |
| 14118 | | Expected a keyword |
| 14119 | | |
| 14120 | | > fitmap #2.2 inMap #1.2 |
| 14121 | | |
| 14122 | | Fit molecule Closed_Rsr21-Ct2.pdb (#2.2) to map Closed_P29_J651_004.mrc (#1.2) |
| 14123 | | using 20396 atoms |
| 14124 | | average map value = 0.5299, steps = 96 |
| 14125 | | shifted from previous position = 2.2 |
| 14126 | | rotated from previous position = 0.0243 degrees |
| 14127 | | atoms outside contour = 5814, contour level = 0.25 |
| 14128 | | |
| 14129 | | Position of Closed_Rsr21-Ct2.pdb (#2.2) relative to Closed_P29_J651_004.mrc |
| 14130 | | (#1.2) coordinates: |
| 14131 | | Matrix rotation and translation |
| 14132 | | 0.99999994 0.00035092 0.00004122 -0.05675804 |
| 14133 | | -0.00035093 0.99999991 0.00023301 0.01544387 |
| 14134 | | -0.00004114 -0.00023302 0.99999997 0.02603591 |
| 14135 | | Axis -0.55054223 0.09730088 -0.82911748 |
| 14136 | | Axis point 40.87711022 144.23535640 0.00000000 |
| 14137 | | Rotation angle (degrees) 0.02425026 |
| 14138 | | Shift along axis 0.01116357 |
| 14139 | | |
| 14140 | | |
| 14141 | | > fitmap #2.2 inMap #1.2 |
| 14142 | | |
| 14143 | | Fit molecule Closed_Rsr21-Ct2.pdb (#2.2) to map Closed_P29_J651_004.mrc (#1.2) |
| 14144 | | using 20396 atoms |
| 14145 | | average map value = 0.5299, steps = 48 |
| 14146 | | shifted from previous position = 0.00321 |
| 14147 | | rotated from previous position = 0.0124 degrees |
| 14148 | | atoms outside contour = 5821, contour level = 0.25 |
| 14149 | | |
| 14150 | | Position of Closed_Rsr21-Ct2.pdb (#2.2) relative to Closed_P29_J651_004.mrc |
| 14151 | | (#1.2) coordinates: |
| 14152 | | Matrix rotation and translation |
| 14153 | | 0.99999995 0.00027075 0.00018784 -0.07196012 |
| 14154 | | -0.00027077 0.99999996 0.00009619 0.02685335 |
| 14155 | | -0.00018781 -0.00009624 0.99999998 0.02957657 |
| 14156 | | Axis -0.28026577 0.54714148 -0.78872511 |
| 14157 | | Axis point 75.83157399 253.85711713 0.00000000 |
| 14158 | | Rotation angle (degrees) 0.01966895 |
| 14159 | | Shift along axis 0.01153276 |
| 14160 | | |
| 14161 | | |
| 14162 | | > hide #!1.2 models |
| 14163 | | |
| 14164 | | > show #!1.2 models |
| 14165 | | |
| 14166 | | > hide #!1.2 models |
| 14167 | | |
| 14168 | | > hide #!2.2 models |
| 14169 | | |
| 14170 | | > show #!2.1 models |
| 14171 | | |
| 14172 | | > show #!1.1 models |
| 14173 | | |
| 14174 | | > hide #!1.1 models |
| 14175 | | |
| 14176 | | > fitmap #2.1 inMap #1.1 |
| 14177 | | |
| 14178 | | Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using |
| 14179 | | 14334 atoms |
| 14180 | | average map value = 0.1059, steps = 256 |
| 14181 | | shifted from previous position = 6.71 |
| 14182 | | rotated from previous position = 12.3 degrees |
| 14183 | | atoms outside contour = 11693, contour level = 0.25 |
| 14184 | | |
| 14185 | | Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1) |
| 14186 | | coordinates: |
| 14187 | | Matrix rotation and translation |
| 14188 | | -0.34605883 -0.61582784 -0.70781308 452.68197651 |
| 14189 | | 0.92660434 -0.34264703 -0.15491101 95.51991162 |
| 14190 | | -0.14713154 -0.70947099 0.68920478 213.89900228 |
| 14191 | | Axis -0.32012214 -0.32365583 0.89037561 |
| 14192 | | Axis point 232.27888694 234.97078197 0.00000000 |
| 14193 | | Rotation angle (degrees) 119.98349746 |
| 14194 | | Shift along axis 14.62135558 |
| 14195 | | |
| 14196 | | |
| 14197 | | > show #!1.1 models |
| 14198 | | |
| 14199 | | > fitmap #2.1 inMap #1.1 |
| 14200 | | |
| 14201 | | Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using |
| 14202 | | 14334 atoms |
| 14203 | | average map value = 0.1059, steps = 64 |
| 14204 | | shifted from previous position = 0.00414 |
| 14205 | | rotated from previous position = 0.00474 degrees |
| 14206 | | atoms outside contour = 11697, contour level = 0.25 |
| 14207 | | |
| 14208 | | Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1) |
| 14209 | | coordinates: |
| 14210 | | Matrix rotation and translation |
| 14211 | | -0.34610474 -0.61584749 -0.70777353 452.68996732 |
| 14212 | | 0.92659759 -0.34263541 -0.15497706 95.53219304 |
| 14213 | | -0.14706605 -0.70945954 0.68923054 213.88132249 |
| 14214 | | Axis -0.32007831 -0.32367173 0.89038558 |
| 14215 | | Axis point 232.27069070 234.97487266 0.00000000 |
| 14216 | | Rotation angle (degrees) 119.98377952 |
| 14217 | | Shift along axis 14.61953711 |
| 14218 | | |
| 14219 | | |
| 14220 | | > fitmap #2.1 inMap #1.1 |
| 14221 | | |
| 14222 | | Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using |
| 14223 | | 14334 atoms |
| 14224 | | average map value = 0.1059, steps = 96 |
| 14225 | | shifted from previous position = 0.0113 |
| 14226 | | rotated from previous position = 0.00502 degrees |
| 14227 | | atoms outside contour = 11697, contour level = 0.25 |
| 14228 | | |
| 14229 | | Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1) |
| 14230 | | coordinates: |
| 14231 | | Matrix rotation and translation |
| 14232 | | -0.34607756 -0.61591612 -0.70772710 452.69785423 |
| 14233 | | 0.92661307 -0.34260447 -0.15495291 95.51375708 |
| 14234 | | -0.14703247 -0.70941491 0.68928364 213.85472149 |
| 14235 | | Axis -0.32005463 -0.32365232 0.89040115 |
| 14236 | | Axis point 232.27102169 234.96820683 0.00000000 |
| 14237 | | Rotation angle (degrees) 119.98010060 |
| 14238 | | Shift along axis 14.61519915 |
| 14239 | | |
| 14240 | | |
| 14241 | | > mmaker #2.1 to #2.2 |
| 14242 | | |
| 14243 | | Parameters |
| 14244 | | --- |
| 14245 | | Chain pairing | bb |
| 14246 | | Alignment algorithm | Needleman-Wunsch |
| 14247 | | Similarity matrix | BLOSUM-62 |
| 14248 | | SS fraction | 0.3 |
| 14249 | | Gap open (HH/SS/other) | 18/18/6 |
| 14250 | | Gap extend | 1 |
| 14251 | | SS matrix | | | H | S | O |
| 14252 | | ---|---|---|--- |
| 14253 | | H | 6 | -9 | -6 |
| 14254 | | S | | 6 | -6 |
| 14255 | | O | | | 4 |
| 14256 | | Iteration cutoff | 2 |
| 14257 | | |
| 14258 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14259 | | A (#2.1), sequence alignment score = 2286.5 |
| 14260 | | RMSD between 463 pruned atom pairs is 0.554 angstroms; (across all 468 pairs: |
| 14261 | | 0.626) |
| 14262 | | |
| 14263 | | |
| 14264 | | > fitmap #2.1 inMap #1.1 |
| 14265 | | |
| 14266 | | Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using |
| 14267 | | 14334 atoms |
| 14268 | | average map value = 0.5957, steps = 64 |
| 14269 | | shifted from previous position = 0.157 |
| 14270 | | rotated from previous position = 0.482 degrees |
| 14271 | | atoms outside contour = 2745, contour level = 0.25 |
| 14272 | | |
| 14273 | | Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1) |
| 14274 | | coordinates: |
| 14275 | | Matrix rotation and translation |
| 14276 | | 0.99999992 -0.00036860 0.00015434 0.03360214 |
| 14277 | | 0.00036859 0.99999993 0.00000892 -0.05847336 |
| 14278 | | -0.00015434 -0.00000886 0.99999999 0.03317737 |
| 14279 | | Axis -0.02223603 0.38613254 0.92217527 |
| 14280 | | Axis point 166.27122211 91.56510687 0.00000000 |
| 14281 | | Rotation angle (degrees) 0.02290123 |
| 14282 | | Shift along axis 0.00726970 |
| 14283 | | |
| 14284 | | |
| 14285 | | > fitmap #2.1 inMap #1.1 |
| 14286 | | |
| 14287 | | Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using |
| 14288 | | 14334 atoms |
| 14289 | | average map value = 0.5957, steps = 28 |
| 14290 | | shifted from previous position = 0.00837 |
| 14291 | | rotated from previous position = 0.0162 degrees |
| 14292 | | atoms outside contour = 2751, contour level = 0.25 |
| 14293 | | |
| 14294 | | Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1) |
| 14295 | | coordinates: |
| 14296 | | Matrix rotation and translation |
| 14297 | | 0.99999994 -0.00028578 0.00017460 0.02061477 |
| 14298 | | 0.00028583 0.99999993 -0.00026147 0.01061319 |
| 14299 | | -0.00017453 0.00026152 0.99999995 -0.01155826 |
| 14300 | | Axis 0.61543508 0.41083533 0.67264701 |
| 14301 | | Axis point -23.78939691 52.16999953 0.00000000 |
| 14302 | | Rotation angle (degrees) 0.02434492 |
| 14303 | | Shift along axis 0.00927269 |
| 14304 | | |
| 14305 | | |
| 14306 | | > fitmap #2.1 inMap #1.1 |
| 14307 | | |
| 14308 | | Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using |
| 14309 | | 14334 atoms |
| 14310 | | average map value = 0.5957, steps = 40 |
| 14311 | | shifted from previous position = 0.00369 |
| 14312 | | rotated from previous position = 0.0134 degrees |
| 14313 | | atoms outside contour = 2748, contour level = 0.25 |
| 14314 | | |
| 14315 | | Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1) |
| 14316 | | coordinates: |
| 14317 | | Matrix rotation and translation |
| 14318 | | 0.99999993 -0.00036973 0.00008964 0.05155215 |
| 14319 | | 0.00036974 0.99999993 -0.00006076 -0.04294827 |
| 14320 | | -0.00008962 0.00006079 0.99999999 0.00801005 |
| 14321 | | Axis 0.15775307 0.23264623 0.95968208 |
| 14322 | | Axis point 119.85213693 136.92144571 0.00000000 |
| 14323 | | Rotation angle (degrees) 0.02207417 |
| 14324 | | Shift along axis 0.00582786 |
| 14325 | | |
| 14326 | | |
| 14327 | | > hide #!1.1 models |
| 14328 | | |
| 14329 | | > show #!1.2 models |
| 14330 | | |
| 14331 | | > hide #!2.1 models |
| 14332 | | |
| 14333 | | > show #!1.1 models |
| 14334 | | |
| 14335 | | > hide #!2 models |
| 14336 | | |
| 14337 | | > show #!2 models |
| 14338 | | |
| 14339 | | > hide #!1.1 models |
| 14340 | | |
| 14341 | | > show #!2.1 models |
| 14342 | | |
| 14343 | | > hide #!2.1 models |
| 14344 | | |
| 14345 | | > show #!2.2 models |
| 14346 | | |
| 14347 | | > fitmap #2.2 inMap #1.2 |
| 14348 | | |
| 14349 | | Fit molecule Closed_Rsr21-Ct2.pdb (#2.2) to map Closed_P29_J651_004.mrc (#1.2) |
| 14350 | | using 20396 atoms |
| 14351 | | average map value = 0.5299, steps = 44 |
| 14352 | | shifted from previous position = 0.0124 |
| 14353 | | rotated from previous position = 0.00518 degrees |
| 14354 | | atoms outside contour = 5817, contour level = 0.25 |
