Changes between Initial Version and Version 1 of Ticket #17117


Ignore:
Timestamp:
Mar 18, 2025, 10:28:15 AM (7 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #17117

    • Property Component Unassigned → Window Toolkit
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Summary ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0

  • Ticket #17117 – Description

    initial v1  
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    1307     "name" : "_version.cpython-39-darwin.so"
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    1316     "name" : "_frame.cpython-39-darwin.so"
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    1325     "name" : "_serialize.cpython-39-darwin.so"
    1326   },
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    1334     "name" : "_cmsgpack.cpython-39-darwin.so"
    1335   },
    1336   {
    1337     "source" : "P",
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    1340     "size" : 16384,
    1341     "uuid" : "fbf8d47b-2bb8-3f78-890a-f19dcbb40bad",
    1342     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/linalg\/lapack_lite.cpython-39-darwin.so",
    1343     "name" : "lapack_lite.cpython-39-darwin.so"
    1344   },
    1345   {
    1346     "source" : "P",
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    1349     "size" : 65536,
    1350     "uuid" : "3bedbea4-7c23-3bad-9ce5-813496293b51",
    1351     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/atomic\/_ribbons.cpython-39-darwin.so",
    1352     "name" : "_ribbons.cpython-39-darwin.so"
    1353   },
    1354   {
    1355     "source" : "P",
    1356     "arch" : "arm64",
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    1358     "size" : 16384,
    1359     "uuid" : "f07242dd-5047-3799-b386-41fcd2016b50",
    1360     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/graphics\/_graphics.cpython-39-darwin.so",
    1361     "name" : "_graphics.cpython-39-darwin.so"
    1362   },
    1363   {
    1364     "source" : "P",
    1365     "arch" : "arm64",
    1366     "base" : 13597949952,
    1367     "size" : 409600,
    1368     "uuid" : "a2249abe-0d9f-3c5a-95e1-1dd0ea609d14",
    1369     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/mmcif\/mmcif.cpython-39-darwin.so",
    1370     "name" : "mmcif.cpython-39-darwin.so"
    1371   },
    1372   {
    1373     "source" : "P",
    1374     "arch" : "arm64",
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    1376     "size" : 409600,
    1377     "uuid" : "68ecb7a1-b0c3-3f74-92a8-607b70894d0c",
    1378     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-39-darwin.so",
    1379     "name" : "_mmcif.cpython-39-darwin.so"
    1380   },
    1381   {
    1382     "source" : "P",
    1383     "arch" : "arm64",
    1384     "base" : 13599424512,
    1385     "size" : 147456,
    1386     "uuid" : "f2a7c02c-70ba-341d-90ac-b566424c2dc7",
    1387     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/pdb\/_pdbio.cpython-39-darwin.so",
    1388     "name" : "_pdbio.cpython-39-darwin.so"
    1389   },
    1390   {
    1391     "source" : "P",
    1392     "arch" : "arm64",
    1393     "base" : 6085623808,
    1394     "size" : 32768,
    1395     "uuid" : "741a95a2-c4dc-3ba3-bee2-0bcbe3139710",
    1396     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/psutil\/_psutil_osx.abi3.so",
    1397     "name" : "_psutil_osx.abi3.so"
    1398   },
    1399   {
    1400     "source" : "P",
    1401     "arch" : "arm64",
    1402     "base" : 6085738496,
    1403     "size" : 16384,
    1404     "uuid" : "065bc7bc-cc26-3df8-a331-eedaf6a57935",
    1405     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/psutil\/_psutil_posix.abi3.so",
    1406     "name" : "_psutil_posix.abi3.so"
    1407   },
    1408   {
    1409     "source" : "P",
    1410     "arch" : "arm64",
    1411     "base" : 13432553472,
    1412     "size" : 1589248,
    1413     "uuid" : "c5672f09-915e-3f0f-8e49-2062281dd942",
    1414     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/lxml\/etree.cpython-39-darwin.so",
    1415     "name" : "etree.cpython-39-darwin.so"
    1416   },
    1417   {
    1418     "source" : "P",
    1419     "arch" : "arm64",
    1420     "base" : 6087131136,
    1421     "size" : 131072,
    1422     "uuid" : "230e85b9-62b9-3a23-888f-508b2bb21bb8",
    1423     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/lxml\/_elementpath.cpython-39-darwin.so",
    1424     "name" : "_elementpath.cpython-39-darwin.so"
    1425   },
    1426   {
    1427     "source" : "P",
    1428     "arch" : "arm64",
    1429     "base" : 6171443200,
    1430     "size" : 16384,
    1431     "uuid" : "b59a5ce9-e782-3729-8ada-e88d61ddd623",
    1432     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-39-darwin.so",
    1433     "name" : "_sw.cpython-39-darwin.so"
    1434   },
    1435   {
    1436     "source" : "P",
    1437     "arch" : "arm64",
    1438     "base" : 6171770880,
    1439     "size" : 16384,
    1440     "uuid" : "c3d03419-8cdf-37bf-b4f9-3d996fb20813",
    1441     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/alignment_algs\/libalign_algs.dylib",
    1442     "name" : "libalign_algs.dylib"
    1443   },
    1444   {
    1445     "source" : "P",
    1446     "arch" : "arm64",
    1447     "base" : 6172327936,
    1448     "size" : 16384,
    1449     "uuid" : "6593a98e-7452-3b02-b940-447003c460e2",
    1450     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/dssp\/_dssp.cpython-39-darwin.so",
    1451     "name" : "_dssp.cpython-39-darwin.so"
    1452   },
    1453   {
    1454     "source" : "P",
    1455     "arch" : "arm64",
    1456     "base" : 6323699712,
    1457     "size" : 32768,
    1458     "uuid" : "7fd04a06-1ad3-30e4-be94-85f11187afc3",
