Changes between Initial Version and Version 1 of Ticket #19798


Ignore:
Timestamp:
Feb 3, 2026, 10:05:51 AM (3 weeks ago)
Author:
Eric Pettersen
Comment:

Reported by James Fleckenstein

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #19798

    • Property Component Unassigned → Graphics
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → glClear: invalid framebuffer operation on statusbar expose

  • Ticket #19798 – Description

    initial v1  
    12411241> aligned_Fig4.cxs
    12421242
    1243 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size
    1244 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    1245 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size
    1246 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1247 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size
    1248 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1249 Opened EatA-G12_composite_map.ccp4 as #4, grid size 356,356,356, pixel 0.86,
    1250 shown at level 8.74, step 1, values float32 
    1251 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size
    1252 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1253 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size
    1254 320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32 
    1255 Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356,
    1256 pixel 0.86, shown at level 4.3, step 1, values float32 
    1257 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14,
    1258 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    1259 float32 
    1260 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
    1261 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    1262 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
    1263 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    1264 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
    1265 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    1266 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
    1267 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    1268 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
    1269 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    1270 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
    1271 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    1272 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
    1273 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    1274 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
    1275 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    1276 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
    1277 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    1278 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
    1279 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1280 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
    1281 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1282 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
    1283 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1284 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
    1285 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1286 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
    1287 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1288 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
    1289 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1290 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
    1291 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1292 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
    1293 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1294 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
    1295 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1296 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
    1297 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1298 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
    1299 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    1300 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid
    1301 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1302 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid
    1303 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1304 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid
    1305 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1306 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid
    1307 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1308 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid
    1309 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1310 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid
    1311 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1312 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid
    1313 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1314 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid
    1315 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1316 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid
    1317 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1318 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid
    1319 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1320 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid
    1321 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    1322 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid
    1323 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1324 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid
    1325 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1326 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid
    1327 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1328 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid
    1329 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1330 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid
    1331 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1332 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid
    1333 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1334 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid
    1335 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1336 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid
    1337 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1338 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid
    1339 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1340 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid
    1341 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1342 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid
    1343 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    1344 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #22.1,
    1345 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    1346 float32 
    1347 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #22.2,
    1348 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    1349 float32 
    1350 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #22.3,
    1351 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    1352 float32 
    1353 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #22.4,
    1354 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    1355 float32 
    1356 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #22.5,
    1357 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    1358 float32 
    1359 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #22.6,
    1360 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    1361 float32 
    1362 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #22.7,
    1363 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    1364 float32 
    1365 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #22.8,
    1366 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    1367 float32 
    1368 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #22.9,
    1369 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    1370 float32 
    1371 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
    1372 #22.10, grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1,
    1373 values float32 
    1374 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #21.1, grid size 356,356,356,
    1375 pixel 0.86, shown at level 4.3, step 1, values float32 
    1376 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #21.2, grid size 356,356,356,
    1377 pixel 0.86, shown at level 4.3, step 1, values float32 
    1378 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #21.3, grid size 356,356,356,
    1379 pixel 0.86, shown at level 4.3, step 1, values float32 
    1380 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #21.4, grid size 356,356,356,
    1381 pixel 0.86, shown at level 4.3, step 1, values float32 
    1382 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #21.5, grid size 356,356,356,
    1383 pixel 0.86, shown at level 4.3, step 1, values float32 
    1384 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #21.6, grid size 356,356,356,
    1385 pixel 0.86, shown at level 4.3, step 1, values float32 
    1386 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #21.7, grid size 356,356,356,
    1387 pixel 0.86, shown at level 4.3, step 1, values float32 
    1388 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #21.8, grid size 356,356,356,
    1389 pixel 0.86, shown at level 4.3, step 1, values float32 
    1390 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #21.9, grid size 356,356,356,
    1391 pixel 0.86, shown at level 4.3, step 1, values float32 
    1392 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #21.10, grid size
    1393 356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32 
    1394 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #21.11, grid size
    1395 356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32 
    1396 Log from Sun Nov 2 19:35:42 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    1397 © 2016-2024 Regents of the University of California. All rights reserved. 
    1398 
    1399 > open C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
    1400 > aligned.cxs
    1401 
    1402 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #1, grid size
    1403 320,320,320, pixel 0.938, shown at level 0.199, step 1, values float32 
    1404 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #2, grid size
    1405 320,320,320, pixel 0.938, shown at level 0.141, step 1, values float32 
    1406 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #3, grid size
    1407 320,320,320, pixel 0.928, shown at level 0.643, step 1, values float32 
    1408 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #5, grid size
    1409 320,320,320, pixel 0.928, shown at level 1.31, step 1, values float32 
    1410 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #6, grid size
    1411 320,320,320, pixel 0.928, shown at level 0.936, step 1, values float32 
    1412 Opened EatA-G12_composite_map.ccp4 as #4, grid size 356,356,356, pixel 0.86,
    1413 shown at level 13.2, step 1, values float32 
    1414 Log from Sun Nov 2 18:27:52 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    1415 © 2016-2024 Regents of the University of California. All rights reserved. 
    1416 
    1417 > open C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-raw-
    1418 > maps.cxs
    1419 
    1420 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #1, grid size
    1421 320,320,320, pixel 0.938, shown at level 0.199, step 1, values float32 
    1422 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #2, grid size
    1423 320,320,320, pixel 0.938, shown at level 0.141, step 1, values float32 
    1424 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #3, grid size
    1425 320,320,320, pixel 0.928, shown at level 0.643, step 1, values float32 
    1426 Opened EatA-G12_cryosparc_P6_J1227_006_volume_map_sharp.mrc as #4, grid size
    1427 352,352,352, pixel 0.86, shown at level 0.0927, step 1, values float32 
    1428 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #5, grid size
    1429 320,320,320, pixel 0.928, shown at level 1.31, step 1, values float32 
    1430 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #6, grid size
    1431 320,320,320, pixel 0.928, shown at level 0.936, step 1, values float32 
    1432 Log from Mon Oct 13 13:12:41 2025 Startup Messages 
    1433 --- 
    1434 note | available bundle cache has not been initialized yet 
    1435  
    1436 UCSF ChimeraX version: 1.8 (2024-06-10) 
    1437 © 2016-2024 Regents of the University of California. All rights reserved. 
    1438 How to cite UCSF ChimeraX 
    1439 
    1440 > open C:/Users/David/Downloads/cryosparc_P18_J419_002_volume_map_sharp.mrc
    1441 > C:/Users/David/Downloads/cryosparc_P18_J417_007_volume_map_sharp.mrc
    1442 
    1443 Opened cryosparc_P18_J419_002_volume_map_sharp.mrc as #1.1, grid size
    1444 320,320,320, pixel 0.928, shown at level 0.237, step 2, values float32 
    1445 Opened cryosparc_P18_J417_007_volume_map_sharp.mrc as #1.2, grid size
    1446 320,320,320, pixel 0.928, shown at level 0.155, step 2, values float32 
    1447 
    1448 > volume #1.2 step 1
    1449 
    1450 > volume #1.1 step 1
    1451 
    1452 > lighting soft
    1453 
    1454 > graphics silhouettes true
    1455 
    1456 > volume #1.2 level 0.2819
    1457 
    1458 > volume #1.1 level 0.6002
    1459 
    1460 > volume #1.2 level 0.2722
    1461 
    1462 > volume #1.2 level 0.4283
    1463 
    1464 > volume #1.2 level 0.4965
    1465 
    1466 > volume #1.2 level 0.516
    1467 
    1468 [Repeated 1 time(s)]
    1469 
    1470 > volume #1.1 level 0.8389
    1471 
    1472 > open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_92/EatA-
    1473 > Fab25_RSR_real_space_refined_092.pdb
    1474 
    1475 Chain information for EatA-Fab25_RSR_real_space_refined_092.pdb #2 
    1476 --- 
    1477 Chain | Description 
    1478 A | No description available 
    1479 B | No description available 
    1480 C | No description available 
    1481  
    1482 
    1483 > select /A:337
    1484 
    1485 7 atoms, 6 bonds, 1 residue, 1 model selected 
    1486 
    1487 > ui mousemode right "rotate selected models"
    1488 
    1489 > view matrix models
    1490 > #2,-0.019575,-0.54161,0.8404,72.703,-0.31976,0.79981,0.508,-15.306,-0.9473,-0.25878,-0.18884,374.61
    1491 
    1492 > view matrix models
    1493 > #2,-0.021078,-0.52928,0.84819,69.83,-0.30047,0.81251,0.49955,-18.318,-0.95356,-0.24432,-0.17616,371.26
    1494 
    1495 > view matrix models
    1496 > #2,-0.43727,-0.47706,0.76237,135.43,-0.29191,0.8771,0.38143,-8.1152,-0.85064,-0.055759,-0.52279,390.47
    1497 
    1498 > ui mousemode right "translate selected models"
    1499 
    1500 > view matrix models
    1501 > #2,-0.43727,-0.47706,0.76237,83.189,-0.29191,0.8771,0.38143,-5.8995,-0.85064,-0.055759,-0.52279,354.74
    1502 
    1503 > ui mousemode right "rotate selected models"
    1504 
    1505 > view matrix models
    1506 > #2,-0.33831,-0.71813,0.60815,130.01,-0.57529,0.66926,0.47025,47.457,-0.7447,-0.19077,-0.63955,379.19
    1507 
    1508 > view matrix models
    1509 > #2,-0.030162,-0.94176,0.33493,165.82,-0.86801,0.19083,0.45841,157.61,-0.49562,-0.27689,-0.82322,388.38
    1510 
    1511 > view matrix models
    1512 > #2,-0.8649,-0.40391,-0.29801,316.37,0.11745,-0.74008,0.66218,115.68,-0.48801,0.53772,0.68753,10.919
    1513 
    1514 > view matrix models
    1515 > #2,0.079061,-0.99665,0.021042,212.71,0.99636,0.078331,-0.033517,-1.4015,0.031757,0.023616,0.99922,-43.345
    1516 
    1517 > view matrix models
    1518 > #2,0.70203,-0.6416,-0.30903,133.1,0.4814,0.74733,-0.45798,49.967,0.52479,0.17275,0.83352,-104.37
    1519 
    1520 > view matrix models
    1521 > #2,-0.072137,-0.84932,0.52293,126.09,-0.45417,-0.43882,-0.77535,402.25,0.88799,-0.29343,-0.35408,116.36
    1522 
    1523 > view matrix models
    1524 > #2,-0.24397,-0.9153,0.32049,194.43,-0.56682,-0.13357,-0.81294,381.57,0.78689,-0.37999,-0.48622,165.54
    1525 
    1526 > view matrix models
    1527 > #2,-0.4587,0.70318,0.54326,-41.767,-0.50135,0.29997,-0.81158,311.26,-0.73365,-0.64464,0.21495,293.33
    1528 
    1529 > view matrix models
    1530 > #2,-0.0796,0.66044,0.74665,-123.9,-0.92844,0.22354,-0.29671,292.33,-0.36286,-0.71683,0.59539,185.8
    1531 
    1532 > view matrix models
    1533 > #2,-0.97691,0.040653,0.20977,181.48,-0.11542,-0.92659,-0.35793,351.21,0.17982,-0.37387,0.90988,7.3657
    1534 
    1535 > ui mousemode right "translate selected models"
    1536 
    1537 > view matrix models
    1538 > #2,-0.97691,0.040653,0.20977,227.65,-0.11542,-0.92659,-0.35793,345.44,0.17982,-0.37387,0.90988,63.812
    1539 
    1540 > view matrix models
    1541 > #2,-0.97691,0.040653,0.20977,250.1,-0.11542,-0.92659,-0.35793,354.72,0.17982,-0.37387,0.90988,38.777
    1542 
    1543 > ui mousemode right "rotate selected models"
    1544 
    1545 > view matrix models
    1546 > #2,-0.9871,-0.15473,0.04117,308.22,0.13002,-0.9247,-0.3578,320.19,0.093432,-0.34783,0.93289,43.18
    1547 
    1548 > ui mousemode right "translate selected models"
    1549 
    1550 > view matrix models
    1551 > #2,-0.9871,-0.15473,0.04117,304.34,0.13002,-0.9247,-0.3578,314.22,0.093432,-0.34783,0.93289,45.843
    1552 
    1553 > view matrix models
    1554 > #2,-0.9871,-0.15473,0.04117,306.57,0.13002,-0.9247,-0.3578,317.84,0.093432,-0.34783,0.93289,55.19
    1555 
    1556 > ui mousemode right "rotate selected models"
    1557 
    1558 > view matrix models
    1559 > #2,-0.99119,-0.13237,0.0042655,310.4,0.12491,-0.94507,-0.30205,311.75,0.044013,-0.29886,0.95328,51.664
    1560 
    1561 > view matrix models
    1562 > #2,-0.98574,-0.16736,-0.017327,318.3,0.16559,-0.94674,-0.27616,301.82,0.029815,-0.2751,0.96095,48.974
    1563 
    1564 > view matrix models
    1565 > #2,-0.99378,-0.11124,0.0044549,307.76,0.10846,-0.97649,-0.1863,298.4,0.025074,-0.18466,0.98248,33.191
    1566 
    1567 > ui mousemode right "translate selected models"
    1568 
    1569 > view matrix models
    1570 > #2,-0.99378,-0.11124,0.0044549,305.58,0.10846,-0.97649,-0.1863,296.07,0.025074,-0.18466,0.98248,30.158
    1571 
    1572 > view matrix models
    1573 > #2,-0.99378,-0.11124,0.0044549,309.28,0.10846,-0.97649,-0.1863,298.31,0.025074,-0.18466,0.98248,28.351
    1574 
    1575 > ui tool show "Fit in Map"
    1576 
    1577 > fitmap #2 inMap #1.2
    1578 
    1579 Fit molecule EatA-Fab25_RSR_real_space_refined_092.pdb (#2) to map
    1580 cryosparc_P18_J417_007_volume_map_sharp.mrc (#1.2) using 5662 atoms 
    1581 average map value = 1.014, steps = 76 
    1582 shifted from previous position = 0.829 
    1583 rotated from previous position = 8.51 degrees 
    1584 atoms outside contour = 979, contour level = 0.51604 
    1585  
    1586 Position of EatA-Fab25_RSR_real_space_refined_092.pdb (#2) relative to
    1587 cryosparc_P18_J417_007_volume_map_sharp.mrc (#1.2) coordinates: 
    1588 Matrix rotation and translation 
    1589 -0.99740771 -0.05876321 -0.04153010 309.91242131 
    1590 0.06885727 -0.94701146 -0.31373233 322.09189835 
    1591 -0.02089356 -0.31577869 0.94860280 59.61845056 
    1592 Axis -0.01582711 -0.15960891 0.98705344 
    1593 Axis point 150.14818166 170.94658144 0.00000000 
    1594 Rotation angle (degrees) 176.29340360 
    1595 Shift along axis 2.53284185 
    1596  
    1597 
    1598 > color #1.1 #b2b2b2b4 models
    1599 
    1600 > color #1.2 #ffffb2b4 models
    1601 
    1602 > select clear
    1603 
    1604 > show atoms
    1605 
    1606 > hide #!1.1 models
    1607 
    1608 > select clear
    1609 
    1610 > hide #!1.2 models
    1611 
    1612 > show #!1.2 models
    1613 
    1614 > volume #1.2 level 0.667
    1615 
    1616 > hide #!1.2 models
    1617 
    1618 > show #!1.2 models
    1619 
    1620 > hide #!1.2 models
    1621 
    1622 > show #!1.2 models
    1623 
    1624 > hide #!1.2 models
    1625 
    1626 > show #!1.2 models
    1627 
    1628 > hide #!1.2 models
    1629 
    1630 > show #!1.2 models
    1631 
    1632 > volume #1.2 color #b2b2b2b4
    1633 
    1634 > hide #!1 models
    1635 
    1636 > show #!1 models
    1637 
    1638 > volume #1.2 level 0.6971
    1639 
    1640 > open "C:/Users/David/Downloads/cryosparc_P18_J326_007_volume_map_sharp
    1641 > (3).mrc"
    1642 
    1643 Opened cryosparc_P18_J326_007_volume_map_sharp (3).mrc as #3, grid size
    1644 270,270,270, pixel 0.928, shown at level 0.253, step 2, values float32 
    1645 
    1646 > volume #3 step 1
    1647 
    1648 > volume #3 level 1.015
    1649 
    1650 > select #3
    1651 
    1652 2 models selected 
    1653 
    1654 > ui mousemode right "rotate selected models"
    1655 
    1656 > view matrix models
    1657 > #3,0.9328,0.14313,0.33076,-50.702,-0.22451,-0.48716,0.84396,107.17,0.28193,-0.8615,-0.42229,249.44
    1658 
    1659 > view matrix models