| 14355 | | |
| 14356 | | Position of Closed_Rsr21-Ct2.pdb (#2.2) relative to Closed_P29_J651_004.mrc |
| 14357 | | (#1.2) coordinates: |
| 14358 | | Matrix rotation and translation |
| 14359 | | 0.99999992 0.00035879 0.00019546 -0.07845402 |
| 14360 | | -0.00035881 0.99999993 0.00007698 0.04457567 |
| 14361 | | -0.00019544 -0.00007705 0.99999998 0.03459009 |
| 14362 | | Axis -0.18524298 0.47008690 -0.86296196 |
| 14363 | | Axis point 116.80668095 215.77843870 0.00000000 |
| 14364 | | Rotation angle (degrees) 0.02382222 |
| 14365 | | Shift along axis 0.00563756 |
| 14366 | | |
| 14367 | | |
| 14368 | | > hide #!1.2 models |
| 14369 | | |
| 14370 | | > show #!1.3 models |
| 14371 | | |
| 14372 | | > hide #!2.2 models |
| 14373 | | |
| 14374 | | > show #!2.3 models |
| 14375 | | |
| 14376 | | > hide #!1.3 models |
| 14377 | | |
| 14378 | | > show #!1.3 models |
| 14379 | | |
| 14380 | | > fitmap #2.3 inMap #1.3 |
| 14381 | | |
| 14382 | | Fit molecule Open_Rsr35-Ct2.pdb (#2.3) to map Open_P29_J701_004.mrc (#1.3) |
| 14383 | | using 20430 atoms |
| 14384 | | average map value = 0.2949, steps = 104 |
| 14385 | | shifted from previous position = 3.53 |
| 14386 | | rotated from previous position = 3.76 degrees |
| 14387 | | atoms outside contour = 7939, contour level = 0.2 |
| 14388 | | |
| 14389 | | Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3) |
| 14390 | | coordinates: |
| 14391 | | Matrix rotation and translation |
| 14392 | | 0.99999958 -0.00019051 -0.00089775 0.18621644 |
| 14393 | | 0.00019039 0.99999997 -0.00013868 -0.01529551 |
| 14394 | | 0.00089778 0.00013851 0.99999959 -0.15553984 |
| 14395 | | Axis 0.14932340 -0.96726299 0.20519462 |
| 14396 | | Axis point 175.78595151 0.00000000 205.56499069 |
| 14397 | | Rotation angle (degrees) 0.05317922 |
| 14398 | | Shift along axis 0.01068532 |
| 14399 | | |
| 14400 | | |
| 14401 | | > fitmap #2.3 inMap #1.3 |
| 14402 | | |
| 14403 | | Fit molecule Open_Rsr35-Ct2.pdb (#2.3) to map Open_P29_J701_004.mrc (#1.3) |
| 14404 | | using 20430 atoms |
| 14405 | | average map value = 0.2949, steps = 48 |
| 14406 | | shifted from previous position = 0.0157 |
| 14407 | | rotated from previous position = 0.00798 degrees |
| 14408 | | atoms outside contour = 7937, contour level = 0.2 |
| 14409 | | |
| 14410 | | Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3) |
| 14411 | | coordinates: |
| 14412 | | Matrix rotation and translation |
| 14413 | | 0.99999945 -0.00016289 -0.00103286 0.20092650 |
| 14414 | | 0.00016273 0.99999997 -0.00015774 -0.01519499 |
| 14415 | | 0.00103289 0.00015757 0.99999945 -0.19544163 |
| 14416 | | Axis 0.14909330 -0.97676325 0.15396343 |
| 14417 | | Axis point 191.51218184 0.00000000 192.30881426 |
| 14418 | | Rotation angle (degrees) 0.06058738 |
| 14419 | | Shift along axis 0.01470784 |
| 14420 | | |
| 14421 | | |
| 14422 | | > fitmap #2.3 inMap #1.3 |
| 14423 | | |
| 14424 | | Fit molecule Open_Rsr35-Ct2.pdb (#2.3) to map Open_P29_J701_004.mrc (#1.3) |
| 14425 | | using 20430 atoms |
| 14426 | | average map value = 0.2949, steps = 44 |
| 14427 | | shifted from previous position = 0.00945 |
| 14428 | | rotated from previous position = 0.01 degrees |
| 14429 | | atoms outside contour = 7933, contour level = 0.2 |
| 14430 | | |
| 14431 | | Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3) |
| 14432 | | coordinates: |
| 14433 | | Matrix rotation and translation |
| 14434 | | 0.99999957 -0.00015733 -0.00091213 0.18403567 |
| 14435 | | 0.00015730 0.99999999 -0.00003129 -0.02941522 |
| 14436 | | 0.00091214 0.00003115 0.99999958 -0.15351458 |
| 14437 | | Axis 0.03371094 -0.98489011 0.16986772 |
| 14438 | | Axis point 170.08865047 0.00000000 201.34858010 |
| 14439 | | Rotation angle (degrees) 0.05306314 |
| 14440 | | Shift along axis 0.00909760 |
| 14441 | | |
| 14442 | | |
| 14443 | | > hide #!1.3 models |
| 14444 | | |
| 14445 | | > show #!2.2 models |
| 14446 | | |
| 14447 | | > hide #!2.3 models |
| 14448 | | |
| 14449 | | > show #!2.3 models |
| 14450 | | |
| 14451 | | > hide #!2.3 models |
| 14452 | | |
| 14453 | | > show #!2.3 models |
| 14454 | | |
| 14455 | | > hide #!2.3 models |
| 14456 | | |
| 14457 | | > show #!2.3 models |
| 14458 | | |
| 14459 | | > hide #!2.2 models |
| 14460 | | |
| 14461 | | > show #!2.2 models |
| 14462 | | |
| 14463 | | > hide #!2.2 models |
| 14464 | | |
| 14465 | | > show #!2.2 models |
| 14466 | | |
| 14467 | | > hide #!2.3 models |
| 14468 | | |
| 14469 | | > show #!2.1 models |
| 14470 | | |
| 14471 | | > hide #!2.2 models |
| 14472 | | |
| 14473 | | > show #!2.2 models |
| 14474 | | |
| 14475 | | > hide #!2.1 models |
| 14476 | | |
| 14477 | | > show #!2.1 models |
| 14478 | | |
| 14479 | | > hide #!2.2 models |
| 14480 | | |
| 14481 | | > show #!2.2 models |
| 14482 | | |
| 14483 | | > hide #!2.2 models |
| 14484 | | |
| 14485 | | > show #!2.2 models |
| 14486 | | |
| 14487 | | > hide #!2.2 models |
| 14488 | | |
| 14489 | | > show #!2.2 models |
| 14490 | | |
| 14491 | | > hide #!2.2 models |
| 14492 | | |
| 14493 | | > show #!2.2 models |
| 14494 | | |
| 14495 | | > hide #!2.1 models |
| 14496 | | |
| 14497 | | > show #!2.1 models |
| 14498 | | |
| 14499 | | > hide #!2.1 models |
| 14500 | | |
| 14501 | | > show #!2.1 models |
| 14502 | | |
| 14503 | | > hide #!2.2 models |
| 14504 | | |
| 14505 | | > show #!2.2 models |
| 14506 | | |
| 14507 | | > hide #!2.1 models |
| 14508 | | |
| 14509 | | > hide #!2.2 models |
| 14510 | | |
| 14511 | | > show #!2.1 models |
| 14512 | | |
| 14513 | | > show #!2.2 models |
| 14514 | | |
| 14515 | | > hide #!2.1 models |
| 14516 | | |
| 14517 | | > hide #!2.2 models |
| 14518 | | |
| 14519 | | > show #!1.2 models |
| 14520 | | |
| 14521 | | > show #!1.1 models |
| 14522 | | |
| 14523 | | > fitmap #1.1 inMap #1.2 |
| 14524 | | |
| 14525 | | Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080 |
| 14526 | | points |
| 14527 | | correlation = 0.9554, correlation about mean = 0.8333, overlap = 6.544e+04 |
| 14528 | | steps = 40, shift = 0.0132, angle = 0.00323 degrees |
| 14529 | | |
| 14530 | | Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc |
| 14531 | | (#1.2) coordinates: |
| 14532 | | Matrix rotation and translation |
| 14533 | | -0.53165456 0.84084486 -0.10160393 138.29871862 |
| 14534 | | -0.59440409 -0.45588234 -0.66246137 467.36416897 |
| 14535 | | -0.60334667 -0.29180682 0.74217355 181.17850074 |
| 14536 | | Axis 0.23684746 0.32061253 -0.91712098 |
| 14537 | | Axis point 214.02602519 230.01629830 0.00000000 |
| 14538 | | Rotation angle (degrees) 128.51223036 |
| 14539 | | Shift along axis 16.43590525 |
| 14540 | | |
| 14541 | | |
| 14542 | | > hide #!1.1 models |
| 14543 | | |
| 14544 | | > show #!1.3 models |
| 14545 | | |
| 14546 | | > fitmap #1.3 inMap #1.2 |
| 14547 | | |
| 14548 | | Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652 |
| 14549 | | points |
| 14550 | | correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04 |
| 14551 | | steps = 60, shift = 0.0156, angle = 0.00323 degrees |
| 14552 | | |
| 14553 | | Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc |
| 14554 | | (#1.2) coordinates: |
| 14555 | | Matrix rotation and translation |
| 14556 | | 0.99847088 0.05404146 0.01163678 -10.30111530 |
| 14557 | | -0.05442446 0.99788338 0.03559124 3.13643466 |
| 14558 | | -0.00968875 -0.03617014 0.99929868 7.17943599 |
| 14559 | | Axis -0.54450170 0.16181110 -0.82300369 |
| 14560 | | Axis point 49.62497877 189.92565671 0.00000000 |
| 14561 | | Rotation angle (degrees) 3.77832215 |
| 14562 | | Shift along axis 0.20778243 |
| 14563 | | |
| 14564 | | |
| 14565 | | > hide #!1.3 models |
| 14566 | | |
| 14567 | | > show #!2.2 models |
| 14568 | | |
| 14569 | | > fitmap #2.2 inMap #1.2 |
| 14570 | | |
| 14571 | | Fit molecule Closed_Rsr21-Ct2.pdb (#2.2) to map Closed_P29_J651_004.mrc (#1.2) |
| 14572 | | using 20396 atoms |
| 14573 | | average map value = 0.5299, steps = 48 |
| 14574 | | shifted from previous position = 0.0107 |
| 14575 | | rotated from previous position = 0.0141 degrees |
| 14576 | | atoms outside contour = 5824, contour level = 0.25 |
| 14577 | | |
| 14578 | | Position of Closed_Rsr21-Ct2.pdb (#2.2) relative to Closed_P29_J651_004.mrc |
| 14579 | | (#1.2) coordinates: |
| 14580 | | Matrix rotation and translation |
| 14581 | | 0.99999990 0.00045273 -0.00000385 -0.05890733 |
| 14582 | | -0.00045273 0.99999988 0.00018531 0.05191103 |
| 14583 | | 0.00000394 -0.00018531 0.99999998 0.02161157 |
| 14584 | | Axis -0.37879465 -0.00796476 -0.92544647 |
| 14585 | | Axis point 114.66064074 128.55070385 0.00000000 |
| 14586 | | Rotation angle (degrees) 0.02802947 |
| 14587 | | Shift along axis 0.00189997 |
| 14588 | | |
| 14589 | | |
| 14590 | | > hide #!2.2 models |
| 14591 | | |
| 14592 | | > show #!2.1 models |
| 14593 | | |
| 14594 | | > hide #!1.2 models |
| 14595 | | |
| 14596 | | > show #!1.1 models |
| 14597 | | |
| 14598 | | > hide #!1.1 models |
| 14599 | | |
| 14600 | | > show #!1.1 models |
| 14601 | | |
| 14602 | | > fitmap #2.1 inMap #1.1 |
| 14603 | | |
| 14604 | | Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using |
| 14605 | | 14334 atoms |
| 14606 | | average map value = 0.5957, steps = 40 |
| 14607 | | shifted from previous position = 0.0121 |
| 14608 | | rotated from previous position = 0.00578 degrees |
| 14609 | | atoms outside contour = 2751, contour level = 0.25 |
| 14610 | | |
| 14611 | | Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1) |
| 14612 | | coordinates: |
| 14613 | | Matrix rotation and translation |
| 14614 | | 0.99999994 -0.00033528 0.00009045 0.04412438 |
| 14615 | | 0.00033528 0.99999994 -0.00001345 -0.04522649 |
| 14616 | | -0.00009045 0.00001348 1.00000000 0.01639942 |
| 14617 | | Axis 0.03875892 0.26026838 0.96475806 |
| 14618 | | Axis point 139.38671802 130.91516584 0.00000000 |
| 14619 | | Rotation angle (degrees) 0.01991165 |
| 14620 | | Shift along axis 0.00576066 |