    1459     "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-39-darwin.so",
    1460     "name" : "_nw.cpython-39-darwin.so"
    1461   },
    1462   {
    1463     "source" : "P",
    1464     "arch" : "arm64e",
    1465     "base" : 6551756800,
    1466     "size" : 241656,
    1467     "uuid" : "eee9d0d3-dffc-37cb-9ced-b27cd0286d8c",
    1468     "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    1469     "name" : "libsystem_kernel.dylib"
    1470   },
    1471   {
    1472     "source" : "P",
    1473     "arch" : "arm64e",
    1474     "base" : 6551998464,
    1475     "size" : 53248,
    1476     "uuid" : "642faf7a-874e-37e6-8aba-2b0cc09a3025",
    1477     "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    1478     "name" : "libsystem_pthread.dylib"
    1479   },
    1480   {
    1481     "source" : "P",
    1482     "arch" : "arm64e",
    1483     "base" : 6550532096,
    1484     "size" : 532476,
    1485     "uuid" : "92699527-645f-3d8d-aed8-1cfb0c034e15",
    1486     "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    1487     "name" : "libsystem_c.dylib"
    1488   },
    1489   {
    1490     "source" : "P",
    1491     "arch" : "arm64e",
    1492     "base" : 6552236032,
    1493     "size" : 32748,
    1494     "uuid" : "984d08b8-f85c-36f5-9e17-5bff7fc779a3",
    1495     "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    1496     "name" : "libsystem_platform.dylib"
    1497   },
    1498   {
    1499     "source" : "P",
    1500     "arch" : "arm64e",
    1501     "base" : 6648705024,
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    1506     "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
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    1514     "uuid" : "5576e4fd-aad2-3608-8c8f-4eec421236f9",
    1515     "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    1516     "name" : "libdispatch.dylib"
    1517   },
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    1540   },
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     70[deleted to fit within ticket limits]
     71
    156872],
    156973  "sharedCache" : {
    … …  
    32531757 
    32541758
    3255 > volume #1 level 0.1462
    3256 
    3257 > hide #!1 models
    3258 
    3259 > ui tool show "Map Eraser"
    3260 
    3261 > select add #3
    3262 
    3263 1 model selected 
    3264 
    3265 > ui mousemode right "translate selected models"
    3266 
    3267 > view matrix models #3,1,0,0,177.62,0,1,0,221.79,0,0,1,116.11
    3268 
    3269 > volume erase #2 center 177.62,221.79,116.11 radius 32.12
    3270 
    3271 > view matrix models #3,1,0,0,188.72,0,1,0,194.5,0,0,1,112.11
    3272 
    3273 > view matrix models #3,1,0,0,212.28,0,1,0,201.47,0,0,1,106.94
    3274 
    3275 > volume erase #2 center 212.28,201.47,106.94 radius 32.12
    3276 
    3277 > view matrix models #3,1,0,0,220.92,0,1,0,166.89,0,0,1,106.53
    3278 
    3279 > view matrix models #3,1,0,0,227.3,0,1,0,168.78,0,0,1,111.01
    3280 
    3281 > volume erase #2 center 227.3,168.78,111.01 radius 32.12
    3282 
    3283 > view matrix models #3,1,0,0,241.37,0,1,0,186.51,0,0,1,178.42
    3284 
    3285 > view matrix models #3,1,0,0,265.96,0,1,0,195.56,0,0,1,150.36
    3286 
    3287 > view matrix models #3,1,0,0,267.41,0,1,0,191.95,0,0,1,151.06
    3288 
    3289 > view matrix models #3,1,0,0,267.98,0,1,0,191.29,0,0,1,150.88
    3290 
    3291 > volume erase #2 center 267.98,191.29,150.88 radius 32.12
    3292 
    3293 > view matrix models #3,1,0,0,249.24,0,1,0,183.14,0,0,1,169.43
    3294 
    3295 > view matrix models #3,1,0,0,247.96,0,1,0,180.13,0,0,1,176.94
    3296 
    3297 > view matrix models #3,1,0,0,247.62,0,1,0,180.93,0,0,1,175.55
    3298 
    3299 > volume erase #2 center 247.62,180.93,175.55 radius 14.85
    3300 
    3301 > view matrix models #3,1,0,0,230.85,0,1,0,183.35,0,0,1,140.43
    3302 
    3303 > view matrix models #3,1,0,0,227.29,0,1,0,181.05,0,0,1,132.78
    3304 
    3305 > volume erase #2 center 227.29,181.05,132.78 radius 14.85
    3306 
    3307 > hide #3 models
    3308 
    3309 > select subtract #3
    3310 
    3311 Nothing selected 
    3312 
    3313 > show #!1 models
    3314 
    3315 > volume #1 level 0.03006
    3316 
    3317 > hide #!2 models
    3318 
    3319 > ui tool show "Map Eraser"
    3320 
    3321 > select add #3
    3322 
    3323 1 model selected 
    3324 
    3325 > volume erase #1 center 139.02,180.94,179.91 radius 22.182
    3326 
    3327 Opened P64_W2_J50_tightTarget.mrc copy as #4, grid size 512,512,512, pixel
    3328 0.74, shown at step 1, values float32 
    3329 
    3330 > volume erase #4 center 135.12,201.97,197.24 radius 22.164
    3331 
    3332 > volume erase #4 center 153.11,212.48,222.77 radius 22.164
    3333 
    3334 > volume erase #4 center 189.01,222.98,218.1 radius 22.164
    3335 
    3336 > volume erase #4 center 207.63,218.66,207.51 radius 22.164
    3337 
    3338 > volume erase #4 center 205.67,233.05,195.36 radius 22.164
    3339 
    3340 > volume erase #4 center 240.61,226.55,200.09 radius 22.164
    3341 
    3342 > volume erase #4 center 234.06,210.34,215.07 radius 22.164
    3343 
    3344 > volume erase #4 center 165.06,178.19,208.63 radius 22.164
    3345 
    3346 > volume erase #4 center 147.44,141.75,161.18 radius 22.164
    3347 
    3348 > volume erase #4 center 168.46,130.94,174.07 radius 22.164
    3349 
    3350 > volume erase #4 center 170.77,147.86,164.7 radius 22.164
    3351 
    3352 > volume erase #4 center 150.68,174.81,163.92 radius 22.164
    3353 
    3354 > volume erase #4 center 158.83,159.78,197.76 radius 22.164
    3355 
    3356 > hide #3 models
    3357 
    3358 > select subtract #3
    3359 
    3360 Nothing selected 
    3361 
    3362 > show #!2 models