    1660 > #3,-0.73672,0.66514,-0.12179,164.83,0.31956,0.50119,0.80417,-82.828,0.59592,0.55353,-0.58179,52.47
    1661 
    1662 > view matrix models
    1663 > #3,-0.85158,0.3777,-0.36353,246.42,-0.041624,0.64256,0.76511,-47.182,0.52257,0.66668,-0.53147,41.862
    1664 
    1665 > ui mousemode right "translate selected models"
    1666 
    1667 > view matrix models
    1668 > #3,-0.85158,0.3777,-0.36353,260.25,-0.041624,0.64256,0.76511,-31.711,0.52257,0.66668,-0.53147,92.385
    1669 
    1670 > view matrix models
    1671 > #3,-0.85158,0.3777,-0.36353,258.85,-0.041624,0.64256,0.76511,-34.724,0.52257,0.66668,-0.53147,92.175
    1672 
    1673 > view matrix models
    1674 > #3,-0.85158,0.3777,-0.36353,258.99,-0.041624,0.64256,0.76511,-34.078,0.52257,0.66668,-0.53147,92.512
    1675 
    1676 > view matrix models
    1677 > #3,-0.85158,0.3777,-0.36353,260.01,-0.041624,0.64256,0.76511,-36.373,0.52257,0.66668,-0.53147,95.203
    1678 
    1679 > view matrix models
    1680 > #3,-0.85158,0.3777,-0.36353,259.5,-0.041624,0.64256,0.76511,-35.892,0.52257,0.66668,-0.53147,96.758
    1681 
    1682 > ui mousemode right "rotate selected models"
    1683 
    1684 > view matrix models
    1685 > #3,-0.85226,0.3822,-0.35719,258.23,-0.04208,0.63049,0.77505,-35.598,0.52143,0.67557,-0.52126,94.513
    1686 
    1687 > view matrix models
    1688 > #3,-0.85502,0.39943,-0.33075,253.11,-0.043716,0.58,0.81344,-33.992,0.51675,0.70997,-0.47845,85.449
    1689 
    1690 > view matrix models
    1691 > #3,-0.8535,0.39017,-0.34541,255.91,-0.04286,0.60805,0.79274,-34.956,0.51933,0.69141,-0.50224,90.421
    1692 
    1693 > ui mousemode right "translate selected models"
    1694 
    1695 > view matrix models
    1696 > #3,-0.8535,0.39017,-0.34541,255.05,-0.04286,0.60805,0.79274,-34.577,0.51933,0.69141,-0.50224,88.647
    1697 
    1698 > view matrix models
    1699 > #3,-0.8535,0.39017,-0.34541,255.7,-0.04286,0.60805,0.79274,-33.419,0.51933,0.69141,-0.50224,86.172
    1700 
    1701 > view matrix models
    1702 > #3,-0.8535,0.39017,-0.34541,259.03,-0.04286,0.60805,0.79274,-33.842,0.51933,0.69141,-0.50224,86.791
    1703 
    1704 > ui tool show "Fit in Map"
    1705 
    1706 > fitmap #3 inMap #1.2
    1707 
    1708 Fit map cryosparc_P18_J326_007_volume_map_sharp (3).mrc in map
    1709 cryosparc_P18_J417_007_volume_map_sharp.mrc using 26648 points 
    1710 correlation = 0.9656, correlation about mean = 0.6735, overlap = 4.744e+04 
    1711 steps = 80, shift = 1.01, angle = 8.23 degrees 
    1712  
    1713 Position of cryosparc_P18_J326_007_volume_map_sharp (3).mrc (#3) relative to
    1714 cryosparc_P18_J417_007_volume_map_sharp.mrc (#1.2) coordinates: 
    1715 Matrix rotation and translation 
    1716 -0.77021232 0.47584786 -0.42466666 247.21624069 
    1717 -0.05822245 0.61060460 0.78979249 -32.46293862 
    1718 0.63512448 0.63303304 -0.44259016 72.03942203 
    1719 Axis -0.13095328 -0.88532548 -0.44615023 
    1720 Axis point 115.48414946 0.00000000 89.71757642 
    1721 Rotation angle (degrees) 143.23517250 
    1722 Shift along axis -35.77391606 
    1723  
    1724 
    1725 > select clear
    1726 
    1727 > hide #!2 models
    1728 
    1729 > volume #3 level 0.8347
    1730 
    1731 > volume #3 color #b2ffffb4
    1732 
    1733 > show #!2 models
    1734 
    1735 > volume #3 level 0.7072
    1736 
    1737 > volume #3 color #b2b2b2b4
    1738 
    1739 > select clear
    1740 
    1741 > hide cartoons
    1742 
    1743 > show cartoons
    1744 
    1745 > select clear
    1746 
    1747 > hide cartoons
    1748 
    1749 > close session
    1750 
    1751 [Repeated 1 time(s)]
    1752 
    1753 > open C:/Users/David/Documents/lab/Berndsen/EatA/SepA/FINAL-
    1754 > MAP/cryosparc_P7_J1169_009_volume_map_sharp.mrc
    1755 
    1756 Opened cryosparc_P7_J1169_009_volume_map_sharp.mrc as #1, grid size
    1757 320,320,320, pixel 0.938, shown at level 0.0423, step 2, values float32 
    1758 
    1759 > volume #1 step 1
    1760 
    1761 > volume #1 level 0.1993
    1762 
    1763 > open C:/Users/David/Documents/lab/Berndsen/EatA/Pic/FINAL-
    1764 > MAP/cryosparc_P7_J1193_002_volume_map_sharp.mrc
    1765 
    1766 Opened cryosparc_P7_J1193_002_volume_map_sharp.mrc as #2, grid size
    1767 320,320,320, pixel 0.938, shown at level 0.0447, step 2, values float32 
    1768 
    1769 > volume #2 step 1
    1770 
    1771 > volume #2 level 0.1409
    1772 
    1773 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab25/FINAL-
    1774 > MAP/cryosparc_P18_J417_007_volume_map_sharp.mrc
    1775 
    1776 Opened cryosparc_P18_J417_007_volume_map_sharp.mrc as #3, grid size
    1777 320,320,320, pixel 0.928, shown at level 0.155, step 2, values float32 
    1778 
    1779 > volume #3 step 1
    1780 
    1781 > volume #3 level 0.6429
    1782 
    1783 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/FINAL-
    1784 > MAP/cryosparc_P6_J1227_006_volume_map_sharp.mrc
    1785 
    1786 Opened cryosparc_P6_J1227_006_volume_map_sharp.mrc as #4, grid size
    1787 352,352,352, pixel 0.86, shown at level 0.0202, step 2, values float32 
    1788 
    1789 > volume #4 step 1
    1790 
    1791 > volume #4 level 0.09272
    1792 
    1793 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab15/FINAL-
    1794 > MAP/cryosparc_P7_J1177_008_volume_map_sharp.mrc
    1795 
    1796 Opened cryosparc_P7_J1177_008_volume_map_sharp.mrc as #5, grid size
    1797 320,320,320, pixel 0.928, shown at level 0.165, step 2, values float32 
    1798 
    1799 > volume #5 step 1
    1800 
    1801 > volume #5 level 1.311
    1802 
    1803 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab40/FINAL-
    1804 > MAP/cryosparc_P7_J1175_008_volume_map_sharp.mrc
    1805 
    1806 Opened cryosparc_P7_J1175_008_volume_map_sharp.mrc as #6, grid size
    1807 320,320,320, pixel 0.928, shown at level 0.168, step 2, values float32 
    1808 
    1809 > volume #6 step 1
    1810 
    1811 > volume #6 level 0.9362
    1812 
    1813 > rename #1 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc
    1814 
    1815 > rename #2 Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc
    1816 
    1817 > hide #!3 models
    1818 
    1819 > show #!3 models
    1820 
    1821 > rename #3 EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc
    1822 
    1823 > rename #4 EatA-G12_cryosparc_P6_J1227_006_volume_map_sharp.mrc
    1824 
    1825 > rename #5 EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc
    1826 
    1827 > hide #!5 models
    1828 
    1829 > show #!5 models
    1830 
    1831 > rename #6 EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc
    1832 
    1833 > hide #!6 models
    1834 
    1835 > show #!6 models
    1836 
    1837 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-raw-
    1838 > maps.cxs includeMaps true
    1839 
    1840 ——— End of log from Mon Oct 13 13:12:41 2025 ———
    1841 
    1842 opened ChimeraX session 
    1843 
    1844 > close #4
    1845 
    1846 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
    1847 > FINAL-MAP/composite_map.ccp4
    1848 
    1849 Opened composite_map.ccp4 as #4, grid size 356,356,356, pixel 0.86, shown at
    1850 level 1.85, step 2, values float32 
    1851 
    1852 > volume #4 step 1
    1853 
    1854 > volume #4 level 7.201
    1855 
    1856 > volume #4 level 14.84
    1857 
    1858 > rename #4 EatA-G12_composite_map.ccp4
    1859 
    1860 > ui tool show "Fit in Map"
    1861 
    1862 > fitmap #1 inMap #2
    1863 
    1864 Fit map SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc in map
    1865 Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc using 38477 points 
    1866 correlation = 0.7563, correlation about mean = 0.4494, overlap = 2288 
    1867 steps = 48, shift = 0.052, angle = 0.402 degrees 
    1868  
    1869 Position of SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) relative
    1870 to Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#2) coordinates: 
    1871 Matrix rotation and translation 
    1872 0.99997596 0.00604647 0.00339383 -1.44058630 
    1873 -0.00605023 0.99998110 0.00109714 0.77765819 
    1874 -0.00338713 -0.00111765 0.99999364 0.68143890 
    1875 Axis -0.15771004 0.48285787 -0.86138018 
    1876 Axis point 126.53476647 238.34552229 0.00000000 
    1877 Rotation angle (degrees) 0.40231685 
    1878 Shift along axis 0.01571535 
    1879  
    1880 
    1881 > fitmap #2 inMap #1
    1882 
    1883 Fit map Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc in map
    1884 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 35000 points 
    1885 correlation = 0.7224, correlation about mean = 0.3946, overlap = 2182 
    1886 steps = 68, shift = 0.0409, angle = 0.201 degrees 
    1887  
    1888 Position of Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#2) relative
    1889 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates: 
    1890 Matrix rotation and translation 
    1891 0.99999400 -0.00305879 -0.00162900 0.75443292 
    1892 0.00305792 0.99999518 -0.00053963 -0.38494907 
    1893 0.00163064 0.00053465 0.99999853 -0.33255063 
    1894 Axis 0.15316592 -0.46474703 0.87209541 
    1895 Axis point 125.59920279 246.17520018 0.00000000 
    1896 Rotation angle (degrees) 0.20093109 
    1897 Shift along axis 0.00444147 
    1898  
    1899 
    1900 > fitmap #3 inMap #1
    1901 
    1902 Fit map EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc in map
    1903 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 46267 points 
    1904 correlation = 0.6022, correlation about mean = 0.3508, overlap = 8169 
    1905 steps = 96, shift = 3.11, angle = 1.41 degrees 
    1906  
    1907 Position of EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#3) relative
    1908 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates: 
    1909 Matrix rotation and translation 
    1910 0.99955034 -0.02544878 -0.01585806 8.29018689 
    1911 0.02529220 0.99963011 -0.00999741 -0.21467164 
    1912 0.01610662 0.00959183 0.99982427 -2.08962239 
    1913 Axis 0.31050527 -0.50666621 0.80428591 
    1914 Axis point -7.00301659 313.65462831 0.00000000 
    1915 Rotation angle (degrees) 1.80764502 
    1916 Shift along axis 1.00225977 
    1917  
    1918 
    1919 > fitmap #4 inMap #1
    1920 
    1921 Fit map EatA-G12_composite_map.ccp4 in map
    1922 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 52467 points 
    1923 correlation = 0.3705, correlation about mean = 0.1076, overlap = 9.509e+04 
    1924 steps = 268, shift = 6.78, angle = 4.91 degrees 
    1925  
    1926 Position of EatA-G12_composite_map.ccp4 (#4) relative to
    1927 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates: 
    1928 Matrix rotation and translation 
    1929 0.99745944 -0.02890438 0.06510909 -9.72422277 
    1930 0.02596410 0.99862406 0.04556149 -15.05643761 
    1931 -0.06633643 -0.04375524 0.99683748 13.76545959 
    1932 Axis -0.53125257 0.78183291 0.32635565 
    1933 Axis point 209.57385733 0.00000000 174.77254945 
    1934 Rotation angle (degrees) 4.82211175 
    1935 Shift along axis -2.11316474 
    1936  
    1937 
    1938 > fitmap #5 inMap #1
    1939 
    1940 Fit map EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc in map
    1941 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 43899 points 
    1942 correlation = 0.3094, correlation about mean = 0.04862, overlap = 7279 
    1943 steps = 84, shift = 3.48, angle = 1.65 degrees 
    1944  
    1945 Position of EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#5) relative
    1946 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates: 
    1947 Matrix rotation and translation 
    1948 0.99977862 -0.00827493 0.01934541 -1.34946115 
    1949 0.00863280 0.99979179 -0.01848921 3.19592240 
    1950 -0.01918838 0.01865212 0.99964189 -2.92764885 
    1951 Axis 0.66174115 0.68655052 0.30124247 
    1952 Axis point -160.69088043 0.00000000 82.25789483 
    1953 Rotation angle (degrees) 1.60812158 
    1954 Shift along axis 0.41923605 
    1955  
    1956 
    1957 > fitmap #6 inMap #1
    1958 
    1959 Fit map EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc in map
    1960 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 54987 points 
    1961 correlation = 0.291, correlation about mean = 0.06381, overlap = 7178 
    1962 steps = 96, shift = 4.11, angle = 1.07 degrees 
    1963  
    1964 Position of EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#6) relative
    1965 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates: 
    1966 Matrix rotation and translation 
    1967 0.99997507 -0.00632438 0.00313999 1.25675053 
    1968 0.00638150 0.99980804 -0.01852454 3.99519091 
    1969 -0.00302223 0.01854412 0.99982348 -5.71979696 
    1970 Axis 0.93448813 0.15534766 0.32031085 
    1971 Axis point 0.00000000 309.82806636 212.77029129 
    1972 Rotation angle (degrees) 1.13646017 
    1973 Shift along axis -0.03705102 
    1974  
    1975 
    1976 > select clear
    1977 
    1978 > hide #!6 models
    1979 
    1980 > hide #!5 models
    1981 
    1982 > hide #!4 models
    1983 
    1984 > hide #!3 models
    1985 
    1986 > hide #!2 models
    1987 
    1988 > show #!2 models
    1989 
    1990 > fitmap #2 inMap #1
    1991 
    1992 Fit map Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc in map
    1993 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 35000 points 
    1994 correlation = 0.7223, correlation about mean = 0.3943, overlap = 2183 
    1995 steps = 44, shift = 0.00419, angle = 0.00269 degrees 
    1996  
    1997 Position of Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#2) relative
    1998 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates: 
    1999 Matrix rotation and translation 
    2000 0.99999404 -0.00305035 -0.00161912 0.74963161 
    2001 0.00304955 0.99999523 -0.00049448 -0.39244236 
    2002 0.00162062 0.00048954 0.99999857 -0.32149008 
    2003 Axis 0.14104581 -0.46437327 0.87433606 
    2004 Axis point 128.02436252 245.18440835 0.00000000 
    2005 Rotation angle (degrees) 0.19986541 
    2006 Shift along axis 0.00688177 
    2007  
    2008 
    2009 > hide #!2 models
    2010 
    2011 > show #!3 models
    2012 
    2013 > fitmap #3 inMap #1
    2014 
    2015 Fit map EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc in map
    2016 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 46267 points 
    2017 correlation = 0.6024, correlation about mean = 0.3511, overlap = 8172 
    2018 steps = 48, shift = 0.0156, angle = 0.0113 degrees 
    2019  
    2020 Position of EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#3) relative
    2021 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates: 
    2022 Matrix rotation and translation 
    2023 0.99955105 -0.02535693 -0.01595992 8.30017154 
    2024 0.02519708 0.99963109 -0.01013856 -0.18582137 
    2025 0.01621112 0.00973186 0.99982123 -2.11478903 
    2026 Axis 0.31474924 -0.50959222 0.80078005 
    2027 Axis point -8.51584380 314.90160964 0.00000000 
    2028 Rotation angle (degrees) 1.80886906 
    2029 Shift along axis 1.01368494 
    2030  
    2031 
    2032 > hide #!3 models
    2033 
    2034 > show #!4 models
    2035 
    2036 > fitmap #4 inMap #1
    2037 
    2038 Fit map EatA-G12_composite_map.ccp4 in map
    2039 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 52467 points 
    2040 correlation = 0.3706, correlation about mean = 0.1079, overlap = 9.509e+04 
    2041 steps = 96, shift = 0.0067, angle = 0.0034 degrees 
    2042  
    2043 Position of EatA-G12_composite_map.ccp4 (#4) relative to
    2044 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates: 
    2045 Matrix rotation and translation 
    2046 0.99746191 -0.02892500 0.06506212 -9.71065540 
    2047 0.02598869 0.99862471 0.04553325 -15.06134195 
    2048 -0.06628969 -0.04372680 0.99684183 13.75403731 
    2049 Axis -0.53119534 0.78168752 0.32679679 
    2050 Axis point 209.61127127 0.00000000 174.73954373 
    2051 Rotation angle (degrees) 4.81956456 
    2052 Shift along axis -2.12023295 
    2053  
    2054 
    2055 > volume #4 level 13.17
    2056 
    2057 > show #!5 models
    2058 
    2059 > select #5
    2060 
    2061 2 models selected 
    2062 
    2063 > ui mousemode right "translate selected models"
    2064 
    2065 > view matrix models
    2066 > #5,0.99974,-0.0021662,0.022626,-2.7022,0.0025627,0.99984,-0.017509,5.4864,-0.022584,0.017563,0.99959,2.199
    2067 
    2068 > fitmap #5 inMap #1
    2069 
    2070 Fit map EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc in map
    2071 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 43899 points 
    2072 correlation = 0.8972, correlation about mean = 0.6275, overlap = 3.444e+04 
    2073 steps = 48, shift = 1.28, angle = 1.53 degrees 
    2074  
    2075 Position of EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#5) relative
    2076 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates: 
    2077 Matrix rotation and translation 
    2078 0.99986911 -0.01601629 -0.00228928 4.11609932 
    2079 0.01600506 0.99986019 -0.00484082 0.65293412 
    2080 0.00236649 0.00480354 0.99998566 0.36363740 
    2081 Axis 0.28563422 -0.13788868 0.94836692 
    2082 Axis point -51.09423877 231.90014067 0.00000000 
    2083 Rotation angle (degrees) 0.96733406 
    2084 Shift along axis 1.43052827 
    2085  
    2086 
    2087 > select clear
    2088 
    2089 > show #!6 models
    2090 
    2091 > hide #!5 models
    2092 
    2093 > select #6
    2094 
    2095 2 models selected 
    2096 
    2097 > view matrix models
    2098 > #6,0.99998,-0.00021598,0.0064211,0.52976,0.00032798,0.99985,-0.017446,5.7292,-0.0064164,0.017448,0.99983,-1.093
    2099 
    2100 > fitmap #6 inMap #1
    2101 
    2102 Fit map EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc in map
    2103 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 54987 points 
    2104 correlation = 0.8676, correlation about mean = 0.6394, overlap = 3.227e+04 
    2105 steps = 72, shift = 1.03, angle = 1.97 degrees 
    2106  
    2107 Position of EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#6) relative
    2108 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates: 
    2109 Matrix rotation and translation 
    2110 0.99933723 -0.03628553 -0.00291044 7.24151640 
    2111 0.03627797 0.99933833 -0.00260875 -2.46701340 
    2112 0.00300318 0.00250144 0.99999236 0.47482860 
    2113 Axis 0.07001876 -0.08102718 0.99424945 
    2114 Axis point 68.94514654 196.03591104 0.00000000 
    2115 Rotation angle (degrees) 2.09127880 
    2116 Shift along axis 1.17903522 
    2117  
    2118 
    2119 > select clear
    2120 
    2121 > show #!5 models
    2122 
    2123 > show #!4 models
    2124 
    2125 > show #!3 models
    2126 
    2127 > show #!2 models
    2128 
    2129 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
    2130 > aligned.cxs
    2131 
    2132 ——— End of log from Sun Nov 2 18:27:52 2025 ———
    2133 
    2134 opened ChimeraX session 
    2135 
    2136 > close session
    2137 
    2138 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab25/FINAL-
    2139 > MAP/cryosparc_P18_J417_007_volume_map_sharp.mrc
    2140 
    2141 Opened cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size
    2142 320,320,320, pixel 0.928, shown at level 0.155, step 2, values float32 
    2143 
    2144 > volume #1 step 1
    2145 
    2146 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab15/FINAL-
    2147 > MAP/cryosparc_P7_J1177_008_volume_map_sharp.mrc
    2148 
    2149 Opened cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size
    2150 320,320,320, pixel 0.928, shown at level 0.165, step 2, values float32 
    2151 
    2152 > volume #2 step 1
    2153 
    2154 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab40/FINAL-
    2155 > MAP/cryosparc_P7_J1175_008_volume_map_sharp.mrc
    2156 
    2157 Opened cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size
    2158 320,320,320, pixel 0.928, shown at level 0.168, step 2, values float32 
    2159 
    2160 > volume #3 step 1
    2161 
    2162 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
    2163 > FINAL-MAP/composite_map.ccp4
    2164 
    2165 Opened composite_map.ccp4 as #4, grid size 356,356,356, pixel 0.86, shown at
    2166 level 1.85, step 2, values float32 
    2167 
    2168 > volume #4 step 1
    2169 
    2170 > open C:/Users/David/Documents/lab/Berndsen/EatA/SepA/FINAL-
    2171 > MAP/cryosparc_P7_J1169_009_volume_map_sharp.mrc
    2172 
    2173 Opened cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size
    2174 320,320,320, pixel 0.938, shown at level 0.0423, step 2, values float32 
    2175 
    2176 > volume #5 step 1
    2177 
    2178 > open C:/Users/David/Documents/lab/Berndsen/EatA/Pic/FINAL-
    2179 > MAP/cryosparc_P7_J1193_002_volume_map_sharp.mrc
    2180 
    2181 Opened cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size
    2182 320,320,320, pixel 0.938, shown at level 0.0447, step 2, values float32 