| 14621 | | |
| 14622 | | |
| 14623 | | > hide #!1.1 models |
| 14624 | | |
| 14625 | | > show #!1.1 models |
| 14626 | | |
| 14627 | | > hide #!1.1 models |
| 14628 | | |
| 14629 | | > show #!1.3 models |
| 14630 | | |
| 14631 | | > hide #!2.1 models |
| 14632 | | |
| 14633 | | > show #!2.3 models |
| 14634 | | |
| 14635 | | > fitmap #2.3 inMap #1.3 |
| 14636 | | |
| 14637 | | Fit molecule Open_Rsr35-Ct2.pdb (#2.3) to map Open_P29_J701_004.mrc (#1.3) |
| 14638 | | using 20430 atoms |
| 14639 | | average map value = 0.2949, steps = 48 |
| 14640 | | shifted from previous position = 0.0181 |
| 14641 | | rotated from previous position = 0.00972 degrees |
| 14642 | | atoms outside contour = 7939, contour level = 0.2 |
| 14643 | | |
| 14644 | | Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3) |
| 14645 | | coordinates: |
| 14646 | | Matrix rotation and translation |
| 14647 | | 0.99999947 -0.00009973 -0.00102301 0.19106219 |
| 14648 | | 0.00009977 0.99999999 0.00003409 -0.03701575 |
| 14649 | | 0.00102301 -0.00003419 0.99999948 -0.15971900 |
| 14650 | | Axis -0.03319861 -0.99473147 0.09699052 |
| 14651 | | Axis point 157.64348455 0.00000000 187.16936061 |
| 14652 | | Rotation angle (degrees) 0.05892461 |
| 14653 | | Shift along axis 0.01498650 |
| 14654 | | |
| 14655 | | |
| 14656 | | > hide #!1.3 models |
| 14657 | | |
| 14658 | | > hide #!2.3 models |
| 14659 | | |
| 14660 | | > show #!1.2 models |
| 14661 | | |
| 14662 | | > hide #!1.2 models |
| 14663 | | |
| 14664 | | > show #!1.1 models |
| 14665 | | |
| 14666 | | > show #!2.1 models |
| 14667 | | |
| 14668 | | > show #!2.2 models |
| 14669 | | |
| 14670 | | > color #1.1 #b2b2b24d models |
| 14671 | | |
| 14672 | | > color #1.1 #b2b2b200 models |
| 14673 | | |
| 14674 | | > color #1.1 #b2b2b280 models |
| 14675 | | |
| 14676 | | > color #1.1 #b2b2b24d models |
| 14677 | | |
| 14678 | | > color #1.1 #b2b2b2ff models |
| 14679 | | |
| 14680 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 14681 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-PCNA_v10.cxs" |
| 14682 | | |
| 14683 | | > show #!3.1 models |
| 14684 | | |
| 14685 | | > cartoon style nucleic xsection oval width 2.5 thickness 2.5 |
| 14686 | | |
| 14687 | | > cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true |
| 14688 | | > xsection oval width 2.75 thickness 1 arrowScale 1.5 |
| 14689 | | |
| 14690 | | > hide #!3.1 models |
| 14691 | | |
| 14692 | | > hide #!3 models |
| 14693 | | |
| 14694 | | > hide #!2.1 models |
| 14695 | | |
| 14696 | | > show #!2.1 models |
| 14697 | | |
| 14698 | | > mmaker #2.1/A-H to #2.2/A-H pais ss bring #1.1 |
| 14699 | | |
| 14700 | | > matchmaker #2.1/A-H to #2.2/A-H pais ss bring #1.1 |
| 14701 | | |
| 14702 | | Expected a keyword |
| 14703 | | |
| 14704 | | > mmaker #2.1/A-H to #2.2/A-H pair ss bring #1.1 |
| 14705 | | |
| 14706 | | Different number of reference/match chains (8 ref, 5 match) |
| 14707 | | |
| 14708 | | > mmaker #2.1/A-E to #2.2/A-E pair ss bring #1.1 |
| 14709 | | |
| 14710 | | Parameters |
| 14711 | | --- |
| 14712 | | Chain pairing | ss |
| 14713 | | Alignment algorithm | Needleman-Wunsch |
| 14714 | | Similarity matrix | BLOSUM-62 |
| 14715 | | SS fraction | 0.3 |
| 14716 | | Gap open (HH/SS/other) | 18/18/6 |
| 14717 | | Gap extend | 1 |
| 14718 | | SS matrix | | | H | S | O |
| 14719 | | ---|---|---|--- |
| 14720 | | H | 6 | -9 | -6 |
| 14721 | | S | | 6 | -6 |
| 14722 | | O | | | 4 |
| 14723 | | Iteration cutoff | 2 |
| 14724 | | |
| 14725 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14726 | | A (#2.1), sequence alignment score = 2286.5 |
| 14727 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14728 | | B (#2.1), sequence alignment score = 1631.1 |
| 14729 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14730 | | C (#2.1), sequence alignment score = 1685.8 |
| 14731 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14732 | | D (#2.1), sequence alignment score = 1702.7 |
| 14733 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14734 | | E (#2.1), sequence alignment score = 1740.3 |
| 14735 | | RMSD between 1753 pruned atom pairs is 0.557 angstroms; (across all 1782 |
| 14736 | | pairs: 0.653) |
| 14737 | | |
| 14738 | | |
| 14739 | | > mmaker #2.1/A-E to #2.2/A-E pair ss bring #1.1 |
| 14740 | | |
| 14741 | | Parameters |
| 14742 | | --- |
| 14743 | | Chain pairing | ss |
| 14744 | | Alignment algorithm | Needleman-Wunsch |
| 14745 | | Similarity matrix | BLOSUM-62 |
| 14746 | | SS fraction | 0.3 |
| 14747 | | Gap open (HH/SS/other) | 18/18/6 |
| 14748 | | Gap extend | 1 |
| 14749 | | SS matrix | | | H | S | O |
| 14750 | | ---|---|---|--- |
| 14751 | | H | 6 | -9 | -6 |
| 14752 | | S | | 6 | -6 |
| 14753 | | O | | | 4 |
| 14754 | | Iteration cutoff | 2 |
| 14755 | | |
| 14756 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14757 | | A (#2.1), sequence alignment score = 2286.5 |
| 14758 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14759 | | B (#2.1), sequence alignment score = 1631.1 |
| 14760 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14761 | | C (#2.1), sequence alignment score = 1685.8 |
| 14762 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14763 | | D (#2.1), sequence alignment score = 1702.7 |
| 14764 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with Apo_Rsr13-Ct1.pdb, chain |
| 14765 | | E (#2.1), sequence alignment score = 1740.3 |
| 14766 | | RMSD between 1753 pruned atom pairs is 0.557 angstroms; (across all 1782 |
| 14767 | | pairs: 0.653) |
| 14768 | | |
| 14769 | | |
| 14770 | | > hide #!1.1 models |
| 14771 | | |
| 14772 | | > show #!3 models |
| 14773 | | |
| 14774 | | > hide #!1 models |
| 14775 | | |
| 14776 | | > hide #!3 models |
| 14777 | | |
| 14778 | | > show #!2.3 models |
| 14779 | | |
| 14780 | | > hide #!2.1 models |
| 14781 | | |
| 14782 | | > hide #!2.3 models |
| 14783 | | |
| 14784 | | > show #!2.3 models |
| 14785 | | |
| 14786 | | > hide #!2.3 models |
| 14787 | | |
| 14788 | | > show #!2.3 models |
| 14789 | | |
| 14790 | | > show #!1.3 models |
| 14791 | | |
| 14792 | | > mmaker #2.3/A-H to #2.2/A-H pair ss bring #1.3 |
| 14793 | | |
| 14794 | | Parameters |
| 14795 | | --- |
| 14796 | | Chain pairing | ss |
| 14797 | | Alignment algorithm | Needleman-Wunsch |
| 14798 | | Similarity matrix | BLOSUM-62 |
| 14799 | | SS fraction | 0.3 |
| 14800 | | Gap open (HH/SS/other) | 18/18/6 |
| 14801 | | Gap extend | 1 |
| 14802 | | SS matrix | | | H | S | O |
| 14803 | | ---|---|---|--- |
| 14804 | | H | 6 | -9 | -6 |
| 14805 | | S | | 6 | -6 |
| 14806 | | O | | | 4 |
| 14807 | | Iteration cutoff | 2 |
| 14808 | | |
| 14809 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14810 | | A (#2.3), sequence alignment score = 2326.1 |
| 14811 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14812 | | B (#2.3), sequence alignment score = 1631.1 |
| 14813 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14814 | | C (#2.3), sequence alignment score = 1685.8 |
| 14815 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14816 | | D (#2.3), sequence alignment score = 1702.7 |
| 14817 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14818 | | E (#2.3), sequence alignment score = 1740.3 |
| 14819 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14820 | | F (#2.3), sequence alignment score = 1283.2 |
| 14821 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14822 | | G (#2.3), sequence alignment score = 1301.2 |
| 14823 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14824 | | H (#2.3), sequence alignment score = 1292.2 |
| 14825 | | RMSD between 2118 pruned atom pairs is 0.609 angstroms; (across all 2550 |
| 14826 | | pairs: 4.762) |
| 14827 | | |
| 14828 | | |
| 14829 | | > mmaker #2.3/A-H to #2.2/A-H pair ss bring #1.3 |
| 14830 | | |
| 14831 | | Parameters |
| 14832 | | --- |
| 14833 | | Chain pairing | ss |
| 14834 | | Alignment algorithm | Needleman-Wunsch |
| 14835 | | Similarity matrix | BLOSUM-62 |
| 14836 | | SS fraction | 0.3 |
| 14837 | | Gap open (HH/SS/other) | 18/18/6 |
| 14838 | | Gap extend | 1 |
| 14839 | | SS matrix | | | H | S | O |
| 14840 | | ---|---|---|--- |
| 14841 | | H | 6 | -9 | -6 |
| 14842 | | S | | 6 | -6 |
| 14843 | | O | | | 4 |
| 14844 | | Iteration cutoff | 2 |
| 14845 | | |
| 14846 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14847 | | A (#2.3), sequence alignment score = 2326.1 |
| 14848 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14849 | | B (#2.3), sequence alignment score = 1631.1 |
| 14850 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14851 | | C (#2.3), sequence alignment score = 1685.8 |
| 14852 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14853 | | D (#2.3), sequence alignment score = 1702.7 |
| 14854 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14855 | | E (#2.3), sequence alignment score = 1740.3 |
| 14856 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14857 | | F (#2.3), sequence alignment score = 1283.2 |
| 14858 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14859 | | G (#2.3), sequence alignment score = 1301.2 |
| 14860 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14861 | | H (#2.3), sequence alignment score = 1292.2 |
| 14862 | | RMSD between 2118 pruned atom pairs is 0.609 angstroms; (across all 2550 |
| 14863 | | pairs: 4.762) |
| 14864 | | |
| 14865 | | |
| 14866 | | > fitmap #2.3 inMap #1.3 |
| 14867 | | |
| 14868 | | Fit molecule Open_Rsr35-Ct2.pdb (#2.3) to map Open_P29_J701_004.mrc (#1.3) |
| 14869 | | using 20430 atoms |
| 14870 | | average map value = 0.2949, steps = 84 |
| 14871 | | shifted from previous position = 0.00231 |
| 14872 | | rotated from previous position = 0.00928 degrees |
| 14873 | | atoms outside contour = 7941, contour level = 0.2 |
| 14874 | | |
| 14875 | | Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3) |
| 14876 | | coordinates: |
| 14877 | | Matrix rotation and translation |