    3363 
    3364 > hide #!4 models
    3365 
    3366 > show #!4 models
    3367 
    3368 > hide #!4 models
    3369 
    3370 > show #!4 models
    3371 
    3372 > hide #!2 models
    3373 
    3374 > show #3 models
    3375 
    3376 > select add #3
    3377 
    3378 1 model selected 
    3379 
    3380 > volume erase #4 center 163.24,190.1,158.8 radius 22.164
    3381 
    3382 > volume erase #4 center 165.54,184.04,168.19 radius 22.164
    3383 
    3384 > volume erase #4 center 171.2,201.05,166.92 radius 22.164
    3385 
    3386 > undo
    3387 
    3388 [Repeated 2 time(s)]
    3389 
    3390 > show #!1 models
    3391 
    3392 > hide #!1 models
    3393 
    3394 > hide #!2 models
    3395 
    3396 > show #!2 models
    3397 
    3398 > hide #!2 models
    3399 
    3400 > show #!2 models
    3401 
    3402 > show #!1 models
    3403 
    3404 > hide #!1 models
    3405 
    3406 > show #!1 models
    3407 
    3408 > hide #!1 models
    3409 
    3410 > hide #!2 models
    3411 
    3412 > show #!1 models
    3413 
    3414 > hide #!1 models
    3415 
    3416 > hide #!4 models
    3417 
    3418 > show #!4 models
    3419 
    3420 > ui tool show "Side View"
    3421 
    3422 > show #!1 models
    3423 
    3424 > hide #!1 models
    3425 
    3426 > show #!2 models
    3427 
    3428 > show #!1 models
    3429 
    3430 > hide #!2 models
    3431 
    3432 > hide #!4 models
    3433 
    3434 > hide #!1 models
    3435 
    3436 > show #!4 models
    3437 
    3438 > show #!2 models
    3439 
    3440 > hide #!4 models
    3441 
    3442 > show #!4 models
    3443 
    3444 > hide #!2 models
    3445 
    3446 > ui tool show "Map Eraser"
    3447 
    3448 > select add #3
    3449 
    3450 1 model selected 
    3451 
    3452 > volume erase #4 center 223.42,218.19,178.35 radius 17.475
    3453 
    3454 > volume erase #4 center 211.53,221.7,173.87 radius 17.475
    3455 
    3456 > show #!1 models
    3457 
    3458 > hide #!1 models
    3459 
    3460 > show #!2 models
    3461 
    3462 > show #!1 models
    3463 
    3464 > hide #!1 models
    3465 
    3466 > show #!1 models
    3467 
    3468 > hide #!1 models
    3469 
    3470 > hide #3 models
    3471 
    3472 > select subtract #3
    3473 
    3474 Nothing selected 
    3475 
    3476 > lighting soft
    3477 
    3478 > ui tool show "Color Zone"
    3479 
    3480 > color zone #4 near #7 distance 4.44
    3481 
    3482 > color zone #4 near #7 distance 4.6
    3483 
    3484 > color zone #4 near #7 distance 72.5
    3485 
    3486 > lighting simple
    3487 
    3488 > lighting soft
    3489 
    3490 > surface dust #2 size 7.4
    3491 
    3492 > surface dust #4 size 7.4
    3493 
    3494 > color zone #4 near #7 distance 74.79
    3495 
    3496 > color zone #4 near #7 distance 58.36
    3497 
    3498 > lighting simple
    3499 
    3500 > lighting soft
    3501 
    3502 > volume #4 level 0.04729
    3503 
    3504 > lighting simple
    3505 
    3506 > volume #4 level 0.06407
    3507 
    3508 > lighting soft
    3509 
    3510 > save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    3511 > 2/Map_localref.cxs" includeMaps true
    3512 
    3513 ——— End of log from Thu Oct 31 16:48:37 2024 ———
    3514 
    3515 opened ChimeraX session 
    3516 
    3517 > lighting simple
    3518 
    3519 > hide #!2 models
    3520 
    3521 > show #!2 models
    3522 
    3523 > hide #!4 models
    3524 
    3525 > show #!4 models
    3526 
    3527 > open
    3528 > /Users/zbxg977/Desktop/BRISC_project/Phenix/RealSpaceRefine_51/P64_J12_model-
    3529 > coot-56.pdb
    3530 
    3531 Summary of feedback from opening
    3532 /Users/zbxg977/Desktop/BRISC_project/Phenix/RealSpaceRefine_51/P64_J12_model-
    3533 coot-56.pdb 
    3534 --- 
    3535 warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 3
    3536 ALA A 6 1 4 
    3537 Start residue of secondary structure not found: HELIX 2 2 LEU A 7 ARG A 9 1 3 
    3538 Start residue of secondary structure not found: HELIX 3 3 SER A 15 ASN A 24 1
    3539 10 
    3540 Start residue of secondary structure not found: HELIX 4 4 PRO A 96 ALA A 98 1
    3541 3 
    3542 Start residue of secondary structure not found: HELIX 5 5 GLN A 100 ALA A 103
    3543 1 4 
    3544 24 messages similar to the above omitted 
    3545  
    3546 P64_J12_model-coot-56.pdb title: 
    3547 Alphafold monomer V2.0 prediction for brisc and BRCA1-A complex member 2
    3548 (Q9NXR7) [more info...] 
    3549  
    3550 Chain information for P64_J12_model-coot-56.pdb #3 
    3551 --- 
    3552 Chain | Description 
    3553 A | brisc and BRCA1-A complex member 2 
    3554 B C D L S T | No description available 
    3555 F | No description available 
    3556 G | No description available 
    3557 I | No description available 
    3558 J | No description available 
    3559 M | No description available 
    3560 N | No description available 
    3561 O R | No description available 
    3562 Q | No description available 
    3563 U | No description available 
    3564 V | No description available 
    3565 W | No description available 
    3566 X | No description available 
    3567 Y | No description available 
    3568 Z | No description available 
    3569  
    3570 Non-standard residues in P64_J12_model-coot-56.pdb #3 
    3571 --- 
    3572 ZN — (ZN) 
    3573  
    3574 
    3575 > select add #3
    3576 
    3577 53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected 
    3578 
    3579 > hide sel atoms
    3580 
    3581 > show sel cartoons
    3582 
    3583 > hide #!2 models
    3584 
    3585 > hide #!4 models
    3586 
    3587 > select subtract #3
    3588 
    3589 Nothing selected 
    3590 
    3591 > colour #3/G,X,M,U #0096FF
    3592 
    3593 > colour #3/Q,F,J,W #00F900