    2183 
    2184 > volume #6 level 0.152
    2185 
    2186 > volume #5 level 0.192
    2187 
    2188 > volume #4 level 5.018
    2189 
    2190 > volume #1 level 0.642
    2191 
    2192 > volume #2 level 1.134
    2193 
    2194 > volume #3 level 1.087
    2195 
    2196 > select clear
    2197 
    2198 > volume #4 level 8.183
    2199 
    2200 > rename #1 EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc
    2201 
    2202 > rename #2 EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc
    2203 
    2204 > rename #3 EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc
    2205 
    2206 > rename #4 EatA-G12_composite_map.ccp4
    2207 
    2208 > rename #5 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc
    2209 
    2210 > rename #6 Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc
    2211 
    2212 > volume #4 level 8.741
    2213 
    2214 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-raw-
    2215 > maps.cxs
    2216 
    2217 > ui tool show "Fit in Map"
    2218 
    2219 > fitmap #1 inMap #5
    2220 
    2221 Fit map EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc in map
    2222 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 46342 points 
    2223 correlation = 0.6022, correlation about mean = 0.3512, overlap = 8173 
    2224 steps = 68, shift = 3.08, angle = 1.81 degrees 
    2225  
    2226 Position of EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#1) relative
    2227 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: 
    2228 Matrix rotation and translation 
    2229 0.99955229 -0.02532125 -0.01593896 8.29155373 
    2230 0.02516068 0.99963143 -0.01019483 -0.16941286 
    2231 0.01619123 0.00978923 0.99982099 -2.12033109 
    2232 Axis 0.31676330 -0.50928889 0.80017863 
    2233 Axis point -9.22114134 314.90629443 0.00000000 
    2234 Rotation angle (degrees) 1.80764730 
    2235 Shift along axis 1.01609639 
    2236  
    2237 
    2238 > fitmap #2 inMap #5
    2239 
    2240 Fit map EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc in map
    2241 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 50274 points 
    2242 correlation = 0.3046, correlation about mean = 0.05393, overlap = 7630 
    2243 steps = 84, shift = 3.5, angle = 1.54 degrees 
    2244  
    2245 Position of EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) relative
    2246 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: 
    2247 Matrix rotation and translation 
    2248 0.99982218 -0.00815206 0.01700469 -0.97420968 
    2249 0.00847568 0.99978267 -0.01904684 3.32784959 
    2250 -0.01684572 0.01918758 0.99967398 -3.35959410 
    2251 Axis 0.71193720 0.63030531 0.30961367 
    2252 Axis point 0.00000000 183.69110924 160.58390930 
    2253 Rotation angle (degrees) 1.53871345 
    2254 Shift along axis 0.36380889 
    2255  
    2256 
    2257 > fitmap #3 inMap #5
    2258 
    2259 Fit map EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc in map
    2260 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 48158 points 
    2261 correlation = 0.2946, correlation about mean = 0.05986, overlap = 6894 
    2262 steps = 80, shift = 4.1, angle = 1.2 degrees 
    2263  
    2264 Position of EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) relative
    2265 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: 
    2266 Matrix rotation and translation 
    2267 0.99997220 -0.00682084 0.00301169 1.34581291 
    2268 0.00687870 0.99978347 -0.01963912 4.10354957 
    2269 -0.00287708 0.01965929 0.99980260 -5.91301424 
    2270 Axis 0.93495579 0.14010092 0.32592854 
    2271 Axis point 0.00000000 301.28710637 206.29677885 
    2272 Rotation angle (degrees) 1.20422719 
    2273 Shift along axis -0.09403343 
    2274  
    2275 
    2276 > fitmap #4 inMap #5
    2277 
    2278 Fit map EatA-G12_composite_map.ccp4 in map
    2279 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 103755 points 
    2280 correlation = 0.3318, correlation about mean = 0.1473, overlap = 1.142e+05 
    2281 steps = 204, shift = 6.57, angle = 4.69 degrees 
    2282  
    2283 Position of EatA-G12_composite_map.ccp4 (#4) relative to
    2284 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: 
    2285 Matrix rotation and translation 
    2286 0.99764605 -0.02749463 0.06282048 -9.63487758 
    2287 0.02466391 0.99866437 0.04540010 -14.80531015 
    2288 -0.06398483 -0.04374383 0.99699168 13.34581636 
    2289 Axis -0.54507513 0.77535752 0.31892603 
    2290 Axis point 210.01867957 0.00000000 178.34606723 
    2291 Rotation angle (degrees) 4.69043631 
    2292 Shift along axis -1.97134816 
    2293  
    2294 
    2295 > fitmap #6 inMap #5
    2296 
    2297 Fit map Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc in map
    2298 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 3945 points 
    2299 correlation = 0.7433, correlation about mean = 0.3789, overlap = 272.3 
    2300 steps = 64, shift = 0.0759, angle = 0.155 degrees 
    2301  
    2302 Position of Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#6) relative
    2303 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: 
    2304 Matrix rotation and translation 
    2305 0.99999678 -0.00253741 -0.00000990 0.40619973 
    2306 0.00253740 0.99999636 -0.00091286 -0.26745975 
    2307 0.00001222 0.00091283 0.99999958 -0.17040278 
    2308 Axis 0.33851358 -0.00410176 0.94095257 
    2309 Axis point 105.67562579 162.85077747 0.00000000 
    2310 Rotation angle (degrees) 0.15450578 
    2311 Shift along axis -0.02173976 
    2312  
    2313 
    2314 > hide #!2 models
    2315 
    2316 > hide #!3 models
    2317 
    2318 > hide #!1 models
    2319 
    2320 > hide #!6 models
    2321 
    2322 > hide #!4 models
    2323 
    2324 > show #!1 models
    2325 
    2326 > fitmap #1 inMap #5
    2327 
    2328 Fit map EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc in map
    2329 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 46342 points 
    2330 correlation = 0.602, correlation about mean = 0.3509, overlap = 8170 
    2331 steps = 44, shift = 0.0169, angle = 0.00885 degrees 
    2332  
    2333 Position of EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#1) relative
    2334 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: 
    2335 Matrix rotation and translation 
    2336 0.99955149 -0.02539753 -0.01586795 8.28316091 
    2337 0.02523949 0.99963059 -0.01008202 -0.19102707 
    2338 0.01611814 0.00967700 0.99982326 -2.10511374 
    2339 Axis 0.31329444 -0.50716422 0.80288919 
    2340 Axis point -7.96659367 313.92350093 0.00000000 
    2341 Rotation angle (degrees) 1.80707931 
    2342 Shift along axis 1.00177732 
    2343  
    2344 
    2345 > hide #!1 models
    2346 
    2347 > show #!2 models
    2348 
    2349 > select clear
    2350 
    2351 > select #2
    2352 
    2353 2 models selected 
    2354 
    2355 > view matrix models
    2356 > #2,0.99982,-0.0081521,0.017005,-0.93057,0.0084757,0.99978,-0.019047,4.3701,-0.016846,0.019188,0.99967,1.3882
    2357 
    2358 > fitmap #2 inMap #5
    2359 
    2360 Fit map EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc in map
    2361 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 50274 points 
    2362 correlation = 0.8911, correlation about mean = 0.6462, overlap = 3.537e+04 
    2363 steps = 52, shift = 1.05, angle = 1.45 degrees 
    2364  
    2365 Position of EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) relative
    2366 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: 
    2367 Matrix rotation and translation 
    2368 0.99986813 -0.01607165 -0.00233017 4.13572149 
    2369 0.01606034 0.99985953 -0.00479402 0.64189318 
    2370 0.00240689 0.00475597 0.99998579 0.36476558 
    2371 Axis 0.28209163 -0.13992537 0.94912865 
    2372 Axis point -50.33000827 232.76575210 0.00000000 
    2373 Rotation angle (degrees) 0.96989764 
    2374 Shift along axis 1.42304475 
    2375  
    2376 
    2377 > select clear
    2378 
    2379 > show #!3 models
    2380 
    2381 > hide #!2 models
    2382 
    2383 > select #3
    2384 
    2385 2 models selected 
    2386 
    2387 > view matrix models
    2388 > #3,0.99997,-0.0068208,0.0030117,1.6929,0.0068787,0.99978,-0.019639,5.2445,-0.0028771,0.019659,0.9998,-1.9579
    2389 
    2390 > view matrix models
    2391 > #3,0.99997,-0.0068208,0.0030117,2.2648,0.0068787,0.99978,-0.019639,4.6546,-0.0028771,0.019659,0.9998,-1.9045
    2392 
    2393 > fitmap #3 inMap #5
    2394 
    2395 Fit map EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc in map
    2396 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 48158 points 
    2397 correlation = 0.8748, correlation about mean = 0.6251, overlap = 3.162e+04 
    2398 steps = 68, shift = 0.862, angle = 1.97 degrees 
    2399  
    2400 Position of EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) relative
    2401 to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: 
    2402 Matrix rotation and translation 
    2403 0.99933904 -0.03624170 -0.00283274 7.22320571 
    2404 0.03623384 0.99933948 -0.00277662 -2.42208705 
    2405 0.00293150 0.00267214 0.99999213 0.46175203 
    2406 Axis 0.07473445 -0.07906158 0.99406440 
    2407 Axis point 67.81464889 195.61513332 0.00000000 
    2408 Rotation angle (degrees) 2.08913166 
    2409 Shift along axis 1.19032756 
    2410  
    2411 
    2412 > select clear
    2413 
    2414 > hide #!3 models
    2415 
    2416 > show #!4 models
    2417 
    2418 > hide #!4 models
    2419 
    2420 > show #!6 models
    2421 
    2422 > show #!4 models
    2423 
    2424 > show #!3 models
    2425 
    2426 > show #!2 models
    2427 
    2428 > show #!1 models
    2429 
    2430 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
    2431 > aligned.cxs
    2432 
    2433 > volume #2 color #b2b2b2
    2434 
    2435 > volume #3 color #b2b2b2
    2436 
    2437 > volume #4 color #b2b2b2
    2438 
    2439 > volume #5 color #b2b2b2
    2440 
    2441 > volume #6 color #b2b2b2
    2442 
    2443 > select clear
    2444 
    2445 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
    2446 > aligned.cxs
    2447 
    2448 > open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_207/EatA-
    2449 > Fab25_RSR_real_space_refined_207.pdb
    2450 
    2451 Chain information for EatA-Fab25_RSR_real_space_refined_207.pdb #7 
    2452 --- 
    2453 Chain | Description 
    2454 A | No description available 
    2455 B | No description available 
    2456 C | No description available 
    2457  
    2458 
    2459 > fitmap #7 inMap #1
    2460 
    2461 Fit molecule EatA-Fab25_RSR_real_space_refined_207.pdb (#7) to map
    2462 EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#1) using 5662 atoms 
    2463 average map value = 1.043, steps = 76 
    2464 shifted from previous position = 3.03 
    2465 rotated from previous position = 1.83 degrees 
    2466 atoms outside contour = 1292, contour level = 0.642 
    2467  
    2468 Position of EatA-Fab25_RSR_real_space_refined_207.pdb (#7) relative to
    2469 EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#1) coordinates: 
    2470 Matrix rotation and translation 
    2471 0.99999987 -0.00006130 -0.00050676 0.09488947 
    2472 0.00006108 0.99999991 -0.00041961 0.05351513 
    2473 0.00050679 0.00041958 0.99999978 -0.13179049 
    2474 Axis 0.63500256 -0.76693948 0.09260449 
    2475 Axis point 261.40774809 0.00000000 178.39845521 
    2476 Rotation angle (degrees) 0.03785960 
    2477 Shift along axis 0.00700779 
    2478  
    2479 
    2480 > open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_204/EatA-
    2481 > Fab15_RSR_real_space_refined_204.pdb
    2482 
    2483 Chain information for EatA-Fab15_RSR_real_space_refined_204.pdb #8 
    2484 --- 
    2485 Chain | Description 
    2486 A | No description available 
    2487 B | No description available 
    2488 C | No description available 
    2489  
    2490 
    2491 > fitmap #8 inMap #2
    2492 
    2493 Fit molecule EatA-Fab15_RSR_real_space_refined_204.pdb (#8) to map
    2494 EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) using 9396 atoms 
    2495 average map value = 0.344, steps = 64 
    2496 shifted from previous position = 3.35 
    2497 rotated from previous position = 0.828 degrees 
    2498 atoms outside contour = 7515, contour level = 1.134 
    2499  
    2500 Position of EatA-Fab15_RSR_real_space_refined_204.pdb (#8) relative to
    2501 EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) coordinates: 
    2502 Matrix rotation and translation 
    2503 0.99965040 0.02151330 0.01537039 -6.45417615 
    2504 -0.02153677 0.99976713 0.00136347 2.17299353 
    2505 -0.01533748 -0.00169402 0.99988094 -1.87229403 
    2506 Axis -0.05772305 0.57974166 -0.81275313 
    2507 Axis point 12.83952609 291.75461937 0.00000000 
    2508 Rotation angle (degrees) 1.51760461 
    2509 Shift along axis 3.15404245 
    2510  
    2511 
    2512 > fitmap #8 inMap #2
    2513 
    2514 Fit molecule EatA-Fab15_RSR_real_space_refined_204.pdb (#8) to map
    2515 EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) using 9396 atoms 
    2516 average map value = 0.3443, steps = 28 
    2517 shifted from previous position = 0.0234 
    2518 rotated from previous position = 0.0268 degrees 
    2519 atoms outside contour = 7516, contour level = 1.134 
    2520  
    2521 Position of EatA-Fab15_RSR_real_space_refined_204.pdb (#8) relative to
    2522 EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) coordinates: 
    2523 Matrix rotation and translation 
    2524 0.99965171 0.02145081 0.01537268 -6.44056543 
    2525 -0.02148140 0.99976758 0.00182777 2.09728694 
    2526 -0.01532990 -0.00215736 0.99988016 -1.78470343 
    2527 Axis -0.07528901 0.58004774 -0.81109567 
    2528 Axis point 9.47181145 289.34943309 0.00000000 
    2529 Rotation angle (degrees) 1.51654235 
    2530 Shift along axis 3.14899554 
    2531  
    2532 
    2533 > select #8/A:94
    2534 
    2535 12 atoms, 12 bonds, 1 residue, 1 model selected 
    2536 
    2537 > ui mousemode right "translate selected models"
    2538 
    2539 > view matrix models
    2540 > #8,0.9999,0.0053851,0.013011,-1.2078,-0.0053501,0.99998,-0.002719,2.9631,-0.013026,0.0026492,0.99991,3.3856
    2541 
    2542 > fitmap #8 inMap #2
    2543 
    2544 Fit molecule EatA-Fab15_RSR_real_space_refined_204.pdb (#8) to map
    2545 EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) using 9396 atoms 
    2546 average map value = 2.206, steps = 52 
    2547 shifted from previous position = 0.673 
    2548 rotated from previous position = 1.52 degrees 
    2549 atoms outside contour = 2103, contour level = 1.134 
    2550  
    2551 Position of EatA-Fab15_RSR_real_space_refined_204.pdb (#8) relative to
    2552 EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) coordinates: 
    2553 Matrix rotation and translation 
    2554 1.00000000 -0.00005009 -0.00002785 0.01579925 
    2555 0.00005009 0.99999999 -0.00012423 0.02160747 
    2556 0.00002786 0.00012422 0.99999999 -0.02398416 
    2557 Axis 0.90800904 -0.20361929 0.36614035 
    2558 Axis point 0.00000000 196.51454959 175.83117461 
    2559 Rotation angle (degrees) 0.00783869 
    2560 Shift along axis 0.00116460 
    2561  
    2562 
    2563 > select clear
    2564 
    2565 > hide #!6 models
    2566 
    2567 > hide #!5 models
    2568 
    2569 > hide #!4 models
    2570 
    2571 > hide #!3 models
    2572 
    2573 > hide #!2 models
    2574 
    2575 > hide #!8 models
    2576 
    2577 > show #!8 models
    2578 
    2579 > hide #!1 models
    2580 
    2581 > show #!2 models
    2582 
    2583 > hide #!7 models
    2584 
    2585 > hide #!8 models
    2586 
    2587 > hide #!2 models
    2588 
    2589 > show #!3 models
    2590 
    2591 > open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_206/EatA-
    2592 > Fab40_RSR_real_space_refined_206.pdb
    2593 
    2594 Chain information for EatA-Fab40_RSR_real_space_refined_206.pdb #9 
    2595 --- 
    2596 Chain | Description 
    2597 A | No description available 
    2598 B | No description available 
    2599 C | No description available 
    2600  
    2601 
    2602 > fitmap #9 inMap #3
    2603 
    2604 Fit molecule EatA-Fab40_RSR_real_space_refined_206.pdb (#9) to map
    2605 EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) using 8896 atoms 
    2606 average map value = 0.4983, steps = 96 
    2607 shifted from previous position = 3.9 
    2608 rotated from previous position = 1.53 degrees 
    2609 atoms outside contour = 6723, contour level = 1.087 
    2610  
    2611 Position of EatA-Fab40_RSR_real_space_refined_206.pdb (#9) relative to
    2612 EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) coordinates: 
    2613 Matrix rotation and translation 
    2614 0.99930604 0.03206320 -0.01895747 -1.18226441 
    2615 -0.03173743 0.99934750 0.01724283 -2.74417853 
    2616 0.01949796 -0.01662920 0.99967160 0.50386631 
    2617 Axis -0.41391611 -0.46992513 -0.77964339 
    2618 Axis point -66.30254517 17.54447497 0.00000000 
    2619 Rotation angle (degrees) 2.34500008 
    2620 Shift along axis 1.38608071 
    2621  
    2622 
    2623 > select clear
    2624 
    2625 > undo
    2626 
    2627 [Repeated 1 time(s)]
    2628 
    2629 > select #9/B:72
    2630 
    2631 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2632 
    2633 > view matrix models
    2634 > #9,0.99974,-0.0041289,-0.022402,1.7094,0.0044381,0.9999,0.013769,-0.80714,0.022342,-0.013865,0.99965,0.23036
    2635 
    2636 > view matrix models
    2637 > #9,0.99974,-0.0041289,-0.022402,4.6226,0.0044381,0.9999,0.013769,-0.17225,0.022342,-0.013865,0.99965,-0.15439
    2638 
    2639 > fitmap #9 inMap #3
    2640 
    2641 Fit molecule EatA-Fab40_RSR_real_space_refined_206.pdb (#9) to map
    2642 EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) using 8896 atoms 
    2643 average map value = 2.132, steps = 56 
    2644 shifted from previous position = 0.892 
    2645 rotated from previous position = 2.34 degrees 
    2646 atoms outside contour = 1993, contour level = 1.087 
    2647  
    2648 Position of EatA-Fab40_RSR_real_space_refined_206.pdb (#9) relative to
    2649 EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) coordinates: 
    2650 Matrix rotation and translation 
    2651 1.00000000 0.00005262 -0.00007010 0.00210688 
    2652 -0.00005261 0.99999999 0.00008658 -0.01656140 
    2653 0.00007011 -0.00008658 0.99999999 -0.00421317 
    2654 Axis -0.70273045 -0.56902882 -0.42705517 
    2655 Axis point 0.00000000 -0.61595131 127.25149200 
    2656 Rotation angle (degrees) 0.00705908 
    2657 Shift along axis 0.00974260 
    2658  
    2659 
    2660 > select clear
    2661 
    2662 > hide #!9 models
    2663 
    2664 > hide #!3 models
    2665 
    2666 > show #!4 models
    2667 
    2668 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
    2669 > FINAL-MAP/composite_map.pdb
    2670 
    2671 Summary of feedback from opening
    2672 C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-FINAL-
    2673 MAP/composite_map.pdb 
    2674 --- 
    2675 warning | Ignored bad PDB record found on line 10676 
    2676  
    2677 Chain information for composite_map.pdb #10 
    2678 --- 
    2679 Chain | Description 
    2680 A | No description available 
    2681 B | No description available 
    2682 C | No description available 
    2683  
    2684 
    2685 > select #10/A:686
    2686 
    2687 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2688 
    2689 > view matrix models #10,1,0,0,-0.035837,0,1,0,-2.5596,0,0,1,-3.415
    2690 
    2691 > ui mousemode right "rotate selected models"
    2692 
    2693 > view matrix models
    2694 > #10,0.99996,-0.0058184,-0.0074329,1.8538,0.0062096,0.99854,0.053736,-11.465,0.0071093,-0.05378,0.99853,2.7087
    2695 
    2696 > fitmap #10 inMap #4
    2697 
    2698 Fit molecule composite_map.pdb (#10) to map EatA-G12_composite_map.ccp4 (#4)
    2699 using 10667 atoms 
    2700 average map value = 12.24, steps = 96 
    2701 shifted from previous position = 4.09 
    2702 rotated from previous position = 4.57 degrees 
    2703 atoms outside contour = 4611, contour level = 8.741 
    2704  
    2705 Position of composite_map.pdb (#10) relative to EatA-G12_composite_map.ccp4
    2706 (#4) coordinates: 
    2707 Matrix rotation and translation 
    2708 0.99998495 -0.00175123 0.00519942 -0.64123615 
    2709 0.00175732 0.99999777 -0.00116770 -0.07419770 
    2710 -0.00519737 0.00117682 0.99998580 0.55464115 
    2711 Axis 0.20894897 0.92658767 0.31269094 
    2712 Axis point 108.14433051 0.00000000 122.46368821 
    2713 Rotation angle (degrees) 0.32144573 
    2714 Shift along axis -0.02930504 
    2715  
    2716 
    2717 > select clear
    2718 
    2719 > rename #10 EatA-G12_composite_map.pdb
    2720 
    2721 > rename #10 EatA-G12_composite.pdb
    2722 
    2723 > rename #10 EatA-G12_composite_model.pdb
    2724 