| 14878 | | 0.99999961 -0.00012946 -0.00086989 0.16857509 |
| 14879 | | 0.00012945 0.99999999 -0.00000951 -0.03224247 |
| 14880 | | 0.00086989 0.00000939 0.99999962 -0.13983225 |
| 14881 | | Axis 0.01074383 -0.98904979 0.14719066 |
| 14882 | | Axis point 163.05133459 0.00000000 193.55515090 |
| 14883 | | Rotation angle (degrees) 0.05039270 |
| 14884 | | Shift along axis 0.01311855 |
| 14885 | | |
| 14886 | | |
| 14887 | | > mmaker #2.3/A-H to #2.2/A-H pair ss bring #1.3 |
| 14888 | | |
| 14889 | | Parameters |
| 14890 | | --- |
| 14891 | | Chain pairing | ss |
| 14892 | | Alignment algorithm | Needleman-Wunsch |
| 14893 | | Similarity matrix | BLOSUM-62 |
| 14894 | | SS fraction | 0.3 |
| 14895 | | Gap open (HH/SS/other) | 18/18/6 |
| 14896 | | Gap extend | 1 |
| 14897 | | SS matrix | | | H | S | O |
| 14898 | | ---|---|---|--- |
| 14899 | | H | 6 | -9 | -6 |
| 14900 | | S | | 6 | -6 |
| 14901 | | O | | | 4 |
| 14902 | | Iteration cutoff | 2 |
| 14903 | | |
| 14904 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14905 | | A (#2.3), sequence alignment score = 2326.1 |
| 14906 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14907 | | B (#2.3), sequence alignment score = 1631.1 |
| 14908 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14909 | | C (#2.3), sequence alignment score = 1685.8 |
| 14910 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14911 | | D (#2.3), sequence alignment score = 1702.7 |
| 14912 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14913 | | E (#2.3), sequence alignment score = 1740.3 |
| 14914 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14915 | | F (#2.3), sequence alignment score = 1283.2 |
| 14916 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14917 | | G (#2.3), sequence alignment score = 1301.2 |
| 14918 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with Open_Rsr35-Ct2.pdb, chain |
| 14919 | | H (#2.3), sequence alignment score = 1292.2 |
| 14920 | | RMSD between 2118 pruned atom pairs is 0.609 angstroms; (across all 2550 |
| 14921 | | pairs: 4.762) |
| 14922 | | |
| 14923 | | |
| 14924 | | > hide #!2.3 models |
| 14925 | | |
| 14926 | | > hide #!1 models |
| 14927 | | |
| 14928 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 14929 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-PCNA_v11.cxs" |
| 14930 | | |
| 14931 | | > hide #!2 models |
| 14932 | | |
| 14933 | | > show #!3.8 models |
| 14934 | | |
| 14935 | | > hide #!3 models |
| 14936 | | |
| 14937 | | > show #!2 models |
| 14938 | | |
| 14939 | | > hide #!2.2 models |
| 14940 | | |
| 14941 | | > show #!2.1 models |
| 14942 | | |
| 14943 | | > show #!2.2 models |
| 14944 | | |
| 14945 | | > hide #!2.1 models |
| 14946 | | |
| 14947 | | > show #!2.1 models |
| 14948 | | |
| 14949 | | > hide #!2.2 models |
| 14950 | | |
| 14951 | | > select #2.1/B:68 |
| 14952 | | |
| 14953 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 14954 | | |
| 14955 | | > select #2.1/B:67 |
| 14956 | | |
| 14957 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 14958 | | |
| 14959 | | > select #2.1/B:68 |
| 14960 | | |
| 14961 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 14962 | | |
| 14963 | | > show #!2.3 models |
| 14964 | | |
| 14965 | | > hide #!2.1 models |
| 14966 | | |
| 14967 | | > hide #!2.3 models |
| 14968 | | |
| 14969 | | > show #!2.2 models |
| 14970 | | |
| 14971 | | > hide #!2.2 models |
| 14972 | | |
| 14973 | | > show #!2.1 models |
| 14974 | | |
| 14975 | | > select #2/B:68 |
| 14976 | | |
| 14977 | | 12 atoms, 9 bonds, 3 residues, 3 models selected |
| 14978 | | |
| 14979 | | > show #!2.2 models |
| 14980 | | |
| 14981 | | > hide #!2.1 models |
| 14982 | | |
| 14983 | | > hide #!2.2 models |
| 14984 | | |
| 14985 | | > show #!2.3 models |
| 14986 | | |
| 14987 | | > show #!2.2 models |
| 14988 | | |
| 14989 | | > hide #!2.3 models |
| 14990 | | |
| 14991 | | > show #!2.3 models |
| 14992 | | |
| 14993 | | > setattr sel res ss_type 0 |
| 14994 | | |
| 14995 | | Assigning ss_type attribute to 3 items |
| 14996 | | |
| 14997 | | > hide #!2.3 models |
| 14998 | | |
| 14999 | | > hide #!2.2 models |
| 15000 | | |
| 15001 | | > show #!2.3 models |
| 15002 | | |
| 15003 | | > select clear |
| 15004 | | |
| 15005 | | > hide #!2.3 models |
| 15006 | | |
| 15007 | | > show #!2.2 models |
| 15008 | | |
| 15009 | | > show #!2.3 models |
| 15010 | | |
| 15011 | | > hide #!2.2 models |
| 15012 | | |
| 15013 | | > setattr #2/A:357-359 res ss_type 1 |
| 15014 | | |
| 15015 | | Assigning ss_type attribute to 9 items |
| 15016 | | |
| 15017 | | > select #2.3/B:68 |
| 15018 | | |
| 15019 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 15020 | | |
| 15021 | | > select #2.3/A:356 |
| 15022 | | |
| 15023 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 15024 | | |
| 15025 | | > select #2.3/A:357 |
| 15026 | | |
| 15027 | | 8 atoms, 7 bonds, 1 residue, 1 model selected |
| 15028 | | |
| 15029 | | > select #2.3/A:355 |
| 15030 | | |
| 15031 | | 5 atoms, 4 bonds, 1 residue, 1 model selected |
| 15032 | | |
| 15033 | | > select #2.3/A:356 |
| 15034 | | |
| 15035 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 15036 | | |
| 15037 | | > select #2.3/A:355 |
| 15038 | | |
| 15039 | | 5 atoms, 4 bonds, 1 residue, 1 model selected |
| 15040 | | |
| 15041 | | > select #2.3/B:69 |
| 15042 | | |
| 15043 | | 11 atoms, 10 bonds, 1 residue, 1 model selected |
| 15044 | | |
| 15045 | | > select #2.3/B:74 |
| 15046 | | |
| 15047 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 15048 | | |
| 15049 | | > select #2.3/B:69 |
| 15050 | | |
| 15051 | | 11 atoms, 10 bonds, 1 residue, 1 model selected |
| 15052 | | |
| 15053 | | > select #2.3/B:74 |
| 15054 | | |
| 15055 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 15056 | | |
| 15057 | | > hide #!2.3 models |
| 15058 | | |
| 15059 | | > show #!2.2 models |
| 15060 | | |
| 15061 | | > hide #!2.2 models |
| 15062 | | |
| 15063 | | > show #!2.3 models |
| 15064 | | |
| 15065 | | > show #!2.2 models |
| 15066 | | |
| 15067 | | > hide #!2.3 models |
| 15068 | | |
| 15069 | | > show #!2.3 models |
| 15070 | | |
| 15071 | | > hide #!2.2 models |
| 15072 | | |
| 15073 | | > show #!2.1 models |
| 15074 | | |
| 15075 | | > hide #!2.3 models |
| 15076 | | |
| 15077 | | > show #!2.3 models |
| 15078 | | |
| 15079 | | > hide #!2.1 models |
| 15080 | | |
| 15081 | | > hide #!2.3 models |
| 15082 | | |
| 15083 | | > show #!2.1 models |
| 15084 | | |
| 15085 | | > hide #!2.1 models |
| 15086 | | |
| 15087 | | > show #!2.2 models |
| 15088 | | |
| 15089 | | > select #2.2/A:580 |
| 15090 | | |
| 15091 | | 9 atoms, 8 bonds, 1 residue, 1 model selected |
| 15092 | | |
| 15093 | | > hide #!2.2 models |
| 15094 | | |
| 15095 | | > show #!2.1 models |
| 15096 | | |
| 15097 | | > show #!2.2 models |
| 15098 | | |
| 15099 | | > setattr #2/A:573-380 res ss_type 1 |
| 15100 | | |
| 15101 | | Assigning ss_type attribute to 0 items |
| 15102 | | |
| 15103 | | > undo |
| 15104 | | |
| 15105 | | > show #!2.2 models |
| 15106 | | |
| 15107 | | > setattr #2/A:573-580 res ss_type 1 |
| 15108 | | |
| 15109 | | Assigning ss_type attribute to 24 items |
| 15110 | | |
| 15111 | | > select #2/A:573-580 |
| 15112 | | |
| 15113 | | 201 atoms, 204 bonds, 24 residues, 3 models selected |
| 15114 | | |
| 15115 | | > show #!2.3 models |
| 15116 | | |
| 15117 | | > hide #!2.2 models |
| 15118 | | |
| 15119 | | > show #!2.2 models |
| 15120 | | |
| 15121 | | > setattr sel res ss_type 1 |
| 15122 | | |
| 15123 | | Assigning ss_type attribute to 24 items |
| 15124 | | |
| 15125 | | > setattr sel res ss_id 88 |
| 15126 | | |
| 15127 | | Assigning ss_id attribute to 24 items |
| 15128 | | |
| 15129 | | > hide #!2.3 models |
| 15130 | | |
| 15131 | | > hide #!2.2 models |
| 15132 | | |
| 15133 | | > show #!2.2 models |
| 15134 | | |
| 15135 | | > show #!2.3 models |
| 15136 | | |
| 15137 | | > select #2/A:586-592 |
| 15138 | | |
| 15139 | | 186 atoms, 186 bonds, 21 residues, 3 models selected |
| 15140 | | |
| 15141 | | > setattr sel res ss_type 1 |
| 15142 | | |
| 15143 | | Assigning ss_type attribute to 21 items |
| 15144 | | |
| 15145 | | > setattr sel res ss_id 88 |
| 15146 | | |
| 15147 | | Assigning ss_id attribute to 21 items |
| 15148 | | |
| 15149 | | > hide #!2.2 models |
| 15150 | | |
| 15151 | | > hide #!2.3 models |
| 15152 | | |
| 15153 | | > show #!2.2 models |
| 15154 | | |
| 15155 | | > show #!2.3 models |
| 15156 | | |
| 15157 | | > hide #!2.3 models |
| 15158 | | |
| 15159 | | > hide #!2.2 models |
| 15160 | | |
| 15161 | | > select clear |
| 15162 | | |
| 15163 | | > show #!2.2 models |
| 15164 | | |
| 15165 | | > hide #!2.2 models |
| 15166 | | |
| 15167 | | > show #!2.2 models |
| 15168 | | |
| 15169 | | > hide #!2.1 models |
| 15170 | | |
| 15171 | | > show #!2.3 models |
| 15172 | | |
| 15173 | | > show #!2.1 models |
| 15174 | | |
| 15175 | | > hide #!2.2 models |
| 15176 | | |
| 15177 | | > select #2.1/C:71 |
| 15178 | | |
| 15179 | | 12 atoms, 12 bonds, 1 residue, 1 model selected |
| 15180 | | |
| 15181 | | > select #2.1/C:72 |
| 15182 | | |
| 15183 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 15184 | | |
| 15185 | | > hide #!2.1 models |
| 15186 | | |
| 15187 | | > show #!2.1 models |
| 15188 | | |
| 15189 | | > select #2/C:72 |
| 15190 | | |
| 15191 | | 12 atoms, 9 bonds, 3 residues, 3 models selected |
| 15192 | | |
| 15193 | | > show #!2.2 models |
| 15194 | | |
| 15195 | | > hide #!2.2 models |
| 15196 | | |
| 15197 | | > hide #!2.3 models |
| 15198 | | |
| 15199 | | > show #!2.2 models |
| 15200 | | |
| 15201 | | > show #!2.3 models |
| 15202 | | |
| 15203 | | > setattr sel res ss_type 0 |
| 15204 | | |
| 15205 | | Assigning ss_type attribute to 3 items |
| 15206 | | |
| 15207 | | > hide #!2.2 models |
| 15208 | | |
| 15209 | | > hide #!2.1 models |
| 15210 | | |
| 15211 | | > show #!2.2 models |
| 15212 | | |