    3594 
    3595 > colour #3/H,Y,D,I,V #9437FF
    3596 
    3597 > colour #3/L,O,R,S,T,C,B,A #FF9300
    3598 
    3599 > colour #3/E,K,N,P #EF4E5D
    3600 
    3601 > select #3/D
    3602 
    3603 602 atoms, 608 bonds, 76 residues, 1 model selected 
    3604 
    3605 > color sel orange
    3606 
    3607 > select #3/A
    3608 
    3609 1839 atoms, 1884 bonds, 231 residues, 1 model selected 
    3610 
    3611 > color sel #ff7e79ff
    3612 
    3613 > color sel byelement
    3614 
    3615 > color sel #ff2600ff
    3616 
    3617 > color sel #ff7e79ff
    3618 
    3619 > select #3/Z
    3620 
    3621 4866 atoms, 4939 bonds, 3 pseudobonds, 340 residues, 2 models selected 
    3622 
    3623 > color (#!3 & sel) #9437ffff
    3624 
    3625 > select #3/V
    3626 
    3627 1998 atoms, 2019 bonds, 5 pseudobonds, 153 residues, 2 models selected 
    3628 
    3629 > color (#!3 & sel) lime
    3630 
    3631 > ui mousemode right select
    3632 
    3633 > select clear
    3634 
    3635 > select #3/J
    3636 
    3637 4726 atoms, 4795 bonds, 6 pseudobonds, 322 residues, 2 models selected 
    3638 
    3639 > color (#!3 & sel) #ff40ffff
    3640 
    3641 > color (#!3 & sel) #9437ffff
    3642 
    3643 > select clear
    3644 
    3645 > dssp
    3646 
    3647 > show #8 models
    3648 
    3649 > hide #8 models
    3650 
    3651 > select #3/S,T
    3652 
    3653 2394 atoms, 2406 bonds, 152 residues, 1 model selected 
    3654 
    3655 > hide sel cartoons
    3656 
    3657 > show #8 models
    3658 
    3659 > select add #3
    3660 
    3661 53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected 
    3662 
    3663 > select subtract #3
    3664 
    3665 Nothing selected 
    3666 
    3667 > select #3/SQ
    3668 
    3669 Nothing selected 
    3670 
    3671 > select #3/Q
    3672 
    3673 2420 atoms, 2446 bonds, 3 pseudobonds, 183 residues, 2 models selected 
    3674 
    3675 > color (#!3 & sel) #0096ffff
    3676 
    3677 > select #3/M
    3678 
    3679 2382 atoms, 2408 bonds, 4 pseudobonds, 192 residues, 2 models selected 
    3680 
    3681 > color (#!3 & sel) #00f900ff
    3682 
    3683 > select clear
    3684 
    3685 > cartoon style width 1
    3686 
    3687 > cartoon style width 5
    3688 
    3689 > cartoon style width 2
    3690 
    3691 > cartoon style thickness 2
    3692 
    3693 > cartoon style thickness 1
    3694 
    3695 > cartoon style thickness 0.9
    3696 
    3697 > cartoon style width 2
    3698 
    3699 > cartoon style width 3
    3700 
    3701 > lighting soft
    3702 
    3703 > cartoon style width 2
    3704 
    3705 > cartoon style thickness 0.8
    3706 
    3707 > cartoon style thickness 0.7
    3708 
    3709 > lighting full
    3710 
    3711 > lighting soft
    3712 
    3713 > lighting simple
    3714 
    3715 > select #3/N
    3716 
    3717 3760 atoms, 3805 bonds, 237 residues, 1 model selected 
    3718 
    3719 > color sel #ff7e79ff
    3720 
    3721 > select clear
    3722 
    3723 > select #3/X,U
    3724 
    3725 5022 atoms, 5072 bonds, 10 pseudobonds, 378 residues, 2 models selected 
    3726 
    3727 > color (#!3 & sel) #0433ffff
    3728 
    3729 > color (#!3 & sel) #7a81ffff
    3730 
    3731 > color (#!3 & sel) #0433ffff
    3732 
    3733 > color (#!3 & sel) #0096ffff
    3734 
    3735 > color (#!3 & sel) #00fdffff
    3736 
    3737 > color (#!3 & sel) #005493ff
    3738 
    3739 [Repeated 1 time(s)]
    3740 
    3741 > color (#!3 & sel) #005493a3
    3742 
    3743 > color (#!3 & sel) #00549385
    3744 
    3745 > color (#!3 & sel) #00549380
    3746 
    3747 > color (#!3 & sel) #0096ffff
    3748 
    3749 > select clear
    3750 
    3751 > select #3/B:63
    3752 
    3753 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3754 
    3755 > show sel atoms
    3756 
    3757 > style sel stick
    3758 
    3759 Changed 9 atom styles 
    3760 
    3761 > color sel byhetero
    3762 
    3763 > select #3/O:76
    3764 
    3765 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3766 
    3767 > select clear
    3768 
    3769 > select #3/B:63
    3770 
    3771 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3772 
    3773 > hide sel atoms
    3774 
    3775 > select clear
    3776 
    3777 > style #8#!3 stick
    3778 
    3779 Changed 56848 atom styles 
    3780 
    3781 > show #8#!3 surfaces
    3782 
    3783 > surface transparency 50
    3784 
    3785 > surface transparency 80
    3786 
    3787 > hide #!3,8 surfaces
    3788 
    3789 > hide #!8 models
    3790 
    3791 > show #!8 models
    3792 
    3793 > hide #!3 models
    3794 
    3795 > show #!3 models
    3796 
    3797 > hide #!3 models
    3798 
    3799 > show #!3 models
    3800 
    3801 > select #A,Y,W
    3802 
    3803 Expected an objects specifier or a keyword 
    3804 
    3805 > select #3A,Y,W
    3806 
    3807 Expected an objects specifier or a keyword 
    3808 
    3809 > select #3/A,Y,W
    3810 
    3811 9248 atoms, 9394 bonds, 8 pseudobonds, 805 residues, 2 models selected 
    3812 
    3813 > color (#!3 & sel) light gray
    3814 
    3815 [Repeated 1 time(s)]
    3816 
    3817 > color (#!3 & sel) #c0c0c0ff
    3818 
    3819 > select #3/X,U,V
    3820 
    3821 7020 atoms, 7091 bonds, 15 pseudobonds, 531 residues, 2 models selected 
    3822 
    3823 > color (#!3 & sel) #d6d6d6ff
    3824 
    3825 > color (#!3 & sel) #c0c0c0ff
    3826 
    3827 > select #3/Z,N
    3828 
    3829 8626 atoms, 8744 bonds, 3 pseudobonds, 577 residues, 2 models selected 
    3830 
    3831 > color (#!3 & sel) #a9a9a9ff
    3832 
    3833 > color (#!3 & sel) #c0c0c0ff
    3834 
    3835 > select clear
    3836 
    3837 > select #3/I,M,Q
    3838 
    3839 9765 atoms, 9908 bonds, 7 pseudobonds, 758 residues, 2 models selected 