    2725 > hide #10 models
    2726 
    2727 > hide #!4 models
    2728 
    2729 > show #!5 models
    2730 
    2731 > open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_208/SepA-
    2732 > Fab40_RSR_real_space_refined_208.pdb
    2733 
    2734 Chain information for SepA-Fab40_RSR_real_space_refined_208.pdb #11 
    2735 --- 
    2736 Chain | Description 
    2737 A | No description available 
    2738 B | No description available 
    2739 C | No description available 
    2740  
    2741 
    2742 > fitmap #11 inMap #5
    2743 
    2744 Fit molecule SepA-Fab40_RSR_real_space_refined_208.pdb (#11) to map
    2745 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) using 9015 atoms 
    2746 average map value = 0.3748, steps = 44 
    2747 shifted from previous position = 0.0123 
    2748 rotated from previous position = 0.0204 degrees 
    2749 atoms outside contour = 1854, contour level = 0.192 
    2750  
    2751 Position of SepA-Fab40_RSR_real_space_refined_208.pdb (#11) relative to
    2752 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: 
    2753 Matrix rotation and translation 
    2754 0.99999995 -0.00029906 -0.00012303 0.05700002 
    2755 0.00029904 0.99999994 -0.00014720 -0.01810641 
    2756 0.00012307 0.00014716 0.99999998 -0.04998960 
    2757 Axis 0.41425820 -0.34632527 0.84169410 
    2758 Axis point 74.70753495 207.47484727 0.00000000 
    2759 Rotation angle (degrees) 0.02035684 
    2760 Shift along axis -0.01219252 
    2761  
    2762 
    2763 > select clear
    2764 
    2765 > hide #!5 models
    2766 
    2767 > hide #!11 models
    2768 
    2769 > show #!6 models
    2770 
    2771 > volume #6 step 1
    2772 
    2773 > show #!5 models
    2774 
    2775 > hide #!5 models
    2776 
    2777 > show #!5 models
    2778 
    2779 > hide #!5 models
    2780 
    2781 > show #!5 models
    2782 
    2783 > hide #!5 models
    2784 
    2785 > show #!5 models
    2786 
    2787 > hide #!5 models
    2788 
    2789 > show #!5 models
    2790 
    2791 > hide #!5 models
    2792 
    2793 > hide #!6 models
    2794 
    2795 > show #!6 models
    2796 
    2797 > open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_199/Pic-
    2798 > Fab40_RSR_real_space_refined_199.pdb
    2799 
    2800 Chain information for Pic-Fab40_RSR_real_space_refined_199.pdb #12 
    2801 --- 
    2802 Chain | Description 
    2803 A | No description available 
    2804 B | No description available 
    2805 C | No description available 
    2806  
    2807 
    2808 > select clear
    2809 
    2810 > fitmap #12 inMap #6
    2811 
    2812 Fit molecule Pic-Fab40_RSR_real_space_refined_199.pdb (#12) to map
    2813 Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#6) using 8204 atoms 
    2814 average map value = 0.1913, steps = 56 
    2815 shifted from previous position = 0.0802 
    2816 rotated from previous position = 0.146 degrees 
    2817 atoms outside contour = 3282, contour level = 0.152 
    2818  
    2819 Position of Pic-Fab40_RSR_real_space_refined_199.pdb (#12) relative to
    2820 Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#6) coordinates: 
    2821 Matrix rotation and translation 
    2822 0.99999997 0.00022320 0.00014008 -0.04271191 
    2823 -0.00022318 0.99999996 -0.00015177 0.05494657 
    2824 -0.00014012 0.00015174 0.99999998 0.00566468 
    2825 Axis 0.49903799 0.46072299 -0.73395872 
    2826 Axis point 246.49551600 191.04967817 0.00000000 
    2827 Rotation angle (degrees) 0.01742292 
    2828 Shift along axis -0.00015736 
    2829  
    2830 
    2831 > select clear
    2832 
    2833 > volume gaussian #4 sDev 1
    2834 
    2835 Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356,
    2836 pixel 0.86, shown at step 1, values float32 
    2837 
    2838 > volume #13 level 5.614
    2839 
    2840 > volume #13 color #b2b2b2
    2841 
    2842 > select clear
    2843 
    2844 > volume gaussian #6 sDev 1
    2845 
    2846 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14,
    2847 grid size 320,320,320, pixel 0.938, shown at step 1, values float32 
    2848 
    2849 > volume #14 level 0.04989
    2850 
    2851 > hide #!13 models
    2852 
    2853 > hide #!12 models
    2854 
    2855 > color #14 #b2b2b2ff models
    2856 
    2857 > color #12 #b2b2b2ff
    2858 
    2859 > select clear
    2860 
    2861 > show #!12 models
    2862 
    2863 > hide #!12 models
    2864 
    2865 > show #!12 models
    2866 
    2867 > hide #!12 models
    2868 
    2869 > show #!13 models
    2870 
    2871 > hide #!14 models
    2872 
    2873 > show #!1 models
    2874 
    2875 > show #!2 models
    2876 
    2877 > show #!3 models
    2878 
    2879 > show #!4 models
    2880 
    2881 > hide #!4 models
    2882 
    2883 > show #!5 models
    2884 
    2885 > show #!14 models
    2886 
    2887 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
    2888 > aligned.cxs
    2889 
    2890 > show #!12 models
    2891 
    2892 > show #!11 models
    2893 
    2894 > show #10 models
    2895 
    2896 > hide #!13 models
    2897 
    2898 > hide #!14 models
    2899 
    2900 > hide #!5 models
    2901 
    2902 > hide #!3 models
    2903 
    2904 > hide #!2 models
    2905 
    2906 > hide #!1 models
    2907 
    2908 > show #!9 models
    2909 
    2910 > show #!8 models
    2911 
    2912 > show #!7 models
    2913 
    2914 > show #!6 models
    2915 
    2916 > show #!5 models
    2917 
    2918 > hide #!5 models
    2919 
    2920 > hide #!6 models
    2921 
    2922 > select #7,8,9,10,11,12/A:
    2923 
    2924 Expected an objects specifier or a keyword 
    2925 
    2926 > select #7,8,9,10,11,12/A
    2927 
    2928 35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected 
    2929 
    2930 > select #7,8,9,10,11,12
    2931 
    2932 51840 atoms, 52845 bonds, 76 pseudobonds, 7081 residues, 11 models selected 
    2933 
    2934 > color (#10#!7-9,11-12 & sel) byhetero
    2935 
    2936 > color (#10#!7-9,11-12 & sel) #aaffffff
    2937 
    2938 > color (#10#!7-9,11-12 & sel) #ffffffff
    2939 
    2940 > select clear
    2941 
    2942 > select #7,8,9,10,11/A
    2943 
    2944 29785 atoms, 30287 bonds, 35 pseudobonds, 4052 residues, 9 models selected 
    2945 
    2946 > select #7,8,9,10,11/A:1-256
    2947 
    2948 9364 atoms, 9570 bonds, 9 pseudobonds, 1267 residues, 8 models selected 
    2949 
    2950 > color (#10#!7-9,11 & sel) cornflower blue
    2951 
    2952 > select clear
    2953 
    2954 > select #7,8,9,10,11/A:78,106,211
    2955 
    2956 117 atoms, 107 bonds, 15 residues, 5 models selected 
    2957 
    2958 > color sel magenta
    2959 
    2960 > select clear
    2961 
    2962 > select #7,8,9,10,11/A:481-560
    2963 
    2964 474 atoms, 467 bonds, 2 pseudobonds, 90 residues, 7 models selected 
    2965 
    2966 > ui tool show "Color Actions"
    2967 
    2968 > color sel gold
    2969 
    2970 > select clear
    2971 
    2972 > select #7,8,9,10,11/A:611-629
    2973 
    2974 707 atoms, 727 bonds, 95 residues, 5 models selected 
    2975 
    2976 > color sel #7dcdd2ff
    2977 
    2978 > select clear
    2979 
    2980 > select #7,8,9,10,11/A:669-699
    2981 
    2982 1047 atoms, 1047 bonds, 155 residues, 5 models selected 
    2983 
    2984 > color sel #ff0000ff
    2985 
    2986 > select clear
    2987 
    2988 > select #7,8,9,10,11/A:781-794
    2989 
    2990 284 atoms, 292 bonds, 3 pseudobonds, 38 residues, 7 models selected 
    2991 
    2992 > color (#10#!8-9,11 & sel) #778899ff
    2993 
    2994 > select clear
    2995 
    2996 > select #7,8,9,10,11/A:834-856
    2997 
    2998 304 atoms, 304 bonds, 2 pseudobonds, 40 residues, 6 models selected 
    2999 
    3000 > color (#10#!8-9,11 & sel) #ff69b4ff
    3001 
    3002 > select clear
    3003 
    3004 > select #12
    3005 
    3006 8204 atoms, 8370 bonds, 23 pseudobonds, 1192 residues, 2 models selected 
    3007 
    3008 > select #12/A
    3009 
    3010 5739 atoms, 5840 bonds, 14 pseudobonds, 828 residues, 2 models selected 
    3011 
    3012 > select #12/A:1-251
    3013 
    3014 1250 atoms, 1276 bonds, 5 pseudobonds, 178 residues, 2 models selected 
    3015 
    3016 > hide #!7 models
    3017 
    3018 > hide #!8 models
    3019 
    3020 > hide #!9 models
    3021 
    3022 > hide #10 models
    3023 
    3024 > hide #!11 models
    3025 
    3026 > show #!11 models
    3027 
    3028 > select #12/A:1-313
    3029 
    3030 1657 atoms, 1694 bonds, 5 pseudobonds, 240 residues, 2 models selected 
    3031 
    3032 > select #12/A:1-251
    3033 
    3034 1250 atoms, 1276 bonds, 5 pseudobonds, 178 residues, 2 models selected 
    3035 
    3036 > color (#!12 & sel) cornflower blue
    3037 
    3038 > select clear
    3039 
    3040 > select #12/A:72,100,203
    3041 
    3042 15 atoms, 12 bonds, 3 residues, 1 model selected 
    3043 
    3044 > color sel magenta
    3045 
    3046 > select clear
    3047 
    3048 > select #12/A:538-618
    3049 
    3050 409 atoms, 419 bonds, 57 residues, 1 model selected 
    3051 
    3052 > select clear
    3053 
    3054 [Repeated 1 time(s)]
    3055 
    3056 > select #12/A:611-633
    3057 
    3058 148 atoms, 152 bonds, 1 pseudobond, 20 residues, 2 models selected 
    3059 
    3060 > color (#!12 & sel) #7dcdd2ff
    3061 
    3062 > select #12/A:672-702
    3063 
    3064 221 atoms, 224 bonds, 31 residues, 1 model selected 
    3065 
    3066 > color sel #ff0000ff
    3067 
    3068 > select #12/A:785-797
    3069 
    3070 69 atoms, 70 bonds, 1 pseudobond, 11 residues, 2 models selected 
    3071 
    3072 > color (#!12 & sel) #778899ff
    3073 
    3074 > select #12/A:838-863
    3075 
    3076 101 atoms, 101 bonds, 1 pseudobond, 17 residues, 2 models selected 
    3077 
    3078 > color (#!12 & sel) #ff69b4ff
    3079 
    3080 > select clear
    3081 
    3082 > show #10 models
    3083 
    3084 > show #!9 models
    3085 
    3086 > show #!8 models
    3087 
    3088 > show #!7 models
    3089 
    3090 > select #7/B
    3091 
    3092 803 atoms, 824 bonds, 2 pseudobonds, 117 residues, 2 models selected 
    3093 
    3094 > color (#!7 & sel) #663399ff
    3095 
    3096 > select clear
    3097 
    3098 > select #7/C
    3099 
    3100 700 atoms, 716 bonds, 1 pseudobond, 104 residues, 2 models selected 
    3101 
    3102 > color (#!7 & sel) #55ffffff
    3103 
    3104 > color (#!7 & sel) #663399ff
    3105 
    3106 > color (#!7 & sel) #643399ff
    3107 
    3108 > color (#!7 & sel) #633399ff
    3109 
    3110 > color (#!7 & sel) #613399ff
    3111 
    3112 > color (#!7 & sel) #5f3399ff
    3113 
    3114 > color (#!7 & sel) #5d3399ff
    3115 
    3116 > color (#!7 & sel) #5c3399ff
    3117 
    3118 > color (#!7 & sel) #5a3399ff
    3119 
    3120 > color (#!7 & sel) #583399ff
    3121 
    3122 > color (#!7 & sel) #993633ff
    3123 
    3124 > color (#!7 & sel) #995533ff
    3125 
    3126 > color (#!7 & sel) #337799ff
    3127 
    3128 > color (#!7 & sel) #663399ff
    3129 
    3130 > color (#!7 & sel) #663499ff
    3131 
    3132 > color (#!7 & sel) #673499ff
    3133 
    3134 > color (#!7 & sel) #673599ff
    3135 
    3136 > color (#!7 & sel) #999899ff
    3137 
    3138 > color (#!7 & sel) #969399ff
    3139 
    3140 > color (#!7 & sel) #7b5d99ff
    3141 
    3142 > color (#!7 & sel) #010101ff
    3143 
    3144 > color (#!7 & sel) #08060aff
    3145 
    3146 > color (#!7 & sel) #503d64ff
    3147 
    3148 > color (#!7 & sel) #513d65ff
    3149 
    3150 > color (#!7 & sel) #010101ff
    3151 
    3152 > color (#!7 & sel) #0c090fff
    3153 
    3154 > color (#!7 & sel) #7b5d99ff
    3155 
    3156 > ui tool show "Color Zone"
    3157 
    3158 > show #!1 models
    3159 
    3160 Need to color zone map before it can be split 
    3161 
    3162 > color zone #1 near #7 distance 5.57
    3163 
    3164 > volume splitbyzone #1
    3165 
    3166 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
    3167 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    3168 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
    3169 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    3170 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
    3171 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    3172 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
    3173 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    3174 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
    3175 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    3176 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
    3177 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    3178 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
    3179 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    3180 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
    3181 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    3182 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
    3183 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    3184 
    3185 > hide #!7 models
    3186 
    3187 > hide #!8 models
    3188 
    3189 > hide #!9 models
    3190 
    3191 > hide #10 models
    3192 
    3193 > hide #!11 models
    3194 
    3195 > hide #!12 models
    3196 
    3197 > ui tool show "Side View"
    3198 
    3199 > open
    3200 > C:/Users/David/Documents/lab/Berndsen/EatA/models/Fab25/fold_2024_09_05_14_51_fab25_fullfab_model_0.cif
    3201 
    3202 Chain information for fold_2024_09_05_14_51_fab25_fullfab_model_0.cif #16 
    3203 --- 
    3204 Chain | Description 
    3205 A | . 
    3206 B | . 
    3207  
    3208 
    3209 > ui tool show Matchmaker
    3210 
    3211 > matchmaker #16 to #7
    3212 
    3213 Parameters 
    3214 --- 
    3215 Chain pairing | bb 
    3216 Alignment algorithm | Needleman-Wunsch 
    3217 Similarity matrix | BLOSUM-62 
    3218 SS fraction | 0.3 
    3219 Gap open (HH/SS/other) | 18/18/6 
    3220 Gap extend | 1 
    3221 SS matrix |  |  | H | S | O 
    3222 ---|---|---|--- 
    3223 H | 6 | -9 | -6 
    3224 S |  | 6 | -6 
    3225 O |  |  | 4 
    3226 Iteration cutoff | 2 
    3227  
    3228 Matchmaker EatA-Fab25_RSR_real_space_refined_207.pdb, chain B (#7) with
    3229 fold_2024_09_05_14_51_fab25_fullfab_model_0.cif, chain A (#16), sequence
    3230 alignment score = 518.3 
    3231 RMSD between 110 pruned atom pairs is 0.701 angstroms; (across all 117 pairs:
    3232 1.160) 
    3233  
    3234 
    3235 > rename #16 AF_EatA-25_fold_2024_09_05_14_51_fab25_fullfab_model_0.cif
    3236 
    3237 > select #16/A
    3238 
    3239 1652 atoms, 1694 bonds, 223 residues, 1 model selected 
    3240 
    3241 > color sel #663399ff
    3242 
    3243 > select clear
    3244 
    3245 > select #16/A
    3246 
    3247 1652 atoms, 1694 bonds, 223 residues, 1 model selected 
    3248 
    3249 > select #16/B
    3250 
    3251 1616 atoms, 1650 bonds, 211 residues, 1 model selected 
    3252 
    3253 > color sel #7b5d99ff
    3254 
    3255 > select clear
    3256 
    3257 > hide #!15.3 models
    3258 
    3259 > show #!15.3 models
    3260 
    3261 > color zone #15.3 near #16 distance 5.57
    3262 
    3263 > hide #!15.1 models
    3264 
    3265 > show #!15.1 models
    3266 
    3267 > color zone #15.1 near #16 distance 5.57
    3268 
    3269 > hide #16 models
    3270 
    3271 > view
    3272 
    3273 [Repeated 1 time(s)]
    3274 
    3275 > hide #!15 models
    3276 
    3277 > show #!15 models
    3278 
    3279 > show #!7 models
    3280 
    3281 > hide #!7 models
    3282 
    3283 > show #!2 models
    3284 
    3285 > color zone #2 near #8 distance 5.57
    3286 
    3287 > select #8/b
    3288 
    3289 1547 atoms, 1587 bonds, 2 pseudobonds, 204 residues, 2 models selected 
    3290 
    3291 > select #8/B
    3292 
    3293 1547 atoms, 1587 bonds, 2 pseudobonds, 204 residues, 2 models selected 
    3294 
    3295 > color #2,15 #36558fff
    3296 
    3297 > undo
    3298 
    3299 > select clear
    3300 
    3301 > select #8/B
    3302 
    3303 1547 atoms, 1587 bonds, 2 pseudobonds, 204 residues, 2 models selected 
    3304 
    3305 > color #2,15 #ffff7fff
    3306 
    3307 > undo
    3308 
    3309 > select clear
    3310 
    3311 > show #!8 models
    3312 
    3313 > select clear
    3314 
    3315 > select #8/B
    3316 
    3317 1547 atoms, 1587 bonds, 2 pseudobonds, 204 residues, 2 models selected 
    3318 
    3319 > color (#!8 & sel) #36558fff
    3320 
    3321 > select clear
    3322 
    3323 > color zone #2 near #8 distance 5.57
    3324 
    3325 > select #8/C
    3326 
    3327 1583 atoms, 1617 bonds, 3 pseudobonds, 205 residues, 2 models selected 
    3328 
    3329 > color (#!8 & sel) #98a8c5ff
    3330 
    3331 > select clear
    3332 
    3333 > color zone #2 near #8 distance 5.57
    3334 
    3335 > select clear
    3336 
    3337 > view
    3338 
    3339 > hide #!8 models
    3340 
    3341 > volume splitbyzone #2
    3342 
    3343 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
    3344 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3345 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
    3346 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3347 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
    3348 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3349 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
    3350 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3351 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
    3352 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3353 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
    3354 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3355 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
    3356 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3357 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
    3358 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3359 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
    3360 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3361 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
    3362 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3363 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
    3364 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    3365 
    3366 > hide #!17 models
    3367 
    3368 > show #!17 models
    3369 
    3370 > hide #!15 models
    3371 
    3372 > show #!15 models
    3373 
    3374 > show #!4 models
    3375 
    3376 > hide #!4 models
    3377 
    3378 > hide #!15 models
    3379 
    3380 > show #!15 models
    3381 
    3382 > hide #!15 models
    3383 
    3384 > show #!15 models
    3385 
    3386 > hide #!17 models
    3387 
    3388 > show #!17 models
    3389 
    3390 > hide #!17 models
    3391 
    3392 > show #!17 models
    3393 
    3394 > hide #!17 models
    3395 
    3396 > show #!17 models
    3397 
    3398 > hide #!17 models
    3399 
    3400 > show #!17 models
    3401 
    3402 > show #!4 models
    3403 
    3404 > hide #!4 models
    3405 
    3406 > hide #!17 models
    3407 
    3408 > show #!17 models
    3409 
    3410 > hide #!15 models
    3411 
    3412 > hide #!17 models
    3413 
    3414 > show #!17 models
    3415 
    3416 > show #!15 models
    3417 
    3418 > hide #!15 models
    3419 
    3420 > show #!15 models
    3421 
    3422 > hide #!15 models
    3423 
    3424 > show #!15 models
    3425 
    3426 > hide #!15 models
    3427 
    3428 > hide #!17 models
    3429 
    3430 > show #!3 models
    3431 
    3432 > show #!9 models
    3433 
    3434 > select #9/B
    3435 
    3436 1517 atoms, 1557 bonds, 2 pseudobonds, 201 residues, 2 models selected 
    3437 
    3438 > color (#!9 & sel) #ecb0e1ff
    3439 
    3440 > select clear
    3441 
    3442 > select #9/C
    3443 
    3444 1566 atoms, 1602 bonds, 3 pseudobonds, 202 residues, 2 models selected 
    3445 
    3446 > color (#!9 & sel) #f7dff3ff
    3447 
    3448 > color zone #3 near #9 distance 5.57
    3449 
    3450 > volume splitbyzone #3
    3451 
    3452 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid
    3453 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3454 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid
    3455 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3456 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid
    3457 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3458 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid
    3459 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3460 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid
    3461 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3462 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid
    3463 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3464 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid
    3465 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3466 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid
    3467 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3468 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid
    3469 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3470 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid
    3471 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3472 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid
    3473 size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 
    3474 
    3475 > hide #!9 models
    3476 
    3477 > show #!17 models
    3478 
    3479 > hide #!17 models
    3480 
    3481 > show #!17 models
    3482 
    3483 > hide #!17 models
    3484 
    3485 > hide #!18 models
    3486 
    3487 > show #!18 models
    3488 
    3489 > show #!17 models
    3490 
    3491 > hide #!17 models
    3492 
    3493 > show #!17 models
    3494 
    3495 > hide #!17 models
    3496 
    3497 > show #!17 models
    3498 
    3499 > hide #!17 models
    3500 
    3501 > hide #!18 models
    3502 
    3503 > show #!18 models
    3504 
    3505 > show #!17 models
    3506 
    3507 > hide #!17 models
    3508 
    3509 > show #!17 models
    3510 
    3511 > show #!15 models
    3512 
    3513 > hide #!15 models
    3514 
    3515 > hide #!17 models
    3516 
    3517 > hide #!18 models
    3518 
    3519 > show #!4 models
    3520 
    3521 > show #10 models
    3522 
    3523 > select #10/C
    3524 
    3525 1624 atoms, 1660 bonds, 210 residues, 1 model selected 
    3526 
    3527 > select #10/b
    3528 
    3529 1659 atoms, 1702 bonds, 220 residues, 1 model selected 
    3530 
    3531 > color sel #2c514cff
    3532 
    3533 > select #10/C
    3534 
    3535 1624 atoms, 1660 bonds, 210 residues, 1 model selected 
    3536 
    3537 > color sel #515151ff
    3538 
    3539 > color sel #4e5151ff
    3540 
    3541 > color sel #31514cff
    3542 
    3543 > color sel #4e5151ff
    3544 
    3545 > color sel #38514dff
    3546 
    3547 > color sel #010202ff
    3548 
    3549 > color sel #0e1413ff
    3550 
    3551 > color sel #8bcac0ff
    3552 
    3553 > color sel #0e1413ff
    3554 
    3555 > color sel #010202ff
    3556 
    3557 > color sel #010101ff
    3558 
    3559 > color sel #0a0f0eff
    3560 
    3561 > color sel #67968fff
    3562 
    3563 > color sel #0a0f0eff
    3564 
    3565 > color sel #010101ff
    3566 
    3567 > color sel #080b0aff
    3568 
    3569 > color sel #50756fff
    3570 
    3571 > color sel #080b0aff
    3572 
    3573 > color sel #010101ff
    3574 
    3575 > color sel #0c1110ff
    3576 
    3577 > color sel #78afa7ff
    3578 
    3579 > color zone #4 near #10 distance 5.16
    3580 
    3581 > color zone #4 near #10 distance 7.73
    3582 
    3583 > select clear
    3584 
    3585 > hide #10 models
    3586 
    3587 > volume splitbyzone #4
    3588 
    3589 Opened EatA-G12_composite_map.ccp4 0 as #19.1, grid size 356,356,356, pixel
    3590 0.86, shown at level 8.74, step 1, values float32 
    3591 Opened EatA-G12_composite_map.ccp4 1 as #19.2, grid size 356,356,356, pixel
    3592 0.86, shown at level 8.74, step 1, values float32 
    3593 Opened EatA-G12_composite_map.ccp4 2 as #19.3, grid size 356,356,356, pixel
    3594 0.86, shown at level 8.74, step 1, values float32 
    3595 Opened EatA-G12_composite_map.ccp4 3 as #19.4, grid size 356,356,356, pixel
    3596 0.86, shown at level 8.74, step 1, values float32 
    3597 Opened EatA-G12_composite_map.ccp4 4 as #19.5, grid size 356,356,356, pixel
    3598 0.86, shown at level 8.74, step 1, values float32 
    3599 Opened EatA-G12_composite_map.ccp4 5 as #19.6, grid size 356,356,356, pixel
    3600 0.86, shown at level 8.74, step 1, values float32 
    3601 Opened EatA-G12_composite_map.ccp4 6 as #19.7, grid size 356,356,356, pixel
    3602 0.86, shown at level 8.74, step 1, values float32 
    3603 Opened EatA-G12_composite_map.ccp4 7 as #19.8, grid size 356,356,356, pixel
    3604 0.86, shown at level 8.74, step 1, values float32 
    3605 Opened EatA-G12_composite_map.ccp4 8 as #19.9, grid size 356,356,356, pixel
    3606 0.86, shown at level 8.74, step 1, values float32 
    3607 Opened EatA-G12_composite_map.ccp4 9 as #19.10, grid size 356,356,356, pixel
    3608 0.86, shown at level 8.74, step 1, values float32 
    3609 Opened EatA-G12_composite_map.ccp4 10 as #19.11, grid size 356,356,356, pixel
    3610 0.86, shown at level 8.74, step 1, values float32 
    3611 
    3612 > hide #!19 models
    3613 
    3614 > show #!19 models
    3615 
    3616 > show #!15 models
    3617 
    3618 > show #16 models
    3619 
    3620 > hide #16 models
    3621 
    3622 > show #!17 models
    3623 
    3624 > hide #!17 models
    3625 
    3626 > show #!14 models
    3627 
    3628 > hide #!14 models
    3629 
    3630 > show #!13 models
    3631 
    3632 > hide #!13 models
    3633 
    3634 > show #!17 models
    3635 
    3636 > lighting flat
    3637 
    3638 > lighting soft
    3639 
    3640 > show #!18 models
    3641 
    3642 > hide #!18 models
    3643 
    3644 > hide #!19 models
    3645 
    3646 > hide #!17 models
    3647 
    3648 > hide #!15 models
    3649 
    3650 > show #!11 models
    3651 
    3652 > show #!5 models
    3653 
    3654 > select #11/B
    3655 
    3656 1489 atoms, 1529 bonds, 2 pseudobonds, 197 residues, 2 models selected 
    3657 
    3658 > show #!19 models
    3659 
    3660 > hide #!19 models
    3661 
    3662 > show #!19 models
    3663 
    3664 > hide #!5 models
    3665 
    3666 > hide #!11 models
    3667 
    3668 > hide #!19.3 models
    3669 
    3670 > show #!19.3 models
    3671 
    3672 > color #19.3 #77ada5ff models
    3673 
    3674 > color #19.3 #6d9f98ff models
    3675 
    3676 > color #19.3 #5d8882ff models
    3677 
    3678 > color #19.3 #66958eff models
    3679 
    3680 > color #19.3 #6b9c95ff models
    3681 
    3682 > color #19.3 #6ea098ff models
    3683 
    3684 > hide #!19 models
    3685 
    3686 > show #!5 models
    3687 
    3688 > show #!11 models
    3689 
    3690 > select #11/B
    3691 
    3692 1489 atoms, 1529 bonds, 2 pseudobonds, 197 residues, 2 models selected 
    3693 
    3694 > color (#!11 & sel) #ecb0e1ff
    3695 
    3696 > select #11/C
    3697 
    3698 1363 atoms, 1394 bonds, 3 pseudobonds, 177 residues, 2 models selected 
    3699 
    3700 > color (#!11 & sel) #f7dff3ff
    3701 
    3702 > select clear
    3703 
    3704 > color zone #5 near #11 distance 5.63
    3705 
    3706 > hide #!11 models
    3707 
    3708 > show #!11 models
    3709 
    3710 > volume splitbyzone #5
    3711 
    3712 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid
    3713 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3714 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid
    3715 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3716 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid
    3717 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3718 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid
    3719 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3720 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid
    3721 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3722 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid
    3723 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3724 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid
    3725 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3726 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid
    3727 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3728 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid
    3729 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3730 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid
    3731 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3732 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid
    3733 size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 
    3734 
    3735 > hide #!20 models
    3736 
    3737 > show #!20 models
    3738 
    3739 > hide #!11 models
    3740 
    3741 > hide #!20 models
    3742 
    3743 > show #!6 models
    3744 
    3745 > show #!12 models
    3746 
    3747 > select #12/B
    3748 
    3749 1324 atoms, 1361 bonds, 5 pseudobonds, 195 residues, 2 models selected 
    3750 
    3751 > color (#!12 & sel) #ecb0e1ff
    3752 
    3753 > select clear
    3754 
    3755 > select #12/C
    3756 
    3757 1141 atoms, 1169 bonds, 4 pseudobonds, 169 residues, 2 models selected 
    3758 
    3759 > color (#!12 & sel) #f7dff3ff
    3760 
    3761 > select clear
    3762 
    3763 > color zone #6 near #12 distance 5.63
    3764 
    3765 > select clear
    3766 
    3767 > hide #!6 models
    3768 
    3769 > show #!14 models
    3770 
    3771 > color zone #14 near #12 distance 5.63
    3772 
    3773 > select clear
    3774 
    3775 > hide #!14 models
    3776 
    3777 > show #!13 models
    3778 
    3779 > hide #!12 models
    3780 
    3781 > show #!4 models
    3782 
    3783 > color zone #13 near #10 distance 5.16
    3784 
    3785 > color zone #13 near #10 distance 8.41
    3786 
    3787 > volume splitbyzone #13
    3788 
    3789 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #21.1, grid size 356,356,356,
    3790 pixel 0.86, shown at level 5.61, step 1, values float32 
    3791 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #21.2, grid size 356,356,356,
    3792 pixel 0.86, shown at level 5.61, step 1, values float32 
    3793 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #21.3, grid size 356,356,356,
    3794 pixel 0.86, shown at level 5.61, step 1, values float32 
    3795 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #21.4, grid size 356,356,356,
    3796 pixel 0.86, shown at level 5.61, step 1, values float32 
    3797 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #21.5, grid size 356,356,356,
    3798 pixel 0.86, shown at level 5.61, step 1, values float32 
    3799 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #21.6, grid size 356,356,356,
    3800 pixel 0.86, shown at level 5.61, step 1, values float32 
    3801 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #21.7, grid size 356,356,356,
    3802 pixel 0.86, shown at level 5.61, step 1, values float32 
    3803 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #21.8, grid size 356,356,356,
    3804 pixel 0.86, shown at level 5.61, step 1, values float32 
    3805 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #21.9, grid size 356,356,356,
    3806 pixel 0.86, shown at level 5.61, step 1, values float32 
    3807 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #21.10, grid size
    3808 356,356,356, pixel 0.86, shown at level 5.61, step 1, values float32 
    3809 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #21.11, grid size
    3810 356,356,356, pixel 0.86, shown at level 5.61, step 1, values float32 
    3811 
    3812 > show #!6 models
    3813 
    3814 > hide #!4 models
    3815 
    3816 > hide #!6 models
    3817 
    3818 > hide #!21 models
    3819 
    3820 > show #!12 models
    3821 
    3822 > show #!14 models
    3823 
    3824 > color zone #14 near #12 distance 5.63
    3825 
    3826 > color zone #14 near #12 distance 18.16
    3827 
    3828 [Repeated 1 time(s)]
    3829 
    3830 > volume splitbyzone #14
    3831 
    3832 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #22.1,
    3833 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    3834 float32 
    3835 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #22.2,
    3836 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    3837 float32 
    3838 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #22.3,
    3839 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    3840 float32 
    3841 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #22.4,
    3842 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    3843 float32 
    3844 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #22.5,
    3845 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    3846 float32 
    3847 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #22.6,
    3848 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    3849 float32 
    3850 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #22.7,
    3851 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    3852 float32 
    3853 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #22.8,
    3854 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    3855 float32 
    3856 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #22.9,
    3857 grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
    3858 float32 
    3859 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
    3860 #22.10, grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1,
    3861 values float32 
    3862 
    3863 > hide #!12 models
    3864 
    3865 > show #!20 models
    3866 
    3867 > hide #!20 models
    3868 
    3869 > show #!20 models
    3870 
    3871 > hide #!22 models
    3872 
    3873 > show #!22 models
    3874 
    3875 > show #!21 models
    3876 
    3877 > close #21
    3878 
    3879 > show #!19 models
    3880 
    3881 > hide #!19 models
    3882 
    3883 > show #!13 models
    3884 
    3885 > volume #13 level 5.718
    3886 
    3887 > volume #13 level 6.761
    3888 
    3889 > hide #!20 models
    3890 
    3891 > hide #!22 models
    3892 
    3893 > volume #13 level 6.031
    3894 
    3895 > show #10 models
    3896 
    3897 > close #10
    3898 
    3899 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
    3900 > FINAL-MAP/EatA-FabG12_RSR_real_space_refined_010.pdb
    3901 
    3902 Chain information for EatA-FabG12_RSR_real_space_refined_010.pdb #10 
    3903 --- 
    3904 Chain | Description 
    3905 A | No description available 
    3906 B | No description available 
    3907 C | No description available 
    3908  
    3909 
    3910 > fitmap #10 inMap #4
    3911 
    3912 Fit molecule EatA-FabG12_RSR_real_space_refined_010.pdb (#10) to map
    3913 EatA-G12_composite_map.ccp4 (#4) using 10667 atoms 
    3914 average map value = 6.079, steps = 108 
    3915 shifted from previous position = 5.11 
    3916 rotated from previous position = 3.39 degrees 
    3917 atoms outside contour = 7317, contour level = 8.741 
    3918  
    3919 Position of EatA-FabG12_RSR_real_space_refined_010.pdb (#10) relative to
    3920 EatA-G12_composite_map.ccp4 (#4) coordinates: 
    3921 Matrix rotation and translation 
    3922 0.99908719 -0.02008723 -0.03770012 9.06831243 
    3923 0.01942262 0.99965088 -0.01791319 5.20661755 
    3924 0.03804678 0.01716460 0.99912853 -8.56741662 
    3925 Axis 0.37982306 -0.82018902 0.42781352 
    3926 Axis point 181.12453566 0.00000000 281.40187709 
    3927 Rotation angle (degrees) 2.64665903 
    3928 Shift along axis -4.49131303 
    3929  
    3930 
    3931 > select #10/A:289
    3932 
    3933 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3934 
    3935 > ui mousemode right "translate selected models"
    3936 
    3937 > view matrix models
    3938 > #10,0.99859,-0.046447,0.025647,-1.6035,0.045765,0.9986,0.026541,-14.883,-0.026844,-0.02533,0.99932,5.0661
    3939 
    3940 > view matrix models
    3941 > #10,0.99859,-0.046447,0.025647,-1.3589,0.045765,0.9986,0.026541,-14.699,-0.026844,-0.02533,0.99932,6.1492
    3942 
    3943 > fitmap #10 inMap #4
    3944 
    3945 Fit molecule EatA-FabG12_RSR_real_space_refined_010.pdb (#10) to map
    3946 EatA-G12_composite_map.ccp4 (#4) using 10667 atoms 
    3947 average map value = 14.61, steps = 76 
    3948 shifted from previous position = 1.25 
    3949 rotated from previous position = 2.63 degrees 
    3950 atoms outside contour = 3617, contour level = 8.741 
    3951  
    3952 Position of EatA-FabG12_RSR_real_space_refined_010.pdb (#10) relative to
    3953 EatA-G12_composite_map.ccp4 (#4) coordinates: 
    3954 Matrix rotation and translation 
    3955 0.99999917 0.00089157 -0.00093181 0.01897248 
    3956 -0.00089133 0.99999957 0.00025755 0.08599727 
    3957 0.00093204 -0.00025672 0.99999953 -0.10459276 
    3958 Axis -0.19553376 -0.70867599 -0.67789741 
    3959 Axis point 107.68461874 0.00000000 21.57608602 
    3960 Rotation angle (degrees) 0.07534542 
    3961 Shift along axis 0.00624920 
    3962  
    3963 
    3964 > color #13 #b2b2b2b4 models
    3965 
    3966 > view
    3967 
    3968 > select #10
    3969 
    3970 10667 atoms, 10878 bonds, 1434 residues, 1 model selected 
    3971 
    3972 > color sel #ffffffff
    3973 
    3974 > select clear
    3975 
    3976 > select #10/A:1-256
    3977 
    3978 1941 atoms, 1986 bonds, 256 residues, 1 model selected 
    3979 
    3980 > color sel cornflower blue
    3981 
    3982 > select clear
    3983 
    3984 > select #10/A:78,106,211
    3985 
    3986 24 atoms, 22 bonds, 3 residues, 1 model selected 
    3987 
    3988 > color sel magenta
    3989 
    3990 > select clear
    3991 
    3992 > select #10/A:481-560
    3993 
    3994 402 atoms, 401 bonds, 80 residues, 1 model selected 
    3995 
    3996 > ui tool show "Color Actions"
    3997 
    3998 > color sel gold
    3999 
    4000 > select clear
    4001 
    4002 > select #10/A:611-629
    4003 
    4004 142 atoms, 146 bonds, 19 residues, 1 model selected 
    4005 
    4006 > color sel #7dcdd2ff
    4007 
    4008 > select #10/A:669-699
    4009 
    4010 213 atoms, 213 bonds, 31 residues, 1 model selected 
    4011 
    4012 > color sel #ff0000ff
    4013 
    4014 > select #10/A:781-794
    4015 
    4016 100 atoms, 104 bonds, 14 residues, 1 model selected 
    4017 
    4018 > color sel #778899ff
    4019 
    4020 > select #10/A:834-856
    4021 
    4022 170 atoms, 172 bonds, 23 residues, 1 model selected 
    4023 
    4024 > color sel #ff69b4ff
    4025 
    4026 > select #13
    4027 
    4028 2 models selected 
    4029 
    4030 > select clear
    4031 
    4032 > select #10/B
    4033 
    4034 1659 atoms, 1704 bonds, 220 residues, 1 model selected 
    4035 
    4036 > color sel #663399ff
    4037 
    4038 > color sel #2c514cff
    4039 
    4040 > select #10/C
    4041 
    4042 1624 atoms, 1662 bonds, 210 residues, 1 model selected 
    4043 
    4044 > color sel #6ea098ff
    4045 
    4046 > select clear
    4047 
    4048 > color zone #13 near #10 distance 5.16
    4049 
    4050 > color zone #13 near #10 distance 10.13
    4051 
    4052 > color zone #13 near #10 distance 7.12
    4053 
    4054 > color zone #13 near #10 distance 7.51
    4055 
    4056 > color zone #13 near #10 distance 12.16
    4057 
    4058 > hide #10 models
    4059 
    4060 > volume #13 level 6.949
    4061 
    4062 > volume #13 level 4.296
    4063 
    4064 > show #!20 models
    4065 
    4066 > hide #!20 models
    4067 
    4068 > show #!20 models
    4069 
    4070 > show #!22 models
    4071 
    4072 > hide #!22 models
    4073 
    4074 > show #!22 models
    4075 
    4076 > hide #!22 models
    4077 
    4078 > hide #!20 models
    4079 
    4080 > show #!20 models
    4081 
    4082 > hide #!20 models
    4083 
    4084 > volume splitbyzone #13
    4085 
    4086 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #21.1, grid size 356,356,356,
    4087 pixel 0.86, shown at level 4.3, step 1, values float32 
    4088 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #21.2, grid size 356,356,356,
    4089 pixel 0.86, shown at level 4.3, step 1, values float32 
    4090 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #21.3, grid size 356,356,356,
    4091 pixel 0.86, shown at level 4.3, step 1, values float32 
    4092 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #21.4, grid size 356,356,356,
    4093 pixel 0.86, shown at level 4.3, step 1, values float32 
    4094 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #21.5, grid size 356,356,356,
    4095 pixel 0.86, shown at level 4.3, step 1, values float32 
    4096 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #21.6, grid size 356,356,356,
    4097 pixel 0.86, shown at level 4.3, step 1, values float32 
    4098 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #21.7, grid size 356,356,356,
    4099 pixel 0.86, shown at level 4.3, step 1, values float32 
    4100 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #21.8, grid size 356,356,356,
    4101 pixel 0.86, shown at level 4.3, step 1, values float32 
    4102 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #21.9, grid size 356,356,356,
    4103 pixel 0.86, shown at level 4.3, step 1, values float32 
    4104 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #21.10, grid size
    4105 356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32 
    4106 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #21.11, grid size
    4107 356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32 
    4108 
    4109 > open 5J44
    4110 
    4111 5j44 title: 
    4112 Crystal structure of the Secreted Extracellular protein A (SepA) from Shigella
    4113 flexneri [more info...] 