| 15213 | | > hide #!2.3 models |
| 15214 | | |
| 15215 | | > select clear |
| 15216 | | |
| 15217 | | > show #!2.3 models |
| 15218 | | |
| 15219 | | > hide #!2.2 models |
| 15220 | | |
| 15221 | | > show #!2.2 models |
| 15222 | | |
| 15223 | | > hide #!2.3 models |
| 15224 | | |
| 15225 | | > hide #!2.2 models |
| 15226 | | |
| 15227 | | > show #!2.3 models |
| 15228 | | |
| 15229 | | > hide #!2.3 models |
| 15230 | | |
| 15231 | | > show #!2.2 models |
| 15232 | | |
| 15233 | | > select #2/F:2-6 |
| 15234 | | |
| 15235 | | 84 atoms, 84 bonds, 10 residues, 2 models selected |
| 15236 | | |
| 15237 | | > show #!2.3 models |
| 15238 | | |
| 15239 | | > hide #!2.2 models |
| 15240 | | |
| 15241 | | > show #!2.2 models |
| 15242 | | |
| 15243 | | > hide #!2.3 models |
| 15244 | | |
| 15245 | | > setattr sel res ss_type 2 |
| 15246 | | |
| 15247 | | Assigning ss_type attribute to 10 items |
| 15248 | | |
| 15249 | | > show #!2.3 models |
| 15250 | | |
| 15251 | | > hide #!2.2 models |
| 15252 | | |
| 15253 | | > show #!2.2 models |
| 15254 | | |
| 15255 | | > hide #!2.3 models |
| 15256 | | |
| 15257 | | > show #!2.3 models |
| 15258 | | |
| 15259 | | > hide #!2.2 models |
| 15260 | | |
| 15261 | | > show #!2.2 models |
| 15262 | | |
| 15263 | | > hide #!2.3 models |
| 15264 | | |
| 15265 | | > select clear |
| 15266 | | |
| 15267 | | > show #!2.3 models |
| 15268 | | |
| 15269 | | > hide #!2.2 models |
| 15270 | | |
| 15271 | | > show #!2.2 models |
| 15272 | | |
| 15273 | | > show #!2.1 models |
| 15274 | | |
| 15275 | | > hide #!2.2 models |
| 15276 | | |
| 15277 | | > hide #!2.3 models |
| 15278 | | |
| 15279 | | > show #!2.2 models |
| 15280 | | |
| 15281 | | > hide #!2.1 models |
| 15282 | | |
| 15283 | | > show #!2.3 models |
| 15284 | | |
| 15285 | | > hide #!2.2 models |
| 15286 | | |
| 15287 | | > show #!2.2 models |
| 15288 | | |
| 15289 | | > hide #!2.3 models |
| 15290 | | |
| 15291 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 15292 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-PCNA_v12.cxs" |
| 15293 | | |
| 15294 | | > select #2/A:334-338 |
| 15295 | | |
| 15296 | | 114 atoms, 114 bonds, 15 residues, 3 models selected |
| 15297 | | |
| 15298 | | > select #2/B:75-78 |
| 15299 | | |
| 15300 | | 96 atoms, 93 bonds, 12 residues, 3 models selected |
| 15301 | | |
| 15302 | | > show #!2.1 models |
| 15303 | | |
| 15304 | | > show #!2.3 models |
| 15305 | | |
| 15306 | | > setattr sel res ss_type 2 |
| 15307 | | |
| 15308 | | Assigning ss_type attribute to 12 items |
| 15309 | | |
| 15310 | | > hide #!2.1 models |
| 15311 | | |
| 15312 | | > hide #!2.3 models |
| 15313 | | |
| 15314 | | > select clear |
| 15315 | | |
| 15316 | | > hide #!2.2 models |
| 15317 | | |
| 15318 | | > show #!2.1 models |
| 15319 | | |
| 15320 | | > select #2/A:334-338 |
| 15321 | | |
| 15322 | | 114 atoms, 114 bonds, 15 residues, 3 models selected |
| 15323 | | |
| 15324 | | > setattr sel res ss_type 2 |
| 15325 | | |
| 15326 | | Assigning ss_type attribute to 15 items |
| 15327 | | |
| 15328 | | > select clear |
| 15329 | | |
| 15330 | | > select #2.1/A:338 |
| 15331 | | |
| 15332 | | 4 atoms, 3 bonds, 1 residue, 1 model selected |
| 15333 | | |
| 15334 | | > select clear |
| 15335 | | |
| 15336 | | > select #2/D:187-188 |
| 15337 | | |
| 15338 | | 66 atoms, 66 bonds, 6 residues, 3 models selected |
| 15339 | | |
| 15340 | | > select #2/D:63-64,187-188 |
| 15341 | | |
| 15342 | | 135 atoms, 138 bonds, 12 residues, 3 models selected |
| 15343 | | |
| 15344 | | > select #2/D:62-64,187-188 |
| 15345 | | |
| 15346 | | 159 atoms, 162 bonds, 15 residues, 3 models selected |
| 15347 | | |
| 15348 | | > select #2/D:62-64,94-95,187-188 |
| 15349 | | |
| 15350 | | 210 atoms, 210 bonds, 21 residues, 3 models selected |
| 15351 | | |
| 15352 | | > setattr sel res ss_type 2 |
| 15353 | | |
| 15354 | | Assigning ss_type attribute to 21 items |
| 15355 | | |
| 15356 | | > select clear |
| 15357 | | |
| 15358 | | > hide #!2.1 models |
| 15359 | | |
| 15360 | | > show #!2.2 models |
| 15361 | | |
| 15362 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 15363 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-PCNA_v12.cxs" |
| 15364 | | |
| 15365 | | > select #2/A:600-601 |
| 15366 | | |
| 15367 | | 54 atoms, 54 bonds, 6 residues, 3 models selected |
| 15368 | | |
| 15369 | | > setattr sel res ss_type 2 |
| 15370 | | |
| 15371 | | Assigning ss_type attribute to 6 items |
| 15372 | | |
| 15373 | | > select clear |
| 15374 | | |
| 15375 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 15376 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC- |
| 15377 | | > PCNA_dssp_v13.cxs" |
| 15378 | | |
| 15379 | | > select #2.2/F:61 |
| 15380 | | |
| 15381 | | 11 atoms, 10 bonds, 1 residue, 1 model selected |
| 15382 | | |
| 15383 | | > select #2.2/F:171 |
| 15384 | | |
| 15385 | | 5 atoms, 4 bonds, 1 residue, 1 model selected |
| 15386 | | |
| 15387 | | > select #2.2/F:62 |
| 15388 | | |
| 15389 | | 6 atoms, 5 bonds, 1 residue, 1 model selected |
| 15390 | | |
| 15391 | | > select #2/F:58-61 |
| 15392 | | |
| 15393 | | 82 atoms, 82 bonds, 8 residues, 2 models selected |
| 15394 | | |
| 15395 | | > setattr sel res ss_type 2 |
| 15396 | | |
| 15397 | | Assigning ss_type attribute to 8 items |
| 15398 | | |
| 15399 | | > show #!2.3 models |
| 15400 | | |
| 15401 | | > hide #!2.2 models |
| 15402 | | |
| 15403 | | > show #!2.2 models |
| 15404 | | |
| 15405 | | > hide #!2.3 models |
| 15406 | | |
| 15407 | | > show #!2.3 models |
| 15408 | | |
| 15409 | | > select #2/F:58-61 |
| 15410 | | |
| 15411 | | 82 atoms, 82 bonds, 8 residues, 2 models selected |
| 15412 | | |
| 15413 | | > setattr sel res ss_type 2 |
| 15414 | | |
| 15415 | | Assigning ss_type attribute to 8 items |
| 15416 | | |
| 15417 | | > setattr sel res ss_id 88 |
| 15418 | | |
| 15419 | | Assigning ss_id attribute to 8 items |
| 15420 | | |
| 15421 | | > hide #!2.3 models |
| 15422 | | |
| 15423 | | > select clear |
| 15424 | | |
| 15425 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 15426 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC- |
| 15427 | | > PCNA_dssp_v13.cxs" |
| 15428 | | |
| 15429 | | ——— End of log from Fri Feb 10 12:12:25 2023 ——— |
| 15430 | | |
| 15431 | | opened ChimeraX session |
| 15432 | | |
| 15433 | | > show #!2.1 models |
| 15434 | | |
| 15435 | | > hide #!2.2 models |
| 15436 | | |
| 15437 | | > hide #!2.1 models |
| 15438 | | |
| 15439 | | > show #!2.2 models |
| 15440 | | |
| 15441 | | > combine #2.2 modelId #2.4 |
| 15442 | | |
| 15443 | | > hide #!2.2 models |
| 15444 | | |
| 15445 | | > show #!2.2 models |
| 15446 | | |
| 15447 | | > hide #!2.2 models |
| 15448 | | |
| 15449 | | > close #2.4 |
| 15450 | | |
| 15451 | | > show #!2.2 models |
| 15452 | | |
| 15453 | | > combine #2.2/B modelId #2.4 |
| 15454 | | |
| 15455 | | > hide #!2.2 models |
| 15456 | | |
| 15457 | | > delete #2.4 & ~/B |
| 15458 | | |
| 15459 | | > show #!2.2 models |
| 15460 | | |
| 15461 | | > hide #!2.2 models |
| 15462 | | |
| 15463 | | > hide #!2.4 models |
| 15464 | | |
| 15465 | | > show #!2.4 models |
| 15466 | | |
| 15467 | | > undo |
| 15468 | | |
| 15469 | | [Repeated 2 time(s)] |
| 15470 | | |
| 15471 | | > hide #!2.2 models |
| 15472 | | |
| 15473 | | > undo |
| 15474 | | |
| 15475 | | [Repeated 6 time(s)] |
| 15476 | | |
| 15477 | | > hide #!2.4 models |
| 15478 | | |
| 15479 | | > show #!2.4 models |
| 15480 | | |
| 15481 | | > close #2.4 |
| 15482 | | |
| 15483 | | > combine #2.2 modelId #2.4 |
| 15484 | | |
| 15485 | | > hide #!2.2 models |
| 15486 | | |
| 15487 | | > delete #2.4 & ~/C |
| 15488 | | |
| 15489 | | > hide #!2.4 models |
| 15490 | | |
| 15491 | | > show #!2.4 models |
| 15492 | | |
| 15493 | | > close #2.4 |
| 15494 | | |
| 15495 | | > combine #2.2 modelId #2.4 |
| 15496 | | |
| 15497 | | > delete #2.4 & ~/D |
| 15498 | | |
| 15499 | | > hide #!2.4 models |
| 15500 | | |
| 15501 | | > show #!2.4 models |
| 15502 | | |
| 15503 | | > close #2.4 |
| 15504 | | |
| 15505 | | > combine #2.2 modelId #2.4 |
| 15506 | | |
| 15507 | | > delete #2.4 & ~/E |
| 15508 | | |
| 15509 | | > hide #!2.4 models |
| 15510 | | |
| 15511 | | > show #!2.4 models |
| 15512 | | |
| 15513 | | > close #2.4 |
| 15514 | | |
| 15515 | | > combine #2.2 modelId #2.4 |
| 15516 | | |
| 15517 | | > delete #2.4 & ~/F |
| 15518 | | |
| 15519 | | > hide #!2.4 models |
| 15520 | | |
| 15521 | | > show #!2.4 models |
| 15522 | | |
| 15523 | | > close #2.4 |
| 15524 | | |
| 15525 | | > combine #2.2 modelId #2.4 |
| 15526 | | |
| 15527 | | > delete #2.4 & ~/G |
| 15528 | | |
| 15529 | | > hide #!2.4 models |
| 15530 | | |
| 15531 | | > show #!2.4 models |
| 15532 | | |
| 15533 | | > close #2.4 |
| 15534 | | |
| 15535 | | > combine #2.2 modelId #2.4 |
| 15536 | | |
| 15537 | | > delete #2.4 & ~/H |
| 15538 | | |
| 15539 | | > hide #!2.4 models |
| 15540 | | |
| 15541 | | > show #!2.4 models |
| 15542 | | |
| 15543 | | > close #2.4 |
| 15544 | | |
| 15545 | | > show #!2.2 models |
| 15546 | | |
| 15547 | | > rename #4 Rad24-gappedDNA |
| 15548 | | |
| 15549 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 15550 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC- |
| 15551 | | > PCNA_dssp_v14.cxs" |
| 15552 | | |
| 15553 | | > color /A #A8B98A |
| 15554 | | |
| 15555 | | > color /B #BCAAC2 |
| 15556 | | |
| 15557 | | > color /C #F3929D |
| 15558 | | |
| 15559 | | > color /D #E3FB90 |
| 15560 | | |
| 15561 | | > color /E #C5BAE5 |
| 15562 | | |
| 15563 | | > color /F #AEDFE2 |
| 15564 | | |
| 15565 | | > color /G #DF8DD7 |
| 15566 | | |
| 15567 | | > color /H #B5F9A0 |
| 15568 | | |
| 15569 | | > hide #!2.2 models |
| 15570 | | |
| 15571 | | > show #!2.1 models |
| 15572 | | |
| 15573 | | > hide #!2.1 models |
| 15574 | | |
| 15575 | | > show #!2.3 models |
| 15576 | | |
| 15577 | | > hide #!2.3 models |
| 15578 | | |
| 15579 | | > show #!2.2 models |