    3840 
    3841 > color (#!3 & sel) dim gray
    3842 
    3843 > select #3/G,F
    3844 
    3845 7112 atoms, 7179 bonds, 4 pseudobonds, 479 residues, 2 models selected 
    3846 
    3847 > select #3/G,F,J
    3848 
    3849 11838 atoms, 11974 bonds, 10 pseudobonds, 801 residues, 2 models selected 
    3850 
    3851 > color (#!3 & sel) dim gray
    3852 
    3853 > select clear
    3854 
    3855 > ui tool show "Side View"
    3856 
    3857 > spin 360
    3858 
    3859 Unknown command: spin 360 
    3860 
    3861 > roll 360
    3862 
    3863 Expected an axis vector or a keyword 
    3864 
    3865 > roll x 360
    3866 
    3867 [Repeated 2 time(s)]
    3868 
    3869 > roll x 1 360
    3870 
    3871 > roll y 1 360
    3872 
    3873 > roll x 1 90
    3874 
    3875 > roll x 2 90
    3876 
    3877 > roll x -1 90
    3878 
    3879 > roll y 1 360
    3880 
    3881 > roll x -1 90
    3882 
    3883 > roll y 1 360
    3884 
    3885 > wait 20
    3886 
    3887 > roll x -1 90
    3888 
    3889 > roll y 1 360
    3890 
    3891 > wait 150
    3892 
    3893 > roll x -1 90
    3894 
    3895 > roll y 1 360
    3896 
    3897 > wait 250
    3898 
    3899 > roll x -1 90
    3900 
    3901 > roll y 1 360
    3902 
    3903 > wait 500
    3904 
    3905 > roll x -1 90
    3906 
    3907 > roll y 1 360
    3908 
    3909 > wait 450
    3910 
    3911 > roll x -1 90
    3912 
    3913 > roll y 1 360
    3914 
    3915 > wait 420
    3916 
    3917 > roll x -1 90
    3918 
    3919 > roll y 1 360
    3920 
    3921 > wait 400
    3922 
    3923 > roll x -1 90
    3924 
    3925 > color #3,8 #0096ffff
    3926 
    3927 [Repeated 1 time(s)]
    3928 
    3929 > undo
    3930 
    3931 [Repeated 1 time(s)]
    3932 
    3933 > Color #3/G,Q #0096FF
    3934 
    3935 Unknown command: Color #3/G,Q #0096FF 
    3936 
    3937 > Sel #3/G,Q color sel #0096FF
    3938 
    3939 Unknown command: Sel #3/G,Q color sel #0096FF 
    3940 
    3941 > Sel #3/G,Q
    3942 
    3943 Unknown command: Sel #3/G,Q 
    3944 
    3945 > select #3/G,Q
    3946 
    3947 6163 atoms, 6223 bonds, 5 pseudobonds, 433 residues, 2 models selected 
    3948 
    3949 > select #3/G,Q color sel #0096FF
    3950 
    3951 Expected a keyword 
    3952 
    3953 > select #3/G,Q
    3954 
    3955 6163 atoms, 6223 bonds, 5 pseudobonds, 433 residues, 2 models selected 
    3956 
    3957 > color sel #0096FF
    3958 
    3959 > select clear
    3960 
    3961 > color #3/G,Q #0096FF
    3962 
    3963 > color #3,8 #797979ff
    3964 
    3965 > color #3,8 #919191ff
    3966 
    3967 > undo
    3968 
    3969 [Repeated 1 time(s)]
    3970 
    3971 > color #3,8 dim gray
    3972 
    3973 > undo
    3974 
    3975 [Repeated 4 time(s)]
    3976 
    3977 > select clear
    3978 
    3979 > color #3/G,Q #0096FF
    3980 
    3981 > wait 150
    3982 
    3983 > color #3/G,Q dimgray
    3984 
    3985 > color #3/G,Q #0096FF
    3986 
    3987 > wait 50
    3988 
    3989 > color #3/G,Q dimgray
    3990 
    3991 > color fade #3/G,Q #0096FF
    3992 
    3993 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    3994 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    3995 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    3996 
    3997 > wait 50
    3998 
    3999 > color #3/G,Q dimgray
    4000 
    4001 > Crossfade color #3/G,Q #0096FF
    4002 
    4003 Unknown command: Crossfade color #3/G,Q #0096FF 
    4004 
    4005 > wait 50
    4006 
    4007 > color #3/G,Q dimgray
    4008 
    4009 > color #3/G,Q #0096FF
    4010 
    4011 > wait 50
    4012 
    4013 > color #3/G,Q dimgray
    4014 
    4015 > Crossfade; color #3/G,Q #0096FF; wait 50
    4016 
    4017 Unknown command: Crossfade; color #3/G,Q #0096FF; wait 50 
    4018 
    4019 > crossfade
    4020 
    4021 > color #3/G,Q #0096FF
    4022 
    4023 > wait 50
    4024 
    4025 > crossfade
    4026 
    4027 > color #3/G,Q #0096FF
    4028 
    4029 > wait 50
    4030 
    4031 > undo
    4032 
    4033 [Repeated 1 time(s)]
    4034 
    4035 > crossfade
    4036 
    4037 > color #3/G,Q #0096FF
    4038 
    4039 > wait 50
    4040 
    4041 [Repeated 1 time(s)]
    4042 
    4043 > crossfade
    4044 
    4045 > color #3/G,Q dimgray
    4046 
    4047 > wait 50
    4048 
    4049 > select #3/Z:275
    4050 
    4051 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4052 
    4053 > color (#!3 & sel) #9437ffff
    4054 
    4055 [Repeated 1 time(s)]
    4056 
    4057 > undo
    4058 
    4059 [Repeated 1 time(s)]
    4060 
    4061 > select clear
    4062 
    4063 > select #3/Z:274
    4064 
    4065 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4066 
    4067 > color (#!3 & sel) light gray
    4068 
    4069 > select clear
    4070 
    4071 > undo
    4072 
    4073 > color (#!3 & sel) #d6d6d6ff
    4074 
    4075 > color (#!3 & sel) #c0c0c0ff
    4076 
    4077 [Repeated 1 time(s)]
    4078 
    4079 > crossfade
    4080 
    4081 > color #3/Y,Z #9437FF
    4082 
    4083 > wait 50
    4084 
    4085 [Repeated 1 time(s)]
    4086 
    4087 > crossfade
    4088 
    4089 > color #3/Y,Z #C0C0C0
    4090 
    4091 > wait 50
    4092 
    4093 > select clear
    4094 
    4095 > roll x -1 90
    4096 
    4097 > roll x 1 90
    4098 
    4099 > open
    4100 > /Users/zbxg977/Desktop/BRISC_project/BRISC_pentaUb_structure_Dan/cryosparc_P1_DeepEmhancer_J202_highres.mrc
    4101 
    4102 Opened cryosparc_P1_DeepEmhancer_J202_highres.mrc as #5, grid size
    4103 512,512,512, pixel 0.74, shown at level 0.00204, step 2, values float32 
    4104 
    4105 > select add #3
    4106 
    4107 53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected 
    4108 
    4109 > volume #5 step 1
    4110 
    4111 > volume #5 level 0.1134