    4114  
    4115 Chain information for 5j44 #23 
    4116 --- 
    4117 Chain | Description | UniProt 
    4118 A B | Serine protease SepA autotransporter | D2AJC0_SHIF2 1-1033 
    4119  
    4120 Non-standard residues in 5j44 #23 
    4121 --- 
    4122 EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) 
    4123  
    4124 5j44 mmCIF Assemblies 
    4125 --- 
    4126 1| author_and_software_defined_assembly 
    4127 2| author_and_software_defined_assembly 
    4128  
    4129 
    4130 > select #23/B
    4131 
    4132 7507 atoms, 7628 bonds, 1013 residues, 1 model selected 
    4133 
    4134 > delete atoms sel
    4135 
    4136 > delete bonds sel
    4137 
    4138 > select ::name="EPE"::name="HOH"
    4139 
    4140 27 atoms, 15 bonds, 13 residues, 1 model selected 
    4141 
    4142 > delete atoms sel
    4143 
    4144 > delete bonds sel
    4145 
    4146 > select clear
    4147 
    4148 > ui tool show Matchmaker
    4149 
    4150 > matchmaker #23 to #9
    4151 
    4152 Parameters 
    4153 --- 
    4154 Chain pairing | bb 
    4155 Alignment algorithm | Needleman-Wunsch 
    4156 Similarity matrix | BLOSUM-62 
    4157 SS fraction | 0.3 
    4158 Gap open (HH/SS/other) | 18/18/6 
    4159 Gap extend | 1 
    4160 SS matrix |  |  | H | S | O 
    4161 ---|---|---|--- 
    4162 H | 6 | -9 | -6 
    4163 S |  | 6 | -6 
    4164 O |  |  | 4 
    4165 Iteration cutoff | 2 
    4166  
    4167 Matchmaker EatA-Fab40_RSR_real_space_refined_206.pdb, chain A (#9) with 5j44,
    4168 chain A (#23), sequence alignment score = 2951.1 
    4169 RMSD between 757 pruned atom pairs is 0.589 angstroms; (across all 769 pairs:
    4170 1.473) 
    4171  
    4172 
    4173 > hide #23 models
    4174 
    4175 > hide #!21 models
    4176 
    4177 > show #23 models
    4178 
    4179 > show #!18 models
    4180 
    4181 > hide #!18 models
    4182 
    4183 > select #10/A:1-256
    4184 
    4185 1941 atoms, 1986 bonds, 256 residues, 1 model selected 
    4186 
    4187 > select #21
    4188 
    4189 23 models selected 
    4190 
    4191 > show #23 surfaces
    4192 
    4193 > color #23 #ffffffff
    4194 
    4195 > select #21/A:1-256
    4196 
    4197 Nothing selected 
    4198 
    4199 > select #23/A:1-256
    4200 
    4201 1928 atoms, 1969 bonds, 256 residues, 1 model selected 
    4202 
    4203 > color (#!23 & sel) cornflower blue
    4204 
    4205 > select clear
    4206 
    4207 > select #23/A:78,106,211
    4208 
    4209 24 atoms, 22 bonds, 3 residues, 1 model selected 
    4210 
    4211 > color (#!23 & sel) magenta
    4212 
    4213 > select clear
    4214 
    4215 > select #23/A:481-560
    4216 
    4217 621 atoms, 633 bonds, 80 residues, 1 model selected 
    4218 
    4219 > ui tool show "Color Actions"
    4220 
    4221 > color sel gold
    4222 
    4223 > select #23/A:611-629
    4224 
    4225 143 atoms, 147 bonds, 19 residues, 1 model selected 
    4226 
    4227 > color (#!23 & sel) #7dcdd2ff
    4228 
    4229 > select #23/A:669-699
    4230 
    4231 213 atoms, 213 bonds, 31 residues, 1 model selected 
    4232 
    4233 > color (#!23 & sel) #ff0000ff
    4234 
    4235 > select #23/A:781-794
    4236 
    4237 105 atoms, 108 bonds, 14 residues, 1 model selected 
    4238 
    4239 > color (#!23 & sel) #778899ff
    4240 
    4241 > select #23/A:834-856
    4242 
    4243 165 atoms, 167 bonds, 23 residues, 1 model selected 
    4244 
    4245 > color (#!23 & sel) #ff69b4ff
    4246 
    4247 > select clear
    4248 
    4249 > show #!22 models
    4250 
    4251 > show #!21 models
    4252 
    4253 > show #!20 models
    4254 
    4255 > close #19
    4256 
    4257 > show #!18 models
    4258 
    4259 > show #!17 models
    4260 
    4261 > show #!15 models
    4262 
    4263 > hide #!15 models
    4264 
    4265 > show #!15 models
    4266 
    4267 > hide #!15 models
    4268 
    4269 > hide #!23 models
    4270 
    4271 > show #!23 models
    4272 
    4273 > hide #!23 models
    4274 
    4275 > show #!23 models
    4276 
    4277 > hide #!23 models
    4278 
    4279 > show #!23 models
    4280 
    4281 > hide #!23 models
    4282 
    4283 > hide #!22 models
    4284 
    4285 > show #!22 models
    4286 
    4287 > hide #!22 models
    4288 
    4289 > show #!22 models
    4290 
    4291 > show #!23 models
    4292 
    4293 > hide #!23 models
    4294 
    4295 > show #!15 models
    4296 
    4297 > view
    4298 
    4299 > hide #!15 models
    4300 
    4301 > show #!15 models
    4302 
    4303 > hide #!15 models
    4304 
    4305 > show #!15 models
    4306 
    4307 > hide #!15 models
    4308 
    4309 > show #!15 models
    4310 
    4311 > hide #!15 models
    4312 
    4313 > hide #!22 models
    4314 
    4315 > show #!22 models
    4316 
    4317 > hide #!22 models
    4318 
    4319 > hide #!21 models
    4320 
    4321 > hide #!20 models
    4322 
    4323 > hide #!18 models
    4324 
    4325 > show #!23 models
    4326 
    4327 > hide #!17 models
    4328 
    4329 > show #!22 models
    4330 
    4331 > show #!21 models
    4332 
    4333 > show #!20 models
    4334 
    4335 > show #!18 models
    4336 
    4337 > show #!17 models
    4338 
    4339 > show #16 models
    4340 
    4341 > hide #16 models
    4342 
    4343 > show #!15 models
    4344 
    4345 > show #16 models
    4346 
    4347 > hide #16 models
    4348 
    4349 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
    4350 > aligned_Fig4.cxs
    4351 
    4352 ——— End of log from Sun Nov 2 19:35:42 2025 ———
    4353 
    4354 opened ChimeraX session 
    4355 
    4356 > show #16 models
    4357 
    4358 > save C:\Users\David/Desktop/new-snaps/test.png supersample 4 width 3000
    4359 > height 2500
    4360 
    4361 > save C:\Users\David/Desktop/new-snaps/test.png supersample 4 width 3000
    4362 > height 2600
    4363 
    4364 > hide #16 models
    4365 
    4366 > hide #!22 models
    4367 
    4368 > hide #!21 models
    4369 
    4370 > hide #!20 models
    4371 
    4372 > hide #!18 models
    4373 
    4374 > hide #!17 models
    4375 
    4376 > hide #!15 models
    4377 
    4378 > save C:\Users\David/Desktop/new-snaps/5J44.png supersample 4 width 3000
    4379 > height 2500
    4380 
    4381 > hide #!23 models
    4382 
    4383 > show #!15 models
    4384 
    4385 > save C:\Users\David/Desktop/new-snaps/EatA-25.png supersample 4 width 3000
    4386 > height 2500
    4387 
    4388 > save C:\Users\David/Desktop/new-snaps/EatA-25.png supersample 4 width 3000
    4389 > height 2600
    4390 
    4391 > hide #!15 models
    4392 
    4393 > show #!23 models
    4394 
    4395 > save C:\Users\David/Desktop/new-snaps/5J44.png supersample 4 width 3000
    4396 > height 2600
    4397 
    4398 > hide #!23 models
    4399 
    4400 > show #!17 models
    4401 
    4402 > save C:\Users\David/Desktop/new-snaps/EatA-15.png supersample 4 width 3000
    4403 > height 2600
    4404 
    4405 > hide #!17 models
    4406 
    4407 > show #!18 models
    4408 
    4409 > save C:\Users\David/Desktop/new-snaps/EatA-40.png supersample 4 width 3000
    4410 > height 2600
    4411 
    4412 > hide #!18 models
    4413 
    4414 > show #!20 models
    4415 
    4416 > save C:\Users\David/Desktop/new-snaps/SepA-40.png supersample 4 width 3000
    4417 > height 2600
    4418 
    4419 > hide #!20 models
    4420 
    4421 > show #!21 models
    4422 
    4423 > save C:\Users\David/Desktop/new-snaps/EatA-G12.png supersample 4 width 3000
    4424 > height 2600
    4425 
    4426 > show #!22 models
    4427 
    4428 > hide #!21 models
    4429 
    4430 > save C:\Users\David/Desktop/new-snaps/Pic-40.png supersample 4 width 3000
    4431 > height 2600
    4432 
    4433 > hide #!22 models
    4434 
    4435 > show #!23 models
    4436 
    4437 > show #!7 models
    4438 
    4439 > hide #!7 models
    4440 
    4441 > show #16 models
    4442 
    4443 > hide #16 models
    4444 
    4445 > show #!8 models
    4446 
    4447 > hide #!8 models
    4448 
    4449 > show #!8 models
    4450 
    4451 > show #!7 models
    4452 
    4453 > hide #!8 models
    4454 
    4455 > show #!8 models
    4456 
    4457 > show #16 models
    4458 
    4459 > hide #!7 models
    4460 
    4461 > show #!9 models
    4462 
    4463 > show #10 models
    4464 
    4465 > hide #!23 models
    4466 
    4467 > show #!23 models
    4468 
    4469 > hide #!23 models
    4470 
    4471 > show #!23 models
    4472 
    4473 > select #7, #8
    4474 
    4475 Expected an objects specifier or a keyword 
    4476 
    4477 > select #7,8,9,10,11,12/A
    4478 
    4479 35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected 
    4480 
    4481 > hide sel & #10#!8-9 cartoons
    4482 
    4483 > select clear
    4484 
    4485 > select #23
    4486 
    4487 7500 atoms, 7628 bonds, 1006 residues, 1 model selected 
    4488 
    4489 > transparency (#!23 & sel) 60
    4490 
    4491 > select clear
    4492 
    4493 > select #21
    4494 
    4495 23 models selected 
    4496 
    4497 > select #23
    4498 
    4499 7500 atoms, 7628 bonds, 1006 residues, 1 model selected 
    4500 
    4501 > hide sel cartoons
    4502 
    4503 > select clear
    4504 
    4505 > select #23
    4506 
    4507 7500 atoms, 7628 bonds, 1006 residues, 1 model selected 
    4508 
    4509 > lighting full
    4510 
    4511 > lighting simple
    4512 
    4513 > lighting full
    4514 
    4515 > graphics silhouettes false
    4516 
    4517 > lighting shadows false
    4518 
    4519 > lighting flat
    4520 
    4521 > lighting soft
    4522 
    4523 > graphics silhouettes false
    4524 
    4525 > graphics silhouettes true
    4526 
    4527 > select clear
    4528 
    4529 > select #23
    4530 
    4531 7500 atoms, 7628 bonds, 1006 residues, 1 model selected 
    4532 
    4533 > show sel cartoons
    4534 
    4535 > select clear
    4536 
    4537 > select #23
    4538 
    4539 7500 atoms, 7628 bonds, 1006 residues, 1 model selected 
    4540 
    4541 > transparency (#!23 & sel) 0
    4542 
    4543 > select clear
    4544 
    4545 > save C:\Users\David/Desktop/new-snaps/overlay.png supersample 4 width 3000
    4546 > height 2600
    4547 
    4548 > hide #16 models
    4549 
    4550 > show #!15 models
    4551 
    4552 > hide #!8 models
    4553 
    4554 > hide #!9 models
    4555 
    4556 > hide #10 models
    4557 
    4558 > show #!7 models
    4559 
    4560 > hide #!23 models
    4561 
    4562 > color #15.2 #663399b4 models
    4563 
    4564 > color #15.3 #7b5d99b4 models
    4565 
    4566 > color #15.4 #6495edb4 models
    4567 
    4568 > select clear
    4569 
    4570 > save C:\Users\David/Desktop/new-snaps/test.png supersample 4 width 3000
    4571 > height 2600
    4572 
    4573 > hide #!15 models
    4574 
    4575 > show #!1 models
    4576 
    4577 > color #1 #b2b2b2b4 models
    4578 
    4579 > hide #!1 models
    4580 
    4581 > show #!15 models
    4582 
    4583 > select clear
    4584 
    4585 > nucleotides #!7 atoms
    4586 
    4587 > style nucleic & #!7 stick
    4588 
    4589 Changed 0 atom styles 
    4590 
    4591 > splitss
    4592 
    4593 Unknown command: splitss 
    4594 
    4595 > cartoon style coil thickness 0.25
    4596 
    4597 > hide #!15 models
    4598 
    4599 > cartoon style coil thickness 1.25
    4600 
    4601 > cartoon style coil thickness 1
    4602 
    4603 > cartoon style coil thickness 1.25
    4604 
    4605 > cartoon style sheet thickness 1.25
    4606 
    4607 Expected an atoms specifier or a keyword 
    4608 
    4609 > cartoon style ribbon thickness 1.25
    4610 
    4611 Expected an atoms specifier or a keyword 
    4612 
    4613 > show #!15 models
    4614 
    4615 > hide #!15 models
    4616 
    4617 > cartoon style ribbon thickness 10
    4618 
    4619 Expected an atoms specifier or a keyword 
    4620 
    4621 > alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6
    4622 
    4623 > alias cylinders cartoon style protein modeh tube rad 2 sides 24
    4624 
    4625 > alias licorice car style protein modeh default arrows f xsect oval width 1
    4626 > thick 1
    4627 
    4628 > cartoon style ribbon thickness 1.25
    4629 
    4630 Expected an atoms specifier or a keyword 
    4631 
    4632 > cartoon style coil thickness 1.25
    4633 
    4634 > cartoon style nucrib thickness 1.25
    4635 
    4636 Expected an atoms specifier or a keyword 
    4637 
    4638 > alias licorice car style protein modeh default arrows f xsect oval width 1
    4639 > thick 1
    4640 
    4641 > licorice
    4642 
    4643 > show #!15 models
    4644 
    4645 > view
    4646 
    4647 > color #15.9 #ff0000b4 models
    4648 
    4649 > color #15.8 #7dcdd2b4 models
    4650 
    4651 > hide #!15.2 models
    4652 
    4653 > show #!15.2 models
    4654 
    4655 > hide #!15 models
    4656 
    4657 > select #7/C:66
    4658 
    4659 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4660 
    4661 > select clear
    4662 
    4663 > select #7/C:66
    4664 
    4665 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4666 
    4667 > show sel atoms
    4668 
    4669 > select clear
    4670 
    4671 > select #7/C:66
    4672 
    4673 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4674 
    4675 > show sel atoms
    4676 
    4677 > select clear
    4678 
    4679 > select #7/C:65
    4680 
    4681 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4682 
    4683 > show sel atoms
    4684 
    4685 > select clear
    4686 
    4687 > select #7/C:69
    4688 
    4689 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4690 
    4691 > show sel atoms
    4692 
    4693 > select clear
    4694 
    4695 > style #!7 sphere
    4696 
    4697 Changed 5662 atom styles 
    4698 
    4699 > style #!7 stick
    4700 
    4701 Changed 5662 atom styles 
    4702 
    4703 > hide #!7 atoms
    4704 
    4705 > show #!14 models
    4706 
    4707 > hide #!14 models
    4708 
    4709 > show #!15 models
    4710 
    4711 > hide #!15.2 models
    4712 
    4713 > hide #!15.3 models
    4714 
    4715 > hide #!15.1 models
    4716 
    4717 > show #!15.1 models
    4718 
    4719 > hide #!15.1 models
    4720 
    4721 > show #!15.1 models
    4722 
    4723 > hide #!15.1 models
    4724 
    4725 > view
    4726 
    4727 > show #!15.1 models
    4728 
    4729 > hide #!15.1 models
    4730 
    4731 > show #!15.1 models
    4732 
    4733 > color #15.1 #b2b2b2b2 models
    4734 
    4735 > color #15.1 #b2b2b2b4 models
    4736 
    4737 > undo
    4738 
    4739 [Repeated 9 time(s)]
    4740 
    4741 > show #!15.1 models
    4742 
    4743 > color #15.1 #b2b2b2b4 models
    4744 
    4745 > show #!15.2 models
    4746 
    4747 > show #!15.3 models
    4748 
    4749 > show #!23 models
    4750 
    4751 > hide #!23 models
    4752 
    4753 > hide #!15 models
    4754 
    4755 > show #!15 models
    4756 
    4757 > color #15.6 #ffffffb4 models
    4758 
    4759 > color #15.7 #ffd700b4 models
    4760 
    4761 > color #15.5 #ff00ffb4 models
    4762 
    4763 > color #16 #663399b4
    4764 
    4765 > color #16 rebeccapurple
    4766 
    4767 > show #16 models
    4768 
    4769 > hide #16 models
    4770 
    4771 > show #16 models
    4772 
    4773 > hide #16 models
    4774 
    4775 > show #16 models
    4776 
    4777 > hide #!15 models
    4778 
    4779 > hide #!7 models
    4780 
    4781 > color #16 rebeccapurple
    4782 
    4783 [Repeated 1 time(s)]
    4784 
    4785 > select clear
    4786 
    4787 > select #16/A
    4788 
    4789 1652 atoms, 1694 bonds, 223 residues, 1 model selected 
    4790 
    4791 > color sel #663399ff
    4792 
    4793 > select clear
    4794 
    4795 > select #16/B
    4796 
    4797 1616 atoms, 1650 bonds, 211 residues, 1 model selected 
    4798 
    4799 > color sel #7b5d99ff
    4800 
    4801 > select clear
    4802 
    4803 > show #!23 models
    4804 
    4805 > hide #!23 models
    4806 
    4807 > show #!23 models
    4808 
    4809 > show #!7 models
    4810 
    4811 > hide #!7 models
    4812 
    4813 > show #!8 models
    4814 
    4815 > show #!9 models
    4816 
    4817 > show #10 models
    4818 
    4819 > show #!15 models
    4820 
    4821 > hide #!23 models
    4822 
    4823 > show #!7 models
    4824 
    4825 > hide #16 models
    4826 
    4827 > hide #!15 models
    4828 
    4829 > show #!15 models
    4830 
    4831 > hide #10 models
    4832 
    4833 > hide #!9 models
    4834 
    4835 > hide #!7 models
    4836 
    4837 > hide #!8 models
    4838 
    4839 > hide #!15 models
    4840 
    4841 > show #!2 models
    4842 
    4843 > show #!8 models
    4844 
    4845 > color #2 #b2b2b2b4 models
    4846 
    4847 > undo
    4848 
    4849 [Repeated 1 time(s)]
    4850 
    4851 > hide #!2 models
    4852 
    4853 > show #!17 models
    4854 
    4855 > hide #!17.1 models
    4856 
    4857 > show #!17.1 models
    4858 
    4859 > color #17.1 #b2b2b2b4 models
    4860 
    4861 > color #17.2 #6495edb4 models
    4862 
    4863 > color #17.3 #ff00ffb4 models
    4864 
    4865 > color #17.4 #ffffffb4 models
    4866 
    4867 > color #17.5 #ffd70005 models
    4868 
    4869 > color #17.5 #ffd700b4 models
    4870 
    4871 > color #17.6 #7dcdd2b4 models
    4872 
    4873 > color #17.7 #ff0000b4 models
    4874 
    4875 > color #17.8 #778899b4 models
    4876 
    4877 > color #17.9 #ff69b4b4 models
    4878 
    4879 > color #17.10 #36558fb4 models
    4880 
    4881 > color #17.11 #98a8c5b4 models
    4882 
    4883 > select clear
    4884 
    4885 [Repeated 1 time(s)]
    4886 
    4887 > select #7,8,9,10,11,12/A
    4888 
    4889 35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected 
    4890 
    4891 > show sel & #!8 cartoons
    4892 
    4893 > select clear
    4894 
    4895 > show #!15 models
    4896 
    4897 > show #!7 models
    4898 
    4899 > hide #!15 models
    4900 
    4901 > show #!15 models
    4902 
    4903 > hide #!15 models
    4904 
    4905 > show #!15 models
    4906 
    4907 > hide #!15 models
    4908 
    4909 > hide #!7 models
    4910 
    4911 > save C:\Users\David/Desktop/new-snaps/test.png supersample 4 width 3000
    4912 > height 2600
    4913 
    4914 > show #!23 models
    4915 
    4916 > hide #!17 models
    4917 
    4918 > hide #!17.1 models
    4919 
    4920 > show #!17.1 models
    4921 
    4922 > hide #!17 models
    4923 
    4924 > show #!17 models
    4925 
    4926 > hide #!23 models
    4927 
    4928 > show #!15 models
    4929 
    4930 > show #!23 models
    4931 
    4932 > hide #!23 models
    4933 
    4934 > hide #!17 models
    4935 
    4936 > hide #!8 models
    4937 
    4938 > show #!7 models
    4939 
    4940 > save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4.png supersample 4 width
    4941 > 3000 height 2600
    4942 
    4943 > color #15.2 #66339978 models
    4944 
    4945 > color #15.3 #7b5d9978 models
    4946 
    4947 > color #15.4 #6495ed78 models
    4948 
    4949 > color #15.5 #ff00ff78 models
    4950 
    4951 > color #15.6 #ffffff78 models
    4952 
    4953 > color #15.7 #ffd70078 models
    4954 
    4955 > color #15.8 #7dcdd278 models
    4956 
    4957 > color #15.9 #ff000078 models
    4958 
    4959 > save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4-1.png supersample 4 width
    4960 > 3000 height 2600
    4961 
    4962 > color #15.2 #6633998c models
    4963 
    4964 > color #15.3 #7b5d998c models
    4965 
    4966 > color #15.4 #6495ed01 models
    4967 
    4968 > color #15.4 #6495ed8c models
    4969 
    4970 > color #15.5 #ff00ff8c models
    4971 
    4972 > color #15.6 #ffffff8c models
    4973 
    4974 > color #15.7 #ffd7008c models
    4975 
    4976 > color #15.8 #7dcdd28c models
    4977 
    4978 > color #15.9 #ff000077 models
    4979 
    4980 > color #15.9 #ff00008c models
    4981 
    4982 > save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4-140.png supersample 4
    4983 > width 3000 height 2600
    4984 
    4985 > hide #!15 models
    4986 
    4987 > hide #!7 models
    4988 
    4989 > show #!8 models
    4990 
    4991 > show #!2 models
    4992 
    4993 > hide #!2 models
    4994 
    4995 > show #!15 models
    4996 
    4997 > show #!23 models
    4998 
    4999 > hide #!23 models
    5000 
    5001 > show #!21 models
    5002 
    5003 > hide #!21 models
    5004 
    5005 > hide #!15 models
    5006 
    5007 > show #!17 models
    5008 