| 15580 | | |
| 15581 | | > show #!3 models |
| 15582 | | |
| 15583 | | > hide #!2 models |
| 15584 | | |
| 15585 | | > hide #!3.8 models |
| 15586 | | |
| 15587 | | > show #!3.1 models |
| 15588 | | |
| 15589 | | > show #!3.2 models |
| 15590 | | |
| 15591 | | > hide #!3.1 models |
| 15592 | | |
| 15593 | | > show #!3.1 models |
| 15594 | | |
| 15595 | | > hide #!3.2 models |
| 15596 | | |
| 15597 | | > hide #!3 models |
| 15598 | | |
| 15599 | | > show #!2 models |
| 15600 | | |
| 15601 | | > mmaker #3.1/A-H to #2.2/A-H pair ss bring #3.2-8 |
| 15602 | | |
| 15603 | | Parameters |
| 15604 | | --- |
| 15605 | | Chain pairing | ss |
| 15606 | | Alignment algorithm | Needleman-Wunsch |
| 15607 | | Similarity matrix | BLOSUM-62 |
| 15608 | | SS fraction | 0.3 |
| 15609 | | Gap open (HH/SS/other) | 18/18/6 |
| 15610 | | Gap extend | 1 |
| 15611 | | SS matrix | | | H | S | O |
| 15612 | | ---|---|---|--- |
| 15613 | | H | 6 | -9 | -6 |
| 15614 | | S | | 6 | -6 |
| 15615 | | O | | | 4 |
| 15616 | | Iteration cutoff | 2 |
| 15617 | | |
| 15618 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA-2DNA-wBRCT, |
| 15619 | | chain A (#3.1), sequence alignment score = 332.6 |
| 15620 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with ScRFC-PCNA-2DNA-wBRCT, |
| 15621 | | chain B (#3.1), sequence alignment score = 1577.7 |
| 15622 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with ScRFC-PCNA-2DNA-wBRCT, |
| 15623 | | chain C (#3.1), sequence alignment score = 1640.2 |
| 15624 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with ScRFC-PCNA-2DNA-wBRCT, |
| 15625 | | chain D (#3.1), sequence alignment score = 1543.9 |
| 15626 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with ScRFC-PCNA-2DNA-wBRCT, |
| 15627 | | chain E (#3.1), sequence alignment score = 1656.5 |
| 15628 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with ScRFC-PCNA-2DNA-wBRCT, |
| 15629 | | chain F (#3.1), sequence alignment score = 1122.1 |
| 15630 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with ScRFC-PCNA-2DNA-wBRCT, |
| 15631 | | chain G (#3.1), sequence alignment score = 1214.2 |
| 15632 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA-2DNA-wBRCT, |
| 15633 | | chain H (#3.1), sequence alignment score = 1193.2 |
| 15634 | | RMSD between 354 pruned atom pairs is 1.089 angstroms; (across all 2504 pairs: |
| 15635 | | 19.089) |
| 15636 | | |
| 15637 | | |
| 15638 | | > show #!3 models |
| 15639 | | |
| 15640 | | > hide #!3.1 models |
| 15641 | | |
| 15642 | | > show #!3.1 models |
| 15643 | | |
| 15644 | | > hide #!3.1 models |
| 15645 | | |
| 15646 | | > show #!3.1 models |
| 15647 | | |
| 15648 | | > hide #!2 models |
| 15649 | | |
| 15650 | | > show #!3.8 models |
| 15651 | | |
| 15652 | | > hide #!3.1 models |
| 15653 | | |
| 15654 | | > show #!2 models |
| 15655 | | |
| 15656 | | > hide #!3 models |
| 15657 | | |
| 15658 | | > show #!3 models |
| 15659 | | |
| 15660 | | > hide #!3 models |
| 15661 | | |
| 15662 | | > show #!3 models |
| 15663 | | |
| 15664 | | > mmaker #3.8/A-H to #2.2/A-H pair ss bring #3.1-7 |
| 15665 | | |
| 15666 | | Parameters |
| 15667 | | --- |
| 15668 | | Chain pairing | ss |
| 15669 | | Alignment algorithm | Needleman-Wunsch |
| 15670 | | Similarity matrix | BLOSUM-62 |
| 15671 | | SS fraction | 0.3 |
| 15672 | | Gap open (HH/SS/other) | 18/18/6 |
| 15673 | | Gap extend | 1 |
| 15674 | | SS matrix | | | H | S | O |
| 15675 | | ---|---|---|--- |
| 15676 | | H | 6 | -9 | -6 |
| 15677 | | S | | 6 | -6 |
| 15678 | | O | | | 4 |
| 15679 | | Iteration cutoff | 2 |
| 15680 | | |
| 15681 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15682 | | chain A (#3.8), sequence alignment score = 379.8 |
| 15683 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15684 | | chain B (#3.8), sequence alignment score = 1486.5 |
| 15685 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15686 | | chain C (#3.8), sequence alignment score = 1525.5 |
| 15687 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15688 | | chain D (#3.8), sequence alignment score = 1468.3 |
| 15689 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15690 | | chain E (#3.8), sequence alignment score = 1400.7 |
| 15691 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15692 | | chain G (#3.8), sequence alignment score = 1144 |
| 15693 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15694 | | chain H (#3.8), sequence alignment score = 1202.2 |
| 15695 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15696 | | chain F (#3.8), sequence alignment score = 1187.8 |
| 15697 | | RMSD between 439 pruned atom pairs is 1.189 angstroms; (across all 2426 pairs: |
| 15698 | | 32.359) |
| 15699 | | |
| 15700 | | |
| 15701 | | > hide #!3 models |
| 15702 | | |
| 15703 | | > show #!3 models |
| 15704 | | |
| 15705 | | > hide #!2 models |
| 15706 | | |
| 15707 | | > show #!2 models |
| 15708 | | |
| 15709 | | > hide #!3 models |
| 15710 | | |
| 15711 | | > show #!3 models |
| 15712 | | |
| 15713 | | > hide #!3 models |
| 15714 | | |
| 15715 | | > show #!3 models |
| 15716 | | |
| 15717 | | > hide #!2 models |
| 15718 | | |
| 15719 | | > show #!3.1 models |
| 15720 | | |
| 15721 | | > hide #!3.1 models |
| 15722 | | |
| 15723 | | > show #!3.1 models |
| 15724 | | |
| 15725 | | > hide #!3.1 models |
| 15726 | | |
| 15727 | | > show #!3.1 models |
| 15728 | | |
| 15729 | | > hide #!3.8 models |
| 15730 | | |
| 15731 | | > show #!3.8 models |
| 15732 | | |
| 15733 | | > hide #!3.8 models |
| 15734 | | |
| 15735 | | > show #!3.8 models |
| 15736 | | |
| 15737 | | > hide #!3.8 models |
| 15738 | | |
| 15739 | | > show #!3.8 models |
| 15740 | | |
| 15741 | | > hide #!3.1 models |
| 15742 | | |
| 15743 | | > show #!3.1 models |
| 15744 | | |
| 15745 | | > hide #!3.8 models |
| 15746 | | |
| 15747 | | > show #!3.8 models |
| 15748 | | |
| 15749 | | > hide #!3.8 models |
| 15750 | | |
| 15751 | | > show #!3.8 models |
| 15752 | | |
| 15753 | | > mmaker #3.8/A-H to #3.1/A-H pair ss |
| 15754 | | |
| 15755 | | Parameters |
| 15756 | | --- |
| 15757 | | Chain pairing | ss |
| 15758 | | Alignment algorithm | Needleman-Wunsch |
| 15759 | | Similarity matrix | BLOSUM-62 |
| 15760 | | SS fraction | 0.3 |
| 15761 | | Gap open (HH/SS/other) | 18/18/6 |
| 15762 | | Gap extend | 1 |
| 15763 | | SS matrix | | | H | S | O |
| 15764 | | ---|---|---|--- |
| 15765 | | H | 6 | -9 | -6 |
| 15766 | | S | | 6 | -6 |
| 15767 | | O | | | 4 |
| 15768 | | Iteration cutoff | 2 |
| 15769 | | |
| 15770 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 15771 | | chain A (#3.8), sequence alignment score = 1956.8 |
| 15772 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain B (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 15773 | | chain B (#3.8), sequence alignment score = 1484.1 |
| 15774 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain C (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 15775 | | chain C (#3.8), sequence alignment score = 1539.9 |
| 15776 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain D (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 15777 | | chain D (#3.8), sequence alignment score = 1540.3 |
| 15778 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 15779 | | chain E (#3.8), sequence alignment score = 1431.7 |
| 15780 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 15781 | | chain G (#3.8), sequence alignment score = 1166.2 |
| 15782 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 15783 | | chain H (#3.8), sequence alignment score = 1234.2 |
| 15784 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 15785 | | chain F (#3.8), sequence alignment score = 1166.8 |
| 15786 | | RMSD between 606 pruned atom pairs is 0.928 angstroms; (across all 2490 pairs: |
| 15787 | | 35.810) |
| 15788 | | |
| 15789 | | |
| 15790 | | > undo |
| 15791 | | |
| 15792 | | > show #!3.8 models |
| 15793 | | |
| 15794 | | > hide #!3.8 models |
| 15795 | | |
| 15796 | | > show #!3.8 models |
| 15797 | | |
| 15798 | | > hide #!3.1 models |
| 15799 | | |
| 15800 | | > mmaker #3.8/A,H to #3.1/A,H pair ss |
| 15801 | | |
| 15802 | | Parameters |
| 15803 | | --- |
| 15804 | | Chain pairing | ss |
| 15805 | | Alignment algorithm | Needleman-Wunsch |
| 15806 | | Similarity matrix | BLOSUM-62 |
| 15807 | | SS fraction | 0.3 |
| 15808 | | Gap open (HH/SS/other) | 18/18/6 |
| 15809 | | Gap extend | 1 |
| 15810 | | SS matrix | | | H | S | O |
| 15811 | | ---|---|---|--- |
| 15812 | | H | 6 | -9 | -6 |
| 15813 | | S | | 6 | -6 |
| 15814 | | O | | | 4 |
| 15815 | | Iteration cutoff | 2 |
| 15816 | | |
| 15817 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 15818 | | chain A (#3.8), sequence alignment score = 1956.8 |
| 15819 | | Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb, |
| 15820 | | chain H (#3.8), sequence alignment score = 1174 |
| 15821 | | RMSD between 416 pruned atom pairs is 0.967 angstroms; (across all 695 pairs: |
| 15822 | | 14.894) |
| 15823 | | |
| 15824 | | |
| 15825 | | > show #!3.1 models |
| 15826 | | |
| 15827 | | > hide #!3.8 models |
| 15828 | | |
| 15829 | | > show #!3.8 models |
| 15830 | | |
| 15831 | | > hide #!3.8 models |
| 15832 | | |
| 15833 | | > show #!3.8 models |
| 15834 | | |
| 15835 | | > hide #!3.8 models |
| 15836 | | |
| 15837 | | > show #!3.8 models |
| 15838 | | |
| 15839 | | > hide #!3.8 models |
| 15840 | | |
| 15841 | | > show #!3.8 models |
| 15842 | | |
| 15843 | | > hide #!3.8 models |
| 15844 | | |
| 15845 | | > show #!3.8 models |
| 15846 | | |
| 15847 | | > hide #!3.1 models |
| 15848 | | |
| 15849 | | > show #!2 models |
| 15850 | | |
| 15851 | | > hide #!3 models |
| 15852 | | |
| 15853 | | > show #!3 models |
| 15854 | | |
| 15855 | | > hide #!3 models |
| 15856 | | |
| 15857 | | > show #!3 models |
| 15858 | | |
| 15859 | | > mmaker #3.8/A-H to #2.2/A-H pair ss bring #3.1-7 |
| 15860 | | |
| 15861 | | Parameters |
| 15862 | | --- |