    4112 
    4113 > ui mousemode right "rotate selected models"
    4114 
    4115 > view matrix models
    4116 > #3,0.95422,-0.27698,-0.11292,74.797,0.20162,0.87447,-0.44119,60.309,0.22095,0.39822,0.89028,-89.115
    4117 
    4118 > undo
    4119 
    4120 > select subtract #3
    4121 
    4122 22 models selected 
    4123 
    4124 > select add #5
    4125 
    4126 4 models selected 
    4127 
    4128 > view matrix models
    4129 > #5,0.89102,-0.11592,0.43892,-23.542,0.30523,0.86866,-0.39021,37.491,-0.33604,0.48165,0.80938,-20.252
    4130 
    4131 > view matrix models
    4132 > #5,0.42416,-0.27299,0.86346,9.9416,0.79723,0.56483,-0.21305,5.4897,-0.42955,0.77875,0.45721,-15.846
    4133 
    4134 > ui mousemode right "translate selected models"
    4135 
    4136 > view matrix models
    4137 > #5,0.42416,-0.27299,0.86346,6.061,0.79723,0.56483,-0.21305,-17.432,-0.42955,0.77875,0.45721,24.788
    4138 
    4139 > ui mousemode right "rotate selected models"
    4140 
    4141 > view matrix models
    4142 > #5,0.81844,-0.43282,0.37791,50.121,0.50998,0.24418,-0.8248,164.2,0.26471,0.86778,0.42057,-78.781
    4143 
    4144 > ui mousemode right "translate selected models"
    4145 
    4146 > view matrix models
    4147 > #5,0.81844,-0.43282,0.37791,40.926,0.50998,0.24418,-0.8248,160.85,0.26471,0.86778,0.42057,-105.12
    4148 
    4149 > view matrix models
    4150 > #5,0.81844,-0.43282,0.37791,56.133,0.50998,0.24418,-0.8248,169.15,0.26471,0.86778,0.42057,-100.7
    4151 
    4152 > ui mousemode right "rotate selected models"
    4153 
    4154 > view matrix models
    4155 > #5,-0.79885,-0.084636,0.59554,174.83,-0.6013,0.13968,-0.78672,330.58,-0.016603,-0.98657,-0.16248,364.87
    4156 
    4157 > view matrix models
    4158 > #5,-0.70691,-0.21333,0.67436,176.16,-0.70654,0.25721,-0.65928,305.02,-0.032808,-0.94251,-0.33255,381.88
    4159 
    4160 > view matrix models
    4161 > #5,-0.86037,-0.37738,0.34257,272.5,-0.34072,-0.074004,-0.93725,356.83,0.37905,-0.9231,-0.06491,287.32
    4162 
    4163 > view matrix models
    4164 > #5,0.27598,-0.92698,0.25405,237.73,-0.926,-0.32726,-0.18819,379.89,0.25759,-0.18332,-0.94871,284.51
    4165 
    4166 > ui mousemode right "translate selected models"
    4167 
    4168 > view matrix models
    4169 > #5,0.27598,-0.92698,0.25405,261.38,-0.926,-0.32726,-0.18819,442.24,0.25759,-0.18332,-0.94871,329.72
    4170 
    4171 > view matrix models
    4172 > #5,0.27598,-0.92698,0.25405,270.85,-0.926,-0.32726,-0.18819,441.82,0.25759,-0.18332,-0.94871,354.73
    4173 
    4174 > ui mousemode right "rotate selected models"
    4175 
    4176 > view matrix models
    4177 > #5,-0.76194,0.56796,0.31124,118.96,-0.39996,-0.034665,-0.91588,416.29,-0.5094,-0.82232,0.25357,412.69
    4178 
    4179 > ui mousemode right "translate selected models"
    4180 
    4181 > view matrix models
    4182 > #5,-0.76194,0.56796,0.31124,167.06,-0.39996,-0.034665,-0.91588,433.46,-0.5094,-0.82232,0.25357,417.86
    4183 
    4184 > ui tool show "Fit in Map"
    4185 
    4186 > fitmap #3 inMap #5
    4187 
    4188 Fit molecule P64_J12_model-coot-56.pdb (#3) to map
    4189 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 53424 atoms 
    4190 average map value = 0.07452, steps = 284 
    4191 shifted from previous position = 23.8 
    4192 rotated from previous position = 6.83 degrees 
    4193 atoms outside contour = 43940, contour level = 0.1134 
    4194  
    4195 Position of P64_J12_model-coot-56.pdb (#3) relative to
    4196 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates: 
    4197 Matrix rotation and translation 
    4198 -0.76336194 -0.42876028 -0.48315957 509.75254988 
    4199 0.58594633 -0.14473464 -0.79731974 262.25309824 
    4200 0.27192911 -0.89174912 0.36171543 201.03833376 
    4201 Axis -0.07445072 -0.59533266 0.80002257 
    4202 Axis point 210.03507452 319.31513667 0.00000000 
    4203 Rotation angle (degrees) 140.64127053 
    4204 Shift along axis -33.24407263 
    4205  
    4206 
    4207 > select subtract #5
    4208 
    4209 Nothing selected 
    4210 
    4211 > open /Users/zbxg977/Desktop/penta_Ub_merged.pdb
    4212 
    4213 Chain information for penta_Ub_merged.pdb #6 
    4214 --- 
    4215 Chain | Description 
    4216 A B C L | No description available 
    4217 O | No description available 
    4218  
    4219 
    4220 > select add #6
    4221 
    4222 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    4223 
    4224 > view matrix models #6,1,0,0,14.12,0,1,0,22.571,0,0,1,27.031
    4225 
    4226 > view matrix models #6,1,0,0,15.745,0,1,0,4.9213,0,0,1,39.269
    4227 
    4228 > fitmap #6 inMap #5
    4229 
    4230 Fit molecule penta_Ub_merged.pdb (#6) to map
    4231 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms 
    4232 average map value = 0.03084, steps = 240 
    4233 shifted from previous position = 5.63 
    4234 rotated from previous position = 11.6 degrees 
    4235 atoms outside contour = 3177, contour level = 0.1134 
    4236  
    4237 Position of penta_Ub_merged.pdb (#6) relative to
    4238 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates: 
    4239 Matrix rotation and translation 
    4240 -0.81522555 -0.25341032 -0.52075956 465.22557231 
    4241 0.51830802 0.08193703 -0.85125972 235.13444893 
    4242 0.25838749 -0.96388253 0.06454744 304.69339704 
    4243 Axis -0.10216074 -0.70676837 0.70002975 
    4244 Axis point 150.78544864 0.00000000 367.68057814 
    4245 Rotation angle (degrees) 146.55035104 
    4246 Shift along axis -0.41893617 
    4247  
    4248 
    4249 > hide sel atoms
    4250 
    4251 > show sel cartoons
    4252 
    4253 > hide #!3 models
    4254 
    4255 > ui mousemode right "rotate selected models"
    4256 
    4257 > view matrix models