    5009 > color #17.2 #6495ed8c models
    5010 
    5011 > color #17.3 #ff00ff8c models
    5012 
    5013 > color #17.4 #ffffff8c models
    5014 
    5015 > color #17.5 #ffd7008c models
    5016 
    5017 > color #17.6 #7dcdd28c models
    5018 
    5019 > color #17.7 #ff0000b3 models
    5020 
    5021 > color #17.7 #ff00008c models
    5022 
    5023 > color #17.8 #7788998c models
    5024 
    5025 > color #17.9 #ff69b48c models
    5026 
    5027 > color #17.10 #36558f8c models
    5028 
    5029 > color #17.11 #98a8c58c models
    5030 
    5031 > select clear
    5032 
    5033 > show #!15 models
    5034 
    5035 > hide #!15 models
    5036 
    5037 > save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-140.png supersample 4
    5038 > width 3000 height 2600
    5039 
    5040 > alias licorice car style protein modeh default arrows f xsect oval width 1
    5041 > thick 0.75
    5042 
    5043 > licorice
    5044 
    5045 > save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-140.png supersample 4
    5046 > width 3000 height 2600
    5047 
    5048 [Repeated 1 time(s)]
    5049 
    5050 > graphics silhouettes color black width 3
    5051 
    5052 > save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-140.png supersample 4
    5053 > width 3000 height 2600
    5054 
    5055 > select #7,8,9,10,11/A:78,106,211
    5056 
    5057 117 atoms, 107 bonds, 15 residues, 5 models selected 
    5058 
    5059 > show sel & #!8 atoms
    5060 
    5061 > select clear
    5062 
    5063 > save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-140.png supersample 4
    5064 > width 3000 height 2600
    5065 
    5066 > save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-140-1.png supersample 4
    5067 > width 3000 height 2600
    5068 
    5069 > show #!15 models
    5070 
    5071 > show #!23 models
    5072 
    5073 > hide #!23 models
    5074 
    5075 > show #!23 models
    5076 
    5077 > hide #!23 models
    5078 
    5079 > hide #!17 models
    5080 
    5081 > show #!17 models
    5082 
    5083 > hide #!17 models
    5084 
    5085 > hide #!15 models
    5086 
    5087 > hide #!8 models
    5088 
    5089 > show #!15 models
    5090 
    5091 > show #!8 models
    5092 
    5093 > hide #!8 models
    5094 
    5095 > show #!7 models
    5096 
    5097 > hide #!7 models
    5098 
    5099 > hide #!15 models
    5100 
    5101 > show #!23 models
    5102 
    5103 > save C:\Users\David/Desktop/new-snaps/5J44.png supersample 4 width 3000
    5104 > height 2600
    5105 
    5106 > show #!7 models
    5107 
    5108 > hide #!7 models
    5109 
    5110 > hide #!23 models
    5111 
    5112 > show #!23 models
    5113 
    5114 > hide #!23 models
    5115 
    5116 > show #!15 models
    5117 
    5118 > show #!1 models
    5119 
    5120 > hide #!1 models
    5121 
    5122 > show #!7 models
    5123 
    5124 > save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4.png supersample 4 width
    5125 > 3000 height 2600
    5126 
    5127 > hide #!7 models
    5128 
    5129 > show #!8 models
    5130 
    5131 > hide #!15 models
    5132 
    5133 > show #!17 models
    5134 
    5135 > save C:\Users\David/Desktop/new-snaps/EatA-15_Fig4.png supersample 4 width
    5136 > 3000 height 2600
    5137 
    5138 > hide #!17 models
    5139 
    5140 > show #!18 models
    5141 
    5142 > hide #!8 models
    5143 
    5144 > save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4.png supersample 4 width
    5145 > 3000 height 2600
    5146 
    5147 > color #18.2 #6495ed8c models
    5148 
    5149 > color #18.3 #ff00ff8c models
    5150 
    5151 > color #18.4 #ffffff8c models
    5152 
    5153 > color #18.5 #ffd7008c models
    5154 
    5155 > color #18.6 #7dcdd28c models
    5156 
    5157 > color #18.7 #ff00008c models
    5158 
    5159 > color #18.8 #7788998c models
    5160 
    5161 > color #18.9 #ff69b48c models
    5162 
    5163 > color #18.10 #ecb0e18c models
    5164 
    5165 > color #18.11 #f7dff38c models
    5166 
    5167 > show #!8 models
    5168 
    5169 > hide #!8 models
    5170 
    5171 > show #!9 models
    5172 
    5173 > save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-transp.png supersample 4
    5174 > width 3000 height 2600
    5175 
    5176 > select #7,8,9,10,11,12/A
    5177 
    5178 35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected 
    5179 
    5180 > show sel & #!9 cartoons
    5181 
    5182 > select clear
    5183 
    5184 > select #7,8,9,10,11/A:78,106,211
    5185 
    5186 117 atoms, 107 bonds, 15 residues, 5 models selected 
    5187 
    5188 > show sel & #!9 atoms
    5189 
    5190 > select clear
    5191 
    5192 > save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-transp.png supersample 4
    5193 > width 3000 height 2600
    5194 
    5195 > hide #!18 models
    5196 
    5197 > show #!17 models
    5198 
    5199 > hide #!9 models
    5200 
    5201 > show #!8 models
    5202 
    5203 > hide #!8 models
    5204 
    5205 > color #17.2 cornflowerblue models
    5206 
    5207 [Repeated 1 time(s)]
    5208 
    5209 > color #17.2 #6495ed02 models
    5210 
    5211 > color #17.2 cornflowerblue models
    5212 
    5213 [Repeated 1 time(s)]
    5214 
    5215 > color #17.3 #ff00ff8d models
    5216 
    5217 > color #17.3 magenta models
    5218 
    5219 > color #17.4 white models
    5220 
    5221 > color #17.4 #fffffffe models
    5222 
    5223 > color #17.4 white models
    5224 
    5225 > color #17.5 gold models
    5226 
    5227 [Repeated 1 time(s)]
    5228 
    5229 > color #17.6 #7dcdd2ff models
    5230 
    5231 [Repeated 1 time(s)]
    5232 
    5233 > color #17.7 red models
    5234 
    5235 [Repeated 1 time(s)]
    5236 
    5237 > color #17.8 lightslategrey models
    5238 
    5239 [Repeated 1 time(s)]
    5240 
    5241 > color #17.9 hotpink models
    5242 
    5243 [Repeated 1 time(s)]
    5244 
    5245 > color #17.10 #36558fff models
    5246 
    5247 > color #17.10 #36558ffe models
    5248 
    5249 > color #17.10 #36558fff models
    5250 
    5251 > color #17.11 #98a8c5ff models
    5252 
    5253 [Repeated 1 time(s)]
    5254 
    5255 > color #17.1 #b2b2b2ff models
    5256 
    5257 [Repeated 1 time(s)]
    5258 
    5259 > color #17.2 #6495edfe models
    5260 
    5261 > color #17.2 cornflowerblue models
    5262 
    5263 > save C:\Users\David/Desktop/new-snaps/EatA-15_Fig4-no-transp.png supersample
    5264 > 4 width 3000 height 2600
    5265 
    5266 > color #17 #b2b2b2fe models
    5267 
    5268 > color #17 #b2b2b2ff models
    5269 
    5270 > undo
    5271 
    5272 [Repeated 2 time(s)]
    5273 
    5274 > color #17 #b2b2b2ff models
    5275 
    5276 > close #17
    5277 
    5278 > show #!8 models
    5279 
    5280 > show #!2 models
    5281 
    5282 > color #2 #b2b2b2ff models
    5283 
    5284 > ui tool show "Color Zone"
    5285 
    5286 > color zone #2 near #8 distance 5.57
    5287 
    5288 > volume splitbyzone #2
    5289 
    5290 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
    5291 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5292 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
    5293 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5294 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
    5295 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5296 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
    5297 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5298 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
    5299 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5300 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
    5301 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5302 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
    5303 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5304 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
    5305 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5306 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
    5307 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5308 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
    5309 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5310 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
    5311 size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 
    5312 
    5313 > hide #!17 models
    5314 
    5315 > show #!17 models
    5316 
    5317 > show #!18 models
    5318 
    5319 > hide #!18 models
    5320 
    5321 > hide #!17 models
    5322 
    5323 > show #!17 models
    5324 
    5325 > hide #!8 models
    5326 
    5327 > save C:\Users\David/Desktop/new-snaps/EatA-15_Fig4.png supersample 4 width
    5328 > 3000 height 2600
    5329 
    5330 > show #!8 models
    5331 
    5332 > color #17.2 #6495edb4 models
    5333 
    5334 > color #17.2 #6495ed8c models
    5335 
    5336 > color #17.3 #ff00ff8c models
    5337 
    5338 > color #17.4 #ffffff8c models
    5339 
    5340 > color #17.5 #ffd7008c models
    5341 
    5342 > color #17.6 #7dcdd28c models
    5343 
    5344 > color #17.7 #ff00008c models
    5345 
    5346 > color #17.8 #77889991 models
    5347 
    5348 > color #17.8 #7788998c models
    5349 
    5350 > color #17.9 #ff69b48c models
    5351 
    5352 > color #17.10 #36558f8c models
    5353 
    5354 > color #17.11 #98a8c58c models
    5355 
    5356 > save C:\Users\David/Desktop/new-snaps/EatA-15_Fig4_transp.png supersample 4
    5357 > width 3000 height 2600
    5358 
    5359 > show #!15 models
    5360 
    5361 > hide #!17 models
    5362 
    5363 > hide #!8 models
    5364 
    5365 > show #!7 models
    5366 
    5367 > color #15.1 #b2b2b2ff models
    5368 
    5369 > color #15.2 rebeccapurple models
    5370 
    5371 > color #15.3 #7b5d99ff models
    5372 
    5373 > color #15.2 #663399fe models
    5374 
    5375 > color #15.2 rebeccapurple models
    5376 
    5377 > color #15.4 cornflowerblue models
    5378 
    5379 > color #15.4 #6495edfe models
    5380 
    5381 > color #15.4 cornflowerblue models
    5382 
    5383 > color #15.5 magenta models
    5384 
    5385 [Repeated 1 time(s)]
    5386 
    5387 > color #15.6 white models
    5388 
    5389 [Repeated 1 time(s)]
    5390 
    5391 > color #15.7 gold models
    5392 
    5393 [Repeated 1 time(s)]
    5394 
    5395 > color #15.8 #7dcdd2ff models
    5396 
    5397 [Repeated 1 time(s)]
    5398 
    5399 > color #15.9 red models
    5400 
    5401 [Repeated 1 time(s)]
    5402 
    5403 > save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4-notransp.png supersample
    5404 > 4 width 3000 height 2600
    5405 
    5406 > close #15
    5407 
    5408 > show #!1 models
    5409 
    5410 > color #1 #b2b2b2ff models
    5411 
    5412 > color zone #1 near #7 distance 5.57
    5413 
    5414 > volume splitbyzone #1
    5415 
    5416 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
    5417 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    5418 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
    5419 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    5420 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
    5421 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    5422 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
    5423 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    5424 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
    5425 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    5426 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
    5427 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    5428 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
    5429 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    5430 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
    5431 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    5432 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
    5433 size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 
    5434 
    5435 > hide #!7 models
    5436 
    5437 > save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4.png supersample 4 width
    5438 > 3000 height 2600
    5439 
    5440 > color #15.2 #6633998c models
    5441 
    5442 > color #15.3 #7b5d998c models
    5443 
    5444 > color #15.1 #b2b2b28c models
    5445 
    5446 > color #15.4 #6495ed8c models
    5447 
    5448 > color #15.5 #ff00ff8c models
    5449 
    5450 > color #15.6 #ffffff8c models
    5451 
    5452 > color #15.7 #ffd7008c models
    5453 
    5454 > color #15.8 #7dcdd28c models
    5455 
    5456 > color #15.9 #ff00008c models
    5457 
    5458 > show #!7 models
    5459 
    5460 > select #7,8,9,10,11/A:78,106,211
    5461 
    5462 117 atoms, 107 bonds, 15 residues, 5 models selected 
    5463 
    5464 > show sel & #!7 atoms
    5465 
    5466 > select clear
    5467 
    5468 > save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4-tranps.png supersample 4
    5469 > width 3000 height 2600
    5470 
    5471 > hide #!15 models
    5472 
    5473 > hide #!7 models
    5474 
    5475 > show #10 models
    5476 
    5477 > show #!21 models
    5478 
    5479 > select #7,8,9,10,11,12/A
    5480 
    5481 35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected 
    5482 
    5483 > show sel & #10 cartoons
    5484 
    5485 > hide #!21 models
    5486 
    5487 > show #!21 models
    5488 
    5489 > hide #!21 models
    5490 
    5491 > show #!21 models
    5492 
    5493 > hide #10 models
    5494 
    5495 > select clear
    5496 
    5497 > save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4.png supersample 4 width
    5498 > 3000 height 2600
    5499 
    5500 > show #10 models
    5501 
    5502 > color #21.1 #b2b2b28c models
    5503 
    5504 > color #21.2 #2c514c02 models
    5505 
    5506 > color #21.2 #2c514c8c models
    5507 
    5508 > color #21.3 #6ea0988c models
    5509 
    5510 > color #21.4 #6495ed8c models
    5511 
    5512 > color #21.5 #ff00ff8c models
    5513 
    5514 > color #21.6 #ffffff8c models
    5515 
    5516 > color #21.7 #ffd7008c models
    5517 
    5518 > color #21.8 #7dcdd28c models
    5519 
    5520 > color #21.9 #ff00008c models
    5521 
    5522 > color #21.10 #7788998c models
    5523 
    5524 > color #21.11 #ff69b48c models
    5525 
    5526 > select clear
    5527 
    5528 > save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4-transp.png supersample 4
    5529 > width 3000 height 2600
    5530 
    5531 > select #7,8,9,10,11/A:78,106,211
    5532 
    5533 117 atoms, 107 bonds, 15 residues, 5 models selected 
    5534 
    5535 > show sel & #10 atoms
    5536 
    5537 > select clear
    5538 
    5539 > save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4-transp.png supersample 4
    5540 > width 3000 height 2600
    5541 
    5542 > close #21
    5543 
    5544 > show #!4 models
    5545 
    5546 > volume #4 level 10.16
    5547 
    5548 > hide #!4 models
    5549 
    5550 > show #!4 models
    5551 
    5552 > hide #10 models
    5553 
    5554 > save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4.png supersample 4 width
    5555 > 3000 height 2600
    5556 
    5557 > hide #!4 models
    5558 
    5559 > show #!4 models
    5560 
    5561 > color zone #13 near #10 distance 12.16
    5562 
    5563 > volume splitbyzone #13
    5564 
    5565 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356,
    5566 pixel 0.86, shown at level 4.3, step 1, values float32 
    5567 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356,
    5568 pixel 0.86, shown at level 4.3, step 1, values float32 
    5569 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356,
    5570 pixel 0.86, shown at level 4.3, step 1, values float32 
    5571 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356,
    5572 pixel 0.86, shown at level 4.3, step 1, values float32 
    5573 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356,
    5574 pixel 0.86, shown at level 4.3, step 1, values float32 
    5575 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356,
    5576 pixel 0.86, shown at level 4.3, step 1, values float32 
    5577 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356,
    5578 pixel 0.86, shown at level 4.3, step 1, values float32 
    5579 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356,
    5580 pixel 0.86, shown at level 4.3, step 1, values float32 
    5581 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356,
    5582 pixel 0.86, shown at level 4.3, step 1, values float32 
    5583 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size
    5584 356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32 
    5585 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size
    5586 356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32 
    5587 
    5588 > hide #!4 models
    5589 
    5590 > hide #!19 models
    5591 
    5592 > show #!19 models
    5593 
    5594 > close #19
    5595 
    5596 > show #!13 models
    5597 
    5598 > volume #13 level 5.725
    5599 
    5600 > show #10 models
    5601 
    5602 > hide #10 models
    5603 
    5604 > color zone #13 near #10 distance 12.16
    5605 
    5606 > volume splitbyzone #13
    5607 
    5608 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356,
    5609 pixel 0.86, shown at level 5.72, step 1, values float32 
    5610 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356,
    5611 pixel 0.86, shown at level 5.72, step 1, values float32 
    5612 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356,
    5613 pixel 0.86, shown at level 5.72, step 1, values float32 
    5614 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356,
    5615 pixel 0.86, shown at level 5.72, step 1, values float32 
    5616 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356,
    5617 pixel 0.86, shown at level 5.72, step 1, values float32 
    5618 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356,
    5619 pixel 0.86, shown at level 5.72, step 1, values float32 
    5620 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356,
    5621 pixel 0.86, shown at level 5.72, step 1, values float32 
    5622 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356,
    5623 pixel 0.86, shown at level 5.72, step 1, values float32 
    5624 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356,
    5625 pixel 0.86, shown at level 5.72, step 1, values float32 
    5626 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size
    5627 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 
    5628 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size
    5629 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 
    5630 
    5631 > save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4.png supersample 4 width
    5632 > 3000 height 2600
    5633 
    5634 > show #10 models
    5635 
    5636 > color #19.1 #b2b2b28c models
    5637 
    5638 > color #19.2 #2c514c8c models
    5639 
    5640 > color #19.3 #6ea098fe models
    5641 
    5642 > color #19.3 #6ea09801 models
    5643 
    5644 > color #19.3 #6ea0988c models
    5645 
    5646 > color #19.4 #6495ed8c models
    5647 
    5648 > color #19.5 #ff00ff8c models
    5649 
    5650 > color #19.6 #ffffff8c models
    5651 
    5652 > color #19.7 #ffd7008c models
    5653 
    5654 > color #19.8 #7dcdd28c models
    5655 
    5656 > color #19.9 #ff00008c models
    5657 
    5658 > color #19.10 #7788998c models
    5659 
    5660 > color #19.11 #ff69b48c models
    5661 
    5662 > select clear
    5663 
    5664 > save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4-transp.png supersample 4
    5665 > width 3000 height 2600
    5666 
    5667 > hide #!19 models
    5668 
    5669 > hide #10 models
    5670 
    5671 > show #!11 models
    5672 
    5673 > show #!22 models
    5674 
    5675 > hide #!22 models
    5676 
    5677 > show #!20 models
    5678 
    5679 > hide #!11 models
    5680 
    5681 > save C:\Users\David/Desktop/new-snaps/SepA-40_Fig4.png supersample 4 width
    5682 > 3000 height 2600
    5683 
    5684 > show #!11 models
    5685 
    5686 > color #20.1 #b2b2b28c models
    5687 
    5688 > color #20.2 #6495ed8c models
    5689 
    5690 > color #20.3 #ff00ff8c models
    5691 
    5692 > color #20.4 #ffffff8c models
    5693 
    5694 > color #20.5 #ffd7008c models
    5695 
    5696 > color #20.6 #7dcdd28c models
    5697 
    5698 > color #20.7 #ff00008c models
    5699 
    5700 > color #20.8 #7788998c models
    5701 