| 15863 | | Chain pairing | ss |
| 15864 | | Alignment algorithm | Needleman-Wunsch |
| 15865 | | Similarity matrix | BLOSUM-62 |
| 15866 | | SS fraction | 0.3 |
| 15867 | | Gap open (HH/SS/other) | 18/18/6 |
| 15868 | | Gap extend | 1 |
| 15869 | | SS matrix | | | H | S | O |
| 15870 | | ---|---|---|--- |
| 15871 | | H | 6 | -9 | -6 |
| 15872 | | S | | 6 | -6 |
| 15873 | | O | | | 4 |
| 15874 | | Iteration cutoff | 2 |
| 15875 | | |
| 15876 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15877 | | chain A (#3.8), sequence alignment score = 379.8 |
| 15878 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15879 | | chain B (#3.8), sequence alignment score = 1486.5 |
| 15880 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15881 | | chain C (#3.8), sequence alignment score = 1525.5 |
| 15882 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15883 | | chain D (#3.8), sequence alignment score = 1468.3 |
| 15884 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15885 | | chain E (#3.8), sequence alignment score = 1400.7 |
| 15886 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15887 | | chain G (#3.8), sequence alignment score = 1144 |
| 15888 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15889 | | chain H (#3.8), sequence alignment score = 1202.2 |
| 15890 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15891 | | chain F (#3.8), sequence alignment score = 1187.8 |
| 15892 | | RMSD between 439 pruned atom pairs is 1.189 angstroms; (across all 2426 pairs: |
| 15893 | | 32.359) |
| 15894 | | |
| 15895 | | |
| 15896 | | > hide #!3 models |
| 15897 | | |
| 15898 | | > show #!3 models |
| 15899 | | |
| 15900 | | > hide #!3 models |
| 15901 | | |
| 15902 | | > show #!3 models |
| 15903 | | |
| 15904 | | > hide #!3 models |
| 15905 | | |
| 15906 | | > show #!3 models |
| 15907 | | |
| 15908 | | > hide #!3 models |
| 15909 | | |
| 15910 | | > show #!3 models |
| 15911 | | |
| 15912 | | > hide #!3 models |
| 15913 | | |
| 15914 | | > show #!3 models |
| 15915 | | |
| 15916 | | > hide #!3 models |
| 15917 | | |
| 15918 | | > show #!3 models |
| 15919 | | |
| 15920 | | > hide #!3 models |
| 15921 | | |
| 15922 | | > show #!3 models |
| 15923 | | |
| 15924 | | > hide #!3 models |
| 15925 | | |
| 15926 | | > show #!3 models |
| 15927 | | |
| 15928 | | > hide #!3 models |
| 15929 | | |
| 15930 | | > show #!3 models |
| 15931 | | |
| 15932 | | > hide #!3 models |
| 15933 | | |
| 15934 | | > show #!3 models |
| 15935 | | |
| 15936 | | > hide #!3 models |
| 15937 | | |
| 15938 | | > show #!3 models |
| 15939 | | |
| 15940 | | > hide #!3 models |
| 15941 | | |
| 15942 | | > show #!3 models |
| 15943 | | |
| 15944 | | > hide #!3 models |
| 15945 | | |
| 15946 | | > show #!3 models |
| 15947 | | |
| 15948 | | > hide #!3 models |
| 15949 | | |
| 15950 | | > show #!3 models |
| 15951 | | |
| 15952 | | > hide #!3 models |
| 15953 | | |
| 15954 | | > show #!3 models |
| 15955 | | |
| 15956 | | > hide #!3 models |
| 15957 | | |
| 15958 | | > show #!3 models |
| 15959 | | |
| 15960 | | > hide #!3 models |
| 15961 | | |
| 15962 | | > show #!3 models |
| 15963 | | |
| 15964 | | > mmaker #3.8/A,H to #2.2/A,H pair ss bring #3.1-7 |
| 15965 | | |
| 15966 | | Parameters |
| 15967 | | --- |
| 15968 | | Chain pairing | ss |
| 15969 | | Alignment algorithm | Needleman-Wunsch |
| 15970 | | Similarity matrix | BLOSUM-62 |
| 15971 | | SS fraction | 0.3 |
| 15972 | | Gap open (HH/SS/other) | 18/18/6 |
| 15973 | | Gap extend | 1 |
| 15974 | | SS matrix | | | H | S | O |
| 15975 | | ---|---|---|--- |
| 15976 | | H | 6 | -9 | -6 |
| 15977 | | S | | 6 | -6 |
| 15978 | | O | | | 4 |
| 15979 | | Iteration cutoff | 2 |
| 15980 | | |
| 15981 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15982 | | chain A (#3.8), sequence alignment score = 379.8 |
| 15983 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 15984 | | chain H (#3.8), sequence alignment score = 1233.4 |
| 15985 | | RMSD between 224 pruned atom pairs is 0.661 angstroms; (across all 637 pairs: |
| 15986 | | 16.331) |
| 15987 | | |
| 15988 | | |
| 15989 | | > hide #!3 models |
| 15990 | | |
| 15991 | | > show #!3 models |
| 15992 | | |
| 15993 | | > hide #!3 models |
| 15994 | | |
| 15995 | | > show #!3 models |
| 15996 | | |
| 15997 | | > hide #!3 models |
| 15998 | | |
| 15999 | | > show #!3 models |
| 16000 | | |
| 16001 | | > hide #!3 models |
| 16002 | | |
| 16003 | | > show #!3 models |
| 16004 | | |
| 16005 | | > hide #!3 models |
| 16006 | | |
| 16007 | | > show #!3 models |
| 16008 | | |
| 16009 | | > mmaker #3.8/A,F-H to #2.2/A,F-H pair ss bring #3.1-7 |
| 16010 | | |
| 16011 | | Parameters |
| 16012 | | --- |
| 16013 | | Chain pairing | ss |
| 16014 | | Alignment algorithm | Needleman-Wunsch |
| 16015 | | Similarity matrix | BLOSUM-62 |
| 16016 | | SS fraction | 0.3 |
| 16017 | | Gap open (HH/SS/other) | 18/18/6 |
| 16018 | | Gap extend | 1 |
| 16019 | | SS matrix | | | H | S | O |
| 16020 | | ---|---|---|--- |
| 16021 | | H | 6 | -9 | -6 |
| 16022 | | S | | 6 | -6 |
| 16023 | | O | | | 4 |
| 16024 | | Iteration cutoff | 2 |
| 16025 | | |
| 16026 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 16027 | | chain A (#3.8), sequence alignment score = 379.8 |
| 16028 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 16029 | | chain G (#3.8), sequence alignment score = 1144 |
| 16030 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 16031 | | chain H (#3.8), sequence alignment score = 1202.2 |
| 16032 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 16033 | | chain F (#3.8), sequence alignment score = 1187.8 |
| 16034 | | RMSD between 573 pruned atom pairs is 0.990 angstroms; (across all 1145 pairs: |
| 16035 | | 32.103) |
| 16036 | | |
| 16037 | | |
| 16038 | | > hide #!3 models |
| 16039 | | |
| 16040 | | > show #!3 models |
| 16041 | | |
| 16042 | | > hide #!3 models |
| 16043 | | |
| 16044 | | > show #!3 models |
| 16045 | | |
| 16046 | | > hide #!2 models |
| 16047 | | |
| 16048 | | > show #!2 models |
| 16049 | | |
| 16050 | | > hide #!2 models |
| 16051 | | |
| 16052 | | > show #!2 models |
| 16053 | | |
| 16054 | | > hide #!3 models |
| 16055 | | |
| 16056 | | > show #!3 models |
| 16057 | | |
| 16058 | | > mmaker #3.8/A,F,G,H to #2.2/A,F,G,H pair ss bring #3.1-7 |
| 16059 | | |
| 16060 | | Parameters |
| 16061 | | --- |
| 16062 | | Chain pairing | ss |
| 16063 | | Alignment algorithm | Needleman-Wunsch |
| 16064 | | Similarity matrix | BLOSUM-62 |
| 16065 | | SS fraction | 0.3 |
| 16066 | | Gap open (HH/SS/other) | 18/18/6 |
| 16067 | | Gap extend | 1 |
| 16068 | | SS matrix | | | H | S | O |
| 16069 | | ---|---|---|--- |
| 16070 | | H | 6 | -9 | -6 |
| 16071 | | S | | 6 | -6 |
| 16072 | | O | | | 4 |
| 16073 | | Iteration cutoff | 2 |
| 16074 | | |
| 16075 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 16076 | | chain A (#3.8), sequence alignment score = 379.8 |
| 16077 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 16078 | | chain F (#3.8), sequence alignment score = 1181.2 |
| 16079 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 16080 | | chain G (#3.8), sequence alignment score = 1207 |
| 16081 | | Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA_1SXJ.pdb, |
| 16082 | | chain H (#3.8), sequence alignment score = 1233.4 |
| 16083 | | RMSD between 635 pruned atom pairs is 0.888 angstroms; (across all 1147 pairs: |
| 16084 | | 12.517) |
| 16085 | | |
| 16086 | | |
| 16087 | | > hide #!3 models |
| 16088 | | |
| 16089 | | > show #!3 models |
| 16090 | | |
| 16091 | | > hide #!3 models |
| 16092 | | |
| 16093 | | > show #!3 models |
| 16094 | | |
| 16095 | | > hide #!3 models |
| 16096 | | |
| 16097 | | > show #!3 models |
| 16098 | | |
| 16099 | | > hide #!3 models |
| 16100 | | |
| 16101 | | > show #!3 models |
| 16102 | | |
| 16103 | | > hide #!3 models |
| 16104 | | |
| 16105 | | > show #!3 models |
| 16106 | | |
| 16107 | | > hide #!2 models |
| 16108 | | |
| 16109 | | > show #!2 models |
| 16110 | | |
| 16111 | | > hide #!2 models |
| 16112 | | |
| 16113 | | > show #!2 models |
| 16114 | | |
| 16115 | | > hide #!2 models |
| 16116 | | |
| 16117 | | > show #!2 models |
| 16118 | | |
| 16119 | | > hide #!2 models |
| 16120 | | |
| 16121 | | > show #!3.1 models |
| 16122 | | |
| 16123 | | > hide #!3.8 models |
| 16124 | | |
| 16125 | | > show #!3.8 models |
| 16126 | | |
| 16127 | | > hide #!3.1 models |
| 16128 | | |
| 16129 | | > show #!3.1 models |
| 16130 | | |
| 16131 | | > hide #!3.8 models |
| 16132 | | |
| 16133 | | > show #!3.8 models |
| 16134 | | |
| 16135 | | > hide #!3.8 models |
| 16136 | | |
| 16137 | | > show #!3.8 models |
| 16138 | | |
| 16139 | | > hide #!3.8 models |
| 16140 | | |
| 16141 | | > show #!3.8 models |
| 16142 | | |
| 16143 | | > hide #!3.8 models |
| 16144 | | |
| 16145 | | > show #!3.8 models |
| 16146 | | |
| 16147 | | > hide #!3.8 models |
| 16148 | | |
| 16149 | | > show #!3.8 models |
| 16150 | | |
| 16151 | | > hide #!3.8 models |
| 16152 | | |
| 16153 | | > hide #!3.1 models |
| 16154 | | |
| 16155 | | > show #!2 models |
| 16156 | | |
| 16157 | | > show #!3.8 models |
| 16158 | | |
| 16159 | | > hide #!3.8 models |
| 16160 | | |
| 16161 | | > show #!3.8 models |
| 16162 | | |
| 16163 | | > hide #!2 models |
| 16164 | | |
| 16165 | | > show #!2 models |
| 16166 | | |
| 16167 | | > hide #!3 models |
| 16168 | | |
| 16169 | | > show #!3 models |
| 16170 | | |
| 16171 | | > hide #!3 models |
| 16172 | | |
| 16173 | | > show #!3 models |
| 16174 | | |
| 16175 | | > hide #!3 models |
| 16176 | | |
| 16177 | | > show #!3 models |
| 16178 | | |
| 16179 | | > hide #!3 models |
| 16180 | | |
| 16181 | | > show #!3 models |
| 16182 | | |
| 16183 | | > hide #!3 models |
| 16184 | | |
| 16185 | | > show #!3 models |
| 16186 | | |
| 16187 | | > hide #!3 models |
| 16188 | | |
| 16189 | | > show #!3 models |
| 16190 | | |
| 16191 | | > hide #!3 models |
| 16192 | | |