    4258 > #6,0.9837,-0.11362,0.13936,21.477,0.056651,0.93143,0.35949,-55.449,-0.17065,-0.34573,0.92269,154.42
    4259 
    4260 > view matrix models
    4261 > #6,0.37349,-0.79347,0.48053,230.48,-0.0081346,0.5152,0.85703,-41.298,-0.9276,-0.324,0.18597,433.9
    4262 
    4263 > view matrix models
    4264 > #6,0.30923,-0.43531,0.8455,121.42,-0.36441,0.76697,0.52816,42.616,-0.8784,-0.47144,0.078541,467.05
    4265 
    4266 > ui mousemode right "translate selected models"
    4267 
    4268 > view matrix models
    4269 > #6,0.30923,-0.43531,0.8455,102.31,-0.36441,0.76697,0.52816,47.152,-0.8784,-0.47144,0.078541,461.46
    4270 
    4271 > ui mousemode right "rotate selected models"
    4272 
    4273 > view matrix models
    4274 > #6,0.92947,-0.26671,-0.25485,104.32,-0.27908,-0.96018,-0.012978,433.1,-0.24124,0.083187,-0.96689,379.48
    4275 
    4276 > ui mousemode right "translate selected models"
    4277 
    4278 > view matrix models
    4279 > #6,0.92947,-0.26671,-0.25485,106.56,-0.27908,-0.96018,-0.012978,437.85,-0.24124,0.083187,-0.96689,383.68
    4280 
    4281 > ui mousemode right "rotate selected models"
    4282 
    4283 > view matrix models
    4284 > #6,0.92611,0.0034423,-0.37724,76.233,-0.10302,-0.95964,-0.26168,437.28,-0.36292,0.28121,-0.88838,361.8
    4285 
    4286 > ui mousemode right "translate selected models"
    4287 
    4288 > ui mousemode right "rotate selected models"
    4289 
    4290 > view matrix models
    4291 > #6,0.58955,0.42781,-0.68513,120.44,-0.084315,-0.81099,-0.57896,454.97,-0.80332,0.39909,-0.44205,368.48
    4292 
    4293 > view matrix models
    4294 > #6,0.43235,-0.37451,-0.82026,325.47,-0.65274,-0.75758,0.0018353,481.19,-0.6221,0.53463,-0.57199,323.19
    4295 
    4296 > view matrix models
    4297 > #6,0.66075,-0.25513,-0.70591,234.59,-0.3588,-0.93341,0.0015123,448.38,-0.65929,0.25228,-0.7083,405.14
    4298 
    4299 > view matrix models
    4300 > #6,0.53137,-0.26167,-0.80572,280.2,-0.12418,-0.96488,0.23147,366.1,-0.83799,-0.022937,-0.5452,470.63
    4301 
    4302 > fitmap #6 inMap #5
    4303 
    4304 Fit molecule penta_Ub_merged.pdb (#6) to map
    4305 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms 
    4306 average map value = 0.04473, steps = 216 
    4307 shifted from previous position = 8.49 
    4308 rotated from previous position = 8.17 degrees 
    4309 atoms outside contour = 3016, contour level = 0.1134 
    4310  
    4311 Position of penta_Ub_merged.pdb (#6) relative to
    4312 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates: 
    4313 Matrix rotation and translation 
    4314 0.07651590 0.64458117 0.76069733 -87.66333612 
    4315 0.99486624 0.00132160 -0.10119000 11.31246327 
    4316 -0.06623051 0.76453474 -0.64117092 155.61742874 
    4317 Axis 0.69402741 0.66292501 0.28081378 
    4318 Axis point 0.00000000 7.59449819 100.00864003 
    4319 Rotation angle (degrees) 141.41343192 
    4320 Shift along axis -9.64192415 
    4321  
    4322 
    4323 > view matrix models
    4324 > #6,0.27731,-0.24257,-0.92965,347.92,-0.0086426,-0.96819,0.25005,334.1,-0.96074,-0.061309,-0.27059,467.65
    4325 
    4326 > ui mousemode right "translate selected models"
    4327 
    4328 > view matrix models
    4329 > #6,0.27731,-0.24257,-0.92965,352.22,-0.0086426,-0.96819,0.25005,333.08,-0.96074,-0.061309,-0.27059,463.08
    4330 
    4331 > view matrix models
    4332 > #6,0.27731,-0.24257,-0.92965,355.74,-0.0086426,-0.96819,0.25005,333.93,-0.96074,-0.061309,-0.27059,466.06
    4333 
    4334 > ui mousemode right "rotate selected models"
    4335 
    4336 > view matrix models
    4337 > #6,0.29679,-0.35595,-0.88612,365.66,0.10608,-0.9099,0.40103,274.01,-0.94903,-0.21303,-0.23229,485.65
    4338 
    4339 > ui mousemode right "translate selected models"
    4340 
    4341 > view matrix models
    4342 > #6,0.29679,-0.35595,-0.88612,367.16,0.10608,-0.9099,0.40103,280.02,-0.94903,-0.21303,-0.23229,486.54
    4343 
    4344 > fitmap #6 inMap #5
    4345 
    4346 Fit molecule penta_Ub_merged.pdb (#6) to map
    4347 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms 
    4348 average map value = 0.04044, steps = 88 
    4349 shifted from previous position = 2.76 
    4350 rotated from previous position = 5.25 degrees 
    4351 atoms outside contour = 3054, contour level = 0.1134 
    4352  
    4353 Position of penta_Ub_merged.pdb (#6) relative to
    4354 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates: 
    4355 Matrix rotation and translation 
    4356 0.15609642 0.72235882 0.67367027 -116.00954017 
    4357 0.96951994 0.01835015 -0.24432426 42.58067044 
    4358 -0.18885174 0.69127491 -0.69747689 205.63722394 
    4359 Axis 0.72174910 0.66537520 0.19066746 
    4360 Axis point 0.00000000 21.56062234 131.74159871 
    4361 Rotation angle (degrees) 139.59795370 
    4362 Shift along axis -16.18933184 
    4363  
    4364 
    4365 > view matrix models
    4366 > #6,0.37294,-0.32482,-0.86914,348.3,0.076925,-0.92267,0.37783,289.83,-0.92466,-0.20777,-0.31911,493.61
    4367 
    4368 > fitmap #6 inMap #5
    4369 
    4370 Fit molecule penta_Ub_merged.pdb (#6) to map
    4371 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms 
    4372 average map value = 0.06226, steps = 212 
    4373 shifted from previous position = 3.45 
    4374 rotated from previous position = 19.4 degrees 
    4375 atoms outside contour = 2811, contour level = 0.1134 
    4376  
    4377 Position of penta_Ub_merged.pdb (#6) relative to
    4378 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates: 
    4379 Matrix rotation and translation 
    4380 0.00314523 0.52331352 0.85213441 -73.49266478 
    4381 0.95223623 0.25863119 -0.16234552 -8.10699426 
    4382 -0.30534615 0.81194388 -0.49750464 178.68162582 