    5702 > color #20.9 #ff69b4fe models
    5703 
    5704 > color #20.9 #ff69b48c models
    5705 
    5706 > color #20.10 #ecb0e18c models
    5707 
    5708 > color #20.11 #f7dff38c models
    5709 
    5710 > select #7,8,9,10,11/A:78,106,211
    5711 
    5712 117 atoms, 107 bonds, 15 residues, 5 models selected 
    5713 
    5714 > show sel & #!11 atoms
    5715 
    5716 > save C:\Users\David/Desktop/new-snaps/SepA-40_Fig4-transp.png supersample 4
    5717 > width 3000 height 2600
    5718 
    5719 > hide #!20 models
    5720 
    5721 > show #!22 models
    5722 
    5723 > hide #!11 models
    5724 
    5725 > show #!12 models
    5726 
    5727 > hide #!22 models
    5728 
    5729 > show #!14 models
    5730 
    5731 > volume #14 level 0.05935
    5732 
    5733 > close #22
    5734 
    5735 > color zone #14 near #12 distance 18.16
    5736 
    5737 > volume splitbyzone #14
    5738 
    5739 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1,
    5740 grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
    5741 float32 
    5742 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2,
    5743 grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
    5744 float32 
    5745 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3,
    5746 grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
    5747 float32 
    5748 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4,
    5749 grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
    5750 float32 
    5751 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5,
    5752 grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
    5753 float32 
    5754 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6,
    5755 grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
    5756 float32 
    5757 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7,
    5758 grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
    5759 float32 
    5760 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8,
    5761 grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
    5762 float32 
    5763 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9,
    5764 grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
    5765 float32 
    5766 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
    5767 #21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
    5768 values float32 
    5769 
    5770 > hide #!21 models
    5771 
    5772 > hide #!12 models
    5773 
    5774 > show #!21 models
    5775 
    5776 > save C:\Users\David/Desktop/new-snaps/Pic-40.png supersample 4 width 3000
    5777 > height 2600
    5778 
    5779 > show #!12 models
    5780 
    5781 > color #21.1 #b2b2b28c models
    5782 
    5783 > color #21.2 #6495ed8c models
    5784 
    5785 > color #21.3 #ff00ff8c models
    5786 
    5787 > color #21.4 #ffffff8c models
    5788 
    5789 > color #21.5 #7dcdd28c models
    5790 
    5791 > color #21.6 #ff00008c models
    5792 
    5793 > color #21.7 #7788998c models
    5794 
    5795 > color #21.8 #ff69b48c models
    5796 
    5797 > color #21.9 #ecb0e18c models
    5798 
    5799 > save C:\Users\David/Desktop/new-snaps/Pic-40-tranps.png supersample 4 width
    5800 > 3000 height 2600
    5801 
    5802 > color #21.10 #f7dff38c models
    5803 
    5804 > select #7,8,9,10,11/A:78,106,211
    5805 
    5806 117 atoms, 107 bonds, 15 residues, 5 models selected 
    5807 
    5808 > select #12/A:72,100,203
    5809 
    5810 15 atoms, 12 bonds, 3 residues, 1 model selected 
    5811 
    5812 > show sel atoms
    5813 
    5814 > select clear
    5815 
    5816 > save C:\Users\David/Desktop/new-snaps/Pic-40-tranps.png supersample 4 width
    5817 > 3000 height 2600
    5818 
    5819 > hide #!21 models
    5820 
    5821 > show #!23 models
    5822 
    5823 > show #!7 models
    5824 
    5825 > show #!8 models
    5826 
    5827 > show #!9 models
    5828 
    5829 > show #10 models
    5830 
    5831 > show #!11 models
    5832 
    5833 > hide #!7 models
    5834 
    5835 > show #16 models
    5836 
    5837 > select #7,8,9,10,11,12/A
    5838 
    5839 35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected 
    5840 
    5841 > hide sel & #10#!8-9,11-12 cartoons
    5842 
    5843 > hide sel & #10#!8-9,11-12 atoms
    5844 
    5845 > select clear
    5846 
    5847 > save C:\Users\David/Desktop/new-snaps/overlay.png supersample 4 width 3000
    5848 > height 2600
    5849 
    5850 > hide #!11 models
    5851 
    5852 > hide #!12 models
    5853 
    5854 > save C:\Users\David/Desktop/new-snaps/overlay.png supersample 4 width 3000
    5855 > height 2600
    5856 
    5857 > save C:\Users\David/Desktop/new-snaps/overlay.png supersample 4 width 3000
    5858 > height 2700
    5859 
    5860 > save C:\Users\David/Desktop/new-snaps/overlay.png supersample 4 width 3000
    5861 > height 2600
    5862 
    5863 > hide #!23 models
    5864 
    5865 > select #7,8,9,10,11,12/A
    5866 
    5867 35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected 
    5868 
    5869 > show sel & #10#!8-9 cartoons
    5870 
    5871 > select clear
    5872 
    5873 > hide #!8 models
    5874 
    5875 > hide #!9 models
    5876 
    5877 > hide #10 models
    5878 
    5879 > hide #16 models
    5880 
    5881 > show #!7 models
    5882 
    5883 > show #!15 models
    5884 
    5885 > hide #!15 models
    5886 
    5887 > save C:\Users\David/Desktop/new-snaps/25-1.png supersample 4 width 3000
    5888 > height 2700
    5889 
    5890 > show #!15 models
    5891 
    5892 > hide #!15.3 models
    5893 
    5894 > hide #!15.2 models
    5895 
    5896 > hide #!15.1 models
    5897 
    5898 > save C:\Users\David/Desktop/new-snaps/25-1.png supersample 4 width 3000
    5899 > height 2700
    5900 
    5901 [Repeated 2 time(s)]
    5902 
    5903 > hide #!15 models
    5904 
    5905 > hide #!7 models
    5906 
    5907 > show #!8 models
    5908 
    5909 > show #!17 models
    5910 
    5911 > hide #!17.11 models
    5912 
    5913 > hide #!17.10 models
    5914 
    5915 > save C:\Users\David/Desktop/new-snaps/15-1.png supersample 4 width 3000
    5916 > height 2700
    5917 
    5918 > hide #!17 models
    5919 
    5920 > hide #!8 models
    5921 
    5922 > show #!9 models
    5923 
    5924 > show #!18 models
    5925 
    5926 > hide #!18.11 models
    5927 
    5928 > hide #!18.10 models
    5929 
    5930 > save C:\Users\David/Desktop/new-snaps/40-1.png supersample 4 width 3000
    5931 > height 2700
    5932 
    5933 > hide #!18 models
    5934 
    5935 > hide #!9 models
    5936 
    5937 > show #10 models
    5938 
    5939 > show #!19 models
    5940 
    5941 > hide #!19.10 models
    5942 
    5943 > show #!19.10 models
    5944 
    5945 > hide #!19.3 models
    5946 
    5947 > hide #!19.2 models
    5948 
    5949 > save C:\Users\David/Desktop/new-snaps/G12-1.png supersample 4 width 3000
    5950 > height 2700
    5951 
    5952 > hide #!19 models
    5953 
    5954 > show #!19 models
    5955 
    5956 > hide #!19 models
    5957 
    5958 > hide #10 models
    5959 
    5960 > show #!9 models
    5961 
    5962 > show #!8 models
    5963 
    5964 > hide #!9 models
    5965 
    5966 > show #!17 models
    5967 
    5968 > save C:\Users\David/Desktop/new-snaps/15-1.png supersample 4 width 3000
    5969 > height 2700
    5970 
    5971 [Repeated 1 time(s)]
    5972 
    5973 > hide #!17 models
    5974 
    5975 > hide #!8 models
    5976 
    5977 > show #!9 models
    5978 
    5979 > show #!18 models
    5980 
    5981 > save C:\Users\David/Desktop/new-snaps/40-1.png supersample 4 width 3000
    5982 > height 2700
    5983 
    5984 > hide #!18 models
    5985 
    5986 > hide #!9 models
    5987 
    5988 > show #!7 models
    5989 
    5990 > show #!15 models
    5991 
    5992 > save C:\Users\David/Desktop/new-snaps/25-1.png supersample 4 width 3000
    5993 > height 2700
    5994 
    5995 > view
    5996 
    5997 > save C:\Users\David/Desktop/new-snaps/25-1.png supersample 4 width 3000
    5998 > height 2700
    5999 
    6000 > hide #!15 models
    6001 
    6002 > hide #!7 models
    6003 
    6004 > show #10 models
    6005 
    6006 > hide #10 models
    6007 
    6008 > show #!9 models
    6009 
    6010 > show #!18 models
    6011 
    6012 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
    6013 > aligned_Fig4-edit.cxs
    6014 
    6015 ——— End of log from Sun Nov 2 23:30:54 2025 ———
    6016 
    6017 opened ChimeraX session 
    6018 
    6019 > hide #!9 models
    6020 
    6021 > hide #!18 models
    6022 
    6023 > show #10 models
    6024 
    6025 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
    6026 > FINAL-MAP/composite_map_J1626+J1599+J1295.ccp4
    6027 
    6028 Opened composite_map_J1626+J1599+J1295.ccp4 as #4, grid size 356,356,356,
    6029 pixel 0.86, shown at level 1.85, step 2, values float32 
    6030 
    6031 > volume #4 step 1
    6032 
    6033 > volume #4 level 10.77
    6034 
    6035 > volume #4 level 11
    6036 
    6037 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
    6038 > FINAL-MAP/EatA-FabG12_RSR_real_space_refined_013.pdb
    6039 
    6040 Chain information for EatA-FabG12_RSR_real_space_refined_013.pdb #22 
    6041 --- 
    6042 Chain | Description 
    6043 A | No description available 
    6044 B | No description available 
    6045 C | No description available 
    6046  
    6047 
    6048 > hide #!22 models
    6049 
    6050 > show #!22 models
    6051 
    6052 > select #22
    6053 
    6054 8934 atoms, 9092 bonds, 28 pseudobonds, 1172 residues, 2 models selected 
    6055 
    6056 > color (#!22 & sel) #55ffffff
    6057 
    6058 > color (#!22 & sel) #ffffffff
    6059 
    6060 > hide #!4 models
    6061 
    6062 > select clear
    6063 
    6064 > hide #10 models
    6065 
    6066 > show #10 models
    6067 
    6068 > show #!4 models
    6069 
    6070 > color #4 #b2b2b2b4 models
    6071 
    6072 > hide #10 models
    6073 
    6074 > select #22/A:1-256
    6075 
    6076 1600 atoms, 1633 bonds, 6 pseudobonds, 210 residues, 2 models selected 
    6077 
    6078 > color (#!22 & sel) cornflower blue
    6079 
    6080 > select clear
    6081 
    6082 > select #22/A:78,106,211
    6083 
    6084 24 atoms, 22 bonds, 3 residues, 1 model selected 
    6085 
    6086 > color sel magenta
    6087 
    6088 > select clear
    6089 
    6090 > select #22/A:481-560
    6091 
    6092 151 atoms, 149 bonds, 1 pseudobond, 19 residues, 2 models selected 
    6093 
    6094 > ui tool show "Color Actions"
    6095 
    6096 > color sel gold
    6097 
    6098 > select clear
    6099 
    6100 > select #22/A:611-629
    6101 
    6102 117 atoms, 120 bonds, 1 pseudobond, 15 residues, 2 models selected 
    6103 
    6104 > color (#!22 & sel) #7dcdd2ff
    6105 
    6106 > select #22/A:669-699
    6107 
    6108 185 atoms, 182 bonds, 3 pseudobonds, 27 residues, 2 models selected 
    6109 
    6110 > color (#!22 & sel) #ff0000ff
    6111 
    6112 > select #22/A:781-794
    6113 
    6114 51 atoms, 52 bonds, 1 pseudobond, 7 residues, 2 models selected 
    6115 
    6116 > color (#!22 & sel) #778899ff
    6117 
    6118 > color (#!22 & sel) #ff69b4ff
    6119 
    6120 > select #22/B
    6121 
    6122 1586 atoms, 1627 bonds, 3 pseudobonds, 208 residues, 2 models selected 
    6123 
    6124 > color (#!22 & sel) #2c514cff
    6125 
    6126 > select #22/C
    6127 
    6128 1567 atoms, 1600 bonds, 3 pseudobonds, 202 residues, 2 models selected 
    6129 
    6130 > color (#!22 & sel) #6ea098ff
    6131 
    6132 > select clear
    6133 
    6134 > ui tool show "Color Zone"
    6135 
    6136 > color zone #4 near #22 distance 5.16
    6137 
    6138 > hide #!22 models
    6139 
    6140 > color zone #4 near #22 distance 6.67
    6141 
    6142 > color zone #4 near #22 distance 5.6
    6143 
    6144 > color zone #4 near #22 distance 4.84
    6145 
    6146 > graphics silhouettes width 1
    6147 
    6148 > save C:\Users\David/Desktop/new-snaps/EMDB/EatA-G12-2.png supersample 4
    6149 > width 500 height 500
    6150 
    6151 [Repeated 2 time(s)]
    6152 
    6153 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
    6154 > FINAL-MAP/cryosparc_P6_J1626_007_volume_map_sharp.mrc
    6155 
    6156 Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #24, grid size
    6157 356,356,356, pixel 0.86, shown at level 0.0179, step 2, values float32 
    6158 
    6159 > volume #24 step 1
    6160 
    6161 > volume #24 level 0.06059
    6162 
    6163 > hide #!4 models
    6164 
    6165 > show #!4 models
    6166 
    6167 > volume #24 level 0.0747
    6168 
    6169 > hide #!24 models
    6170 
    6171 > hide #!4 models
    6172 
    6173 > show #!4 models
    6174 
    6175 > save C:\Users\David/Desktop/new-snaps/EMDB/EatA-G12-2.png supersample 4
    6176 > width 500 height 500
    6177 
    6178 > hide #!4 models
    6179 
    6180 > show #!24 models
    6181 
    6182 > color zone #24 near #22 distance 5.16
    6183 
    6184 > color zone #24 near #22 distance 5.53
    6185 
    6186 > color #24 #b2b2b2ff models
    6187 
    6188 > color zone #24 near #22 distance 5.53
    6189 
    6190 > color zone #24 near #22 distance 4.88
    6191 
    6192 > save C:\Users\David/Desktop/new-snaps/EMDB/EatA-G12-consens.png supersample
    6193 > 4 width 500 height 500
    6194 
    6195 > hide #!24 models
    6196 
    6197 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
    6198 > FINAL-
    6199 > MAP/J1599/J1599-resampled/cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc
    6200 
    6201 Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #25, grid size
    6202 356,356,356, pixel 0.86, shown at level 0.0252, step 2, values float32 
    6203 
    6204 > show #!4 models
    6205 
    6206 > volume #25 step 1
    6207 
    6208 > volume #25 level 0.2254
    6209 
    6210 > hide #!4 models
    6211 
    6212 > show #!4 models
    6213 
    6214 > hide #!4 models
    6215 
    6216 > show #!4 models
    6217 
    6218 > hide #!4 models
    6219 
    6220 > show #!4 models
    6221 
    6222 > hide #!4 models
    6223 
    6224 > show #!4 models
    6225 
    6226 > hide #!4 models
    6227 
    6228 > color #25 #b2b2b2ff models
    6229 
    6230 > color zone #24 near #22 distance 4.91
    6231 
    6232 > color zone #25 near #22 distance 5.16
    6233 
    6234 > color zone #25 near #22 distance 4.88
    6235 
    6236 > save C:\Users\David/Desktop/new-snaps/EMDB/EatA-G12-loc-1.png supersample 4
    6237 > width 500 height 500
    6238 
    6239 > hide #!25 models
    6240 
    6241 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
    6242 > FINAL-MAP/J1295/cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc
    6243 
    6244 Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #26, grid size
    6245 356,356,356, pixel 0.86, shown at level 0.0291, step 2, values float32 
    6246 
    6247 > volume #26 step 1
    6248 
    6249 > volume #26 level 0.1905
    6250 
    6251 > show #!4 models
    6252 
    6253 > volume #26 level 0.2291
    6254 
    6255 > hide #!4 models
    6256 
    6257 > color #26 #b2b2b2ff models
    6258 
    6259 > color zone #25 near #22 distance 4.85
    6260 
    6261 > color zone #26 near #22 distance 5.16
    6262 
    6263 > color zone #26 near #22 distance 5.39
    6264 
    6265 > color zone #26 near #22 distance 5.04
    6266 
    6267 > save C:\Users\David/Desktop/new-snaps/EMDB/EatA-G12-loc-2.png supersample 4
    6268 > width 500 height 500
    6269 
    6270 > volume #26 level 0.23
    6271 
    6272 > volume #26 level 0.229
    6273 
    6274 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
    6275 > aligned_Fig4-edit.cxs
    6276 
    6277 ——— End of log from Sun Nov 16 18:26:26 2025 ———
    6278 
    6279 opened ChimeraX session 
    6280 
    6281 > show #!1 models
    6282 
    6283 > show #!2 models
    6284 
    6285 > hide #!2 models
    6286 
    6287 > show #!3 models
    6288 
    6289 > hide #!3 models
    6290 
    6291 > show #!4 models
    6292 
    6293 > hide #!4 models
    6294 
    6295 > show #!5 models
    6296 
    6297 > hide #!5 models
    6298 
    6299 > show #!6 models
    6300 
    6301 > hide #!6 models
    6302 
    6303 > show #!7 models
    6304 
    6305 > hide #!7 models
    6306 
    6307 > show #!8 models
    6308 
    6309 > hide #!8 models
    6310 
    6311 > show #!9 models
    6312 
    6313 > hide #!9 models
    6314 
    6315 > show #10 models
    6316 
    6317 > hide #10 models
    6318 
    6319 > show #!11 models
    6320 
    6321 > hide #!11 models
    6322 
    6323 > show #!12 models
    6324 
    6325 > hide #!12 models
    6326 
    6327 > show #!13 models
    6328 
    6329 > hide #!13 models
    6330 
    6331 > show #!14 models
    6332 
    6333 > hide #!14 models
    6334 
    6335 > show #!15 models
    6336 
    6337 > hide #!15 models
    6338 
    6339 > show #16 models
    6340 
    6341 > hide #16 models
    6342 
    6343 > show #!17 models
    6344 
    6345 > hide #!1 models
    6346 
    6347 > hide #!26 models
    6348 
    6349 > show #!17.10 models
    6350 
    6351 > show #!17.11 models
    6352 
    6353 > hide #!17 models
    6354 
    6355 > show #!18 models
    6356 
    6357 > show #!18.10 models
    6358 
    6359 > show #!18.11 models
    6360 
    6361 > hide #!18 models
    6362 
    6363 > show #!19.2 models
    6364 
    6365 > show #!19.3 models
    6366 
    6367 > show #!4 models
    6368 
    6369 > hide #!4 models
    6370 
    6371 > show #!4 models
    6372 
    6373 > hide #!4 models
    6374 
    6375 > show #!4 models
    6376 
    6377 > hide #!4 models
    6378 
    6379 > show #!4 models
    6380 
    6381 > show #!1 models
    6382 
    6383 > hide #!4 models
    6384 
    6385 > show #!4 models
    6386 
    6387 > hide #!4 models
    6388 
    6389 > show #!5 models
    6390 
    6391 > hide #!5 models
    6392 
    6393 > show #!5 models
    6394 
    6395 > hide #!1 models
    6396 
    6397 > show #!4 models
    6398 
    6399 > hide #!19 models
    6400 
    6401 > hide #!4 models
    6402 
    6403 > hide #!5 models
    6404 
    6405 > show #!4 models
    6406 
    6407 > show #!13 models
    6408 
    6409 > hide #!13 models
    6410 
    6411 > show #!5 models
    6412 
    6413 > hide #!4 models
    6414 
    6415 > show #!4 models
    6416 
    6417 > select #4
    6418 
    6419 2 models selected 
    6420 
    6421 > ui mousemode right "translate selected models"
    6422 
    6423 > view matrix models #4,1,0,0,-0.14988,0,1,0,-3.7143,0,0,1,-3.0634
    6424 
    6425 > ui mousemode right "rotate selected models"
    6426 
    6427 > view matrix models
    6428 > #4,0.99843,0.053725,-0.015885,-4.5976,-0.053323,0.99827,0.024706,1.0648,0.017185,-0.02382,0.99957,-2.5236
    6429 
    6430 > view matrix models
    6431 > #4,0.99867,-0.036628,0.036363,-0.56328,0.036145,0.99925,0.013864,-11.278,-0.036844,-0.012531,0.99924,4.3952
    6432 
    6433 > ui tool show "Fit in Map"
    6434 
    6435 > fitmap #4 inMap #5
    6436 
    6437 Fit map composite_map_J1626+J1599+J1295.ccp4 in map
    6438 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 80208 points 
    6439 correlation = 0.3463, correlation about mean = 0.1333, overlap = 1.079e+05 
    6440 steps = 176, shift = 4.02, angle = 2.47 degrees 
    6441  
    6442 Position of composite_map_J1626+J1599+J1295.ccp4 (#4) relative to
    6443 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: 
    6444 Matrix rotation and translation 
    6445 0.99760209 -0.02760094 0.06346856 -9.70153389 
    6446 0.02472356 0.99865001 0.04568259 -14.87071002 
    6447 -0.06464377 -0.04400387 0.99693773 13.51873268 
    6448 Axis -0.54386119 0.77687675 0.31729722 
    6449 Axis point 210.45522440 0.00000000 177.83322647 
    6450 Rotation angle (degrees) 4.72960394 
    6451 Shift along axis -1.98696477 
    6452  
    6453 
    6454 > select clear
    6455 
    6456 > show #!13 models
    6457 
    6458 > hide #!13 models
    6459 
    6460 > show #!13 models
    6461 
    6462 > hide #!13 models
    6463 
    6464 > hide #!4 models
    6465 
    6466 > hide #!5 models
    6467 
    6468 > show #!4 models
    6469 
    6470 > hide #!4 models
    6471 
    6472 > show #!4 models
    6473 
    6474 > hide #!4 models
    6475 
    6476 > show #!4 models
    6477 
    6478 > show #!22 models
     1243[deleted to fit within ticket limits]
     1244
    64791245
    64801246> ui tool show Matchmaker