| 16193 | | > show #!3 models |
| 16194 | | |
| 16195 | | > hide #!2 models |
| 16196 | | |
| 16197 | | > show #!2 models |
| 16198 | | |
| 16199 | | > hide #!2 models |
| 16200 | | |
| 16201 | | > show #!2 models |
| 16202 | | |
| 16203 | | > hide #!2 models |
| 16204 | | |
| 16205 | | > show #!2 models |
| 16206 | | |
| 16207 | | > hide #!2 models |
| 16208 | | |
| 16209 | | > show #!2 models |
| 16210 | | |
| 16211 | | > hide #!2 models |
| 16212 | | |
| 16213 | | > show #!2 models |
| 16214 | | |
| 16215 | | > hide #!2 models |
| 16216 | | |
| 16217 | | > show #!2 models |
| 16218 | | |
| 16219 | | > hide #!3 models |
| 16220 | | |
| 16221 | | > save "/Users/fengwei.zheng/OneDrive - Van Andel |
| 16222 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC- |
| 16223 | | > PCNA_dssp_v14.cxs" |
| 16224 | | |
| 16225 | | [Repeated 1 time(s)] |
| 16226 | | |
| 16227 | | ——— End of log from Sat Feb 18 16:30:50 2023 ——— |
| 16228 | | |
| 16229 | | opened ChimeraX session |
| 16230 | | |
| 16231 | | > hide #!2 models |
| 16232 | | |
| 16233 | | > show #!1 models |
| 16234 | | |
| 16235 | | > hide #!1.3 models |
| 16236 | | |
| 16237 | | > show #!1.1 models |
| 16238 | | |
| 16239 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 16240 | | > Institute/Documents/Draft/4_Egl1_RFC- |
| 16241 | | > PCNA/0-MM/0-half/J632-Apo/cryosparc_P47_J328_map_locres.mrc" |
| 16242 | | |
| 16243 | | Opened cryosparc_P47_J328_map_locres.mrc as #5, grid size 420,420,420, pixel |
| 16244 | | 0.828, shown at level 4.55, step 2, values float32 |
| 16245 | | |
| 16246 | | > close #5 |
| 16247 | | |
| 16248 | | Uncaught (in promise) TypeError: Cannot read properties of null (reading |
| 16249 | | 'insertBefore') |
| 16250 | | |
| 16251 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 16252 | | > Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Apo_P29_J632_004.mrc" |
| 16253 | | |
| 16254 | | Opened Apo_P29_J632_004.mrc as #5, grid size 420,420,420, pixel 0.828, shown |
| 16255 | | at level 0.1, step 2, values float32 |
| 16256 | | |
| 16257 | | > hide #!1 models |
| 16258 | | |
| 16259 | | > surface dust #0-9 size 10 |
| 16260 | | |
| 16261 | | > open "/Users/fengwei.zheng/OneDrive - Van Andel |
| 16262 | | > Institute/Documents/Draft/4_Egl1_RFC- |
| 16263 | | > PCNA/0-MM/0-half/J632-Apo/cryosparc_P47_J328_map_locres.mrc" |
| 16264 | | |
| 16265 | | Opened cryosparc_P47_J328_map_locres.mrc as #6, grid size 420,420,420, pixel |
| 16266 | | 0.828, shown at level 4.55, step 2, values float32 |
| 16267 | | |
| 16268 | | > hide #!6 models |
| 16269 | | |
| 16270 | | > show #!1 models |
| 16271 | | |
| 16272 | | > volume #5-6 step 1 level 0.25 |
| 16273 | | |
| 16274 | | > hide #!1 models |
| 16275 | | |
| 16276 | | > show #!6 models |
| 16277 | | |
| 16278 | | > volume #6 color #b2ffffb3 |
| 16279 | | |
| 16280 | | > volume #6 color #b2ffff |
| 16281 | | |
| 16282 | | > hide #!6 models |
| 16283 | | |
| 16284 | | > show #!1 models |
| 16285 | | |
| 16286 | | > fitmap #5 inMap #1.1 bring #6 |
| 16287 | | |
| 16288 | | Expected a keyword |
| 16289 | | |
| 16290 | | > hide #!1 models |
| 16291 | | |
| 16292 | | > show #!6 models |
| 16293 | | |
| 16294 | | > hide #!6 models |
| 16295 | | |
| 16296 | | > color sample #5 map #6 palette 2.5,blue:3.5,cyan:4.5,lime:5.5,yellow:6.5,red |
| 16297 | | > key true |
| 16298 | | |
| 16299 | | Map values for surface "surface": minimum 0, mean 3.582, maximum 8.703 |
| 16300 | | |
| 16301 | | > key rainbow :2.5 :3.5 :4.5 :5.5 :6.5 showTool true |
| 16302 | | |
| 16303 | | > ui mousemode right "color key" |
| 16304 | | |
| 16305 | | > key pos 0.71847,0.0652488 |
| 16306 | | |
| 16307 | | > ui mousemode right translate |
| 16308 | | |
| 16309 | | > volume #5 level 0.3 |
| 16310 | | |
| 16311 | | > volume #6 level 0.3 |
| 16312 | | |
| 16313 | | > volume #5 level 0.35 |
| 16314 | | |
| 16315 | | > show #!1 models |
| 16316 | | |
| 16317 | | > select add #5 |
| 16318 | | |
| 16319 | | 2 models selected |
| 16320 | | |
| 16321 | | > ui mousemode right "rotate selected models" |
| 16322 | | |
| 16323 | | > view matrix models |
| 16324 | | > #5,-0.19588,0.9379,-0.28631,81.544,-0.22909,-0.32765,-0.9166,446.33,-0.95349,-0.11395,0.27905,311.26 |
| 16325 | | |
| 16326 | | > view matrix models |
| 16327 | | > #5,0.46722,0.88022,0.08315,-85.883,0.73165,-0.33212,-0.5953,229.04,-0.49638,0.33897,-0.79919,353.33 |
| 16328 | | |
| 16329 | | > view matrix models |
| 16330 | | > #5,-0.91246,-0.40891,-0.014391,392.32,-0.17295,0.35357,0.91928,-24.803,-0.37082,0.8413,-0.39334,167.12 |
| 16331 | | |
| 16332 | | > view matrix models |
| 16333 | | > #5,-0.44742,-0.81801,-0.3615,453.29,-0.36901,-0.19934,0.9078,109.31,-0.81465,0.53956,-0.21266,261.43 |
| 16334 | | |
| 16335 | | > ui mousemode right "translate selected models" |
| 16336 | | |
| 16337 | | > view matrix models |
| 16338 | | > #5,-0.44742,-0.81801,-0.3615,400.08,-0.36901,-0.19934,0.9078,133.36,-0.81465,0.53956,-0.21266,277.53 |
| 16339 | | |
| 16340 | | > ui mousemode right "rotate selected models" |
| 16341 | | |
| 16342 | | > view matrix models |
| 16343 | | > #5,-0.84663,0.17613,-0.5022,312.96,-0.40253,-0.82922,0.38778,348.43,-0.34813,0.53045,0.77293,20.014 |
| 16344 | | |
| 16345 | | > view matrix models |
| 16346 | | > #5,-0.61922,-0.56425,-0.54607,416.85,-0.31942,-0.45429,0.83162,185.17,-0.71731,0.68938,0.10107,176.5 |
| 16347 | | |
| 16348 | | > view matrix models |
| 16349 | | > #5,-0.37265,-0.89215,-0.25533,381.47,-0.40393,-0.091769,0.91018,119.32,-0.83545,0.44232,-0.32617,319.45 |
| 16350 | | |
| 16351 | | > view matrix models |
| 16352 | | > #5,-0.072232,-0.93202,0.35513,226.24,-0.63915,0.3166,0.70089,123.29,-0.76568,-0.17636,-0.61857,473.38 |
| 16353 | | |
| 16354 | | > view matrix models |
| 16355 | | > #5,0.023712,-0.64624,0.76277,83.605,-0.82405,0.41935,0.38091,194.44,-0.56603,-0.63759,-0.52259,505.74 |
| 16356 | | |
| 16357 | | > view matrix models |
| 16358 | | > #5,-0.81564,0.23975,-0.52655,300.88,0.37275,-0.47828,-0.79518,375.64,-0.44248,-0.84485,0.30074,370.57 |
| 16359 | | |
| 16360 | | > view matrix models |
| 16361 | | > #5,-0.881,0.36967,-0.29528,245.55,-0.011821,-0.64111,-0.76736,463.38,-0.47298,-0.67255,0.56918,294.98 |
| 16362 | | |
| 16363 | | > view matrix models |
| 16364 | | > #5,-0.67682,0.72785,-0.11023,113.11,-0.36601,-0.46264,-0.80746,497.16,-0.63871,-0.50616,0.57953,290.48 |
| 16365 | | |
| 16366 | | > view matrix models |
| 16367 | | > #5,-0.38284,0.92206,0.056951,-1.33,-0.68291,-0.24095,-0.68962,487.82,-0.62215,-0.30291,0.72193,224.83 |
| 16368 | | |
| 16369 | | > ui mousemode right "translate selected models" |
| 16370 | | |
| 16371 | | > view matrix models |
| 16372 | | > #5,-0.38284,0.92206,0.056951,75.238,-0.68291,-0.24095,-0.68962,457.3,-0.62215,-0.30291,0.72193,195.05 |
| 16373 | | |
| 16374 | | > fitmap #5 inMap #1.1 bring #6 |
| 16375 | | |
| 16376 | | Expected a keyword |
| 16377 | | |
| 16378 | | > fitmap #5 inMap #1.1 |
| 16379 | | |
| 16380 | | Fit map Apo_P29_J632_004.mrc in map Apo_P29_J632_004.mrc using 125313 points |
| 16381 | | correlation = 0.4658, correlation about mean = 0.09559, overlap = 1.801e+04 |
| 16382 | | steps = 172, shift = 7.57, angle = 13.6 degrees |
| 16383 | | |
| 16384 | | Position of Apo_P29_J632_004.mrc (#5) relative to Apo_P29_J632_004.mrc (#1.1) |
| 16385 | | coordinates: |
| 16386 | | Matrix rotation and translation |
| 16387 | | 0.99998757 0.00327691 -0.00375862 -4.26903411 |
| 16388 | | -0.00327343 0.99999421 0.00093028 -2.14580035 |
| 16389 | | 0.00376164 -0.00091797 0.99999251 0.64788562 |
| 16390 | | Axis -0.18222236 -0.74143457 -0.64580941 |
| 16391 | | Axis point -509.16948697 0.00000000 -1039.55451000 |
| 16392 | | Rotation angle (degrees) 0.29057229 |
| 16393 | | Shift along axis 1.95047339 |
| 16394 | | |
| 16395 | | |
| 16396 | | > fitmap #5 inMap #1.1 |
| 16397 | | |
| 16398 | | Fit map Apo_P29_J632_004.mrc in map Apo_P29_J632_004.mrc using 125313 points |
| 16399 | | correlation = 0.4652, correlation about mean = 0.09547, overlap = 1.803e+04 |
| 16400 | | steps = 28, shift = 0.0166, angle = 0.02 degrees |
| 16401 | | |
| 16402 | | Position of Apo_P29_J632_004.mrc (#5) relative to Apo_P29_J632_004.mrc (#1.1) |
| 16403 | | coordinates: |
| 16404 | | Matrix rotation and translation |
| 16405 | | 0.99998635 0.00360551 -0.00378107 -4.30762066 |
| 16406 | | -0.00360157 0.99999296 0.00104822 -2.10325239 |
| 16407 | | 0.00378482 -0.00103459 0.99999230 0.66406669 |
| 16408 | | Axis -0.19548324 -0.71009875 -0.67642152 |
| 16409 | | Axis point -514.70544884 0.00000000 -1039.87371878 |
| 16410 | | Rotation angle (degrees) 0.30523641 |
| 16411 | | Shift along axis 1.88639551 |
| 16412 | | |
| 16413 | | |
| 16414 | | > view matrix models |
| 16415 | | > #5,-0.53655,0.83803,-0.09912,140.43,-0.5944,-0.45869,-0.66053,467.88,-0.59901,-0.29549,0.74423,179.01 |
| 16416 | | |
| 16417 | | > fitmap #5 inMap #1.1 |
| 16418 | | |
| 16419 | | Fit map Apo_P29_J632_004.mrc in map Apo_P29_J632_004.mrc using 125313 points |
| 16420 | | correlation = 1, correlation about mean = 1, overlap = 6.736e+04 |
| 16421 | | steps = 56, shift = 1.65, angle = 0.31 degrees |
| 16422 | | |
| 16423 | | Position of Apo_P29_J632_004.mrc (#5) relative to Apo_P29_J632_004.mrc (#1.1) |
| 16424 | | coordinates: |
| 16425 | | Matrix rotation and translation |
| 16426 | | 1.00000000 -0.00003582 0.00005096 -0.00778457 |
| 16427 | | 0.00003582 1.00000000 -0.00007979 0.00476406 |
| 16428 | | -0.00005096 0.00007979 1.00000000 -0.00887981 |
| 16429 | | Axis 0.78825025 0.50341701 0.35388255 |
| 16430 | | Axis point 0.00000000 80.77940671 103.11450309 |
| 16431 | | Rotation angle (degrees) 0.00579971 |
| 16432 | | Shift along axis -0.00688029 |
| 16433 | | |
| 16434 | | |
| 16435 | | > select clear |
| | 946 | |
| | 947 | [truncated to fit within ticket limits] |
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