    4383 Axis 0.61955240 0.73604400 0.27275273 
    4384 Axis point 25.90526356 0.00000000 114.54079787 
    4385 Rotation angle (degrees) 128.16032758 
    4386 Shift along axis -2.76376043 
    4387  
    4388 
    4389 > select subtract #6
    4390 
    4391 Nothing selected 
    4392 
    4393 > hide #!5 models
    4394 
    4395 > show #!3 models
    4396 
    4397 > color #6 #ff9300ff
    4398 
    4399 > ui tool show "Side View"
    4400 
    4401 > select #6
    4402 
    4403 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    4404 
    4405 > hide #6
    4406 
    4407 > view matrix models
    4408 > #6,0.4434,0.00086618,-0.89632,274.04,0.24539,-0.96191,0.12046,299.3,-0.86208,-0.27336,-0.42673,507.15
    4409 
    4410 > hide cartoons #6
    4411 
    4412 Expected ',' or a keyword 
    4413 
    4414 > view matrix models
    4415 > #6,0.4434,0.00086618,-0.89632,274.06,0.24539,-0.96191,0.12046,299.25,-0.86208,-0.27336,-0.42673,507.17
    4416 
    4417 > ui mousemode right select
    4418 
    4419 > select clear
    4420 
    4421 > crossfade #6
    4422 
    4423 Expected an integer >= 1 or a keyword 
    4424 
    4425 > hide #6 models
    4426 
    4427 > crossfade
    4428 
    4429 > hide #3/O,L,D,C,B
    4430 
    4431 > wait 50
    4432 
    4433 > crossfade
    4434 
    4435 > hide cartoons #3/O,L,D,C,B; wait 50
    4436 
    4437 Expected ',' or a keyword 
    4438 
    4439 > crossfade
    4440 
    4441 > cartoon hide #3/O,L,D,C,B
    4442 
    4443 > wait 50
    4444 
    4445 > undo
    4446 
    4447 > show #6 models
    4448 
    4449 > hide #6 models
    4450 
    4451 > show #6 models
    4452 
    4453 > crossfade
    4454 
    4455 > cartoon hide #3/O,L,D,C,B
    4456 
    4457 > wait 50
    4458 
    4459 > undo
    4460 
    4461 > hide #6 models
    4462 
    4463 > crossfade
    4464 
    4465 > cartoon hide #3/O,L,D,C,B
    4466 
    4467 > wait 50
    4468 
    4469 > crossfade
    4470 
    4471 > cartoon show #3/O,L,A,C,B; wait 50
    4472 
    4473 Expected an atoms specifier or a keyword 
    4474 
    4475 > show #6 models
    4476 
    4477 > crossfade
    4478 
    4479 > cartoon hide #3/O,L,A,C,B
    4480 
    4481 > wait 50
    4482 
    4483 > undo
    4484 
    4485 > crossfade
    4486 
    4487 > cartoon hide #6/O,L,A,C,B
    4488 
    4489 > wait 50
    4490 
    4491 > crossfade
    4492 
    4493 > cartoon hide #3/O,L,D,C,B
    4494 
    4495 > wait 50
    4496 
    4497 > crossfade
    4498 
    4499 > cartoon show #6/O,L,A,C,B; wait 50
    4500 
    4501 Expected an atoms specifier or a keyword 
    4502 
    4503 > undo
    4504 
    4505 > crossfade
    4506 
    4507 > cartoon #6/O,L,A,C,B
    4508 
    4509 > wait 50
    4510 
    4511 > crossfade
    4512 
    4513 > cartoon hide #3/O,L,D,C,B
    4514 
    4515 > wait 50
    4516 
    4517 > crossfade
    4518 
    4519 > cartoon #6/O,L,A,C,B
    4520 
    4521 > wait 50
    4522 
    4523 > roll y 1 90
    4524 
    4525 > hide #!8 models
    4526 
    4527 > show #!8 models
    4528 
    4529 > undo
    4530 
    4531 [Repeated 9 time(s)]
    4532 
    4533 > show #!1 models
    4534 
    4535 > hide #!1 models
    4536 
    4537 > show #!2 models
    4538 
    4539 > hide #!2 models
    4540 
    4541 > show #6 models
    4542 
    4543 > show #!2 models
    4544 
    4545 > hide #!2 models
    4546 
    4547 > hide #6 models
    4548 
    4549 > show #!5 models
    4550 
    4551 > hide #!5 models
    4552 
    4553 > show #6 models
    4554 
    4555 > hide #6 models
    4556 
    4557 > hide #!8 models
    4558 
    4559 > show #!8 models
    4560 
    4561 > hide #!8 models
    4562 
    4563 > show #!8 models
    4564 
    4565 > select add #8
    4566 
    4567 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    4568 
    4569 > show sel cartoons
    4570 
    4571 > ui tool show Matchmaker
    4572 
    4573 [Repeated 1 time(s)]
    4574 
    4575 > matchmaker #8/O to #3/R pairing ss
    4576 
    4577 Parameters 
    4578 --- 
    4579 Chain pairing | ss 
    4580 Alignment algorithm | Needleman-Wunsch 
    4581 Similarity matrix | BLOSUM-62 
    4582 SS fraction | 0.3 
    4583 Gap open (HH/SS/other) | 18/18/6 
    4584 Gap extend | 1 
    4585 SS matrix |  |  | H | S | O 
    4586 ---|---|---|--- 
    4587 H | 6 | -9 | -6 
    4588 S |  | 6 | -6 
    4589 O |  |  | 4 
    4590 Iteration cutoff | 2 
    4591  
    4592 Matchmaker P64_J12_model-coot-56.pdb, chain R (#3) with penta_Ub_merged.pdb,
    4593 chain O (#8), sequence alignment score = 374 
    4594 RMSD between 76 pruned atom pairs is 0.217 angstroms; (across all 76 pairs:
    4595 0.217) 
    4596  
    4597 
    4598 > select clear
    4599 
    4600 > show #6 models
    4601 
    4602 > hide #!8 models
    4603 
    4604 > show #!8 models
    4605 
    4606 > hide #6 models
    4607 
    4608 > show #6 models
    4609 
    4610 > crossfade
    4611 
    4612 > color #3/Q #0096FF, color #3/Z #C0C0C0; wait 50
    4613 
    4614 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    4615 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    4616 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    4617 
    4618 > wait 50
    4619 
    4620 > crossfade
    4621 
    4622 > color #3/Q #0096FF
    4623 
    4624 > color #3/Z #C0C0C0
    4625 
    4626 > wait 50
    4627 
    4628 > select clear
    4629 
    4630 > undo
    4631 
    4632 [Repeated 3 time(s)]
    4633 
    4634 > crossfade
    4635 
    4636 > color #3/Q #0096FF, #3/Z #C0C0C0; wait 50
    4637 
    4638 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    4639 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    4640 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    4641 
    4642 > crossfade
    4643 
    4644 > color #3/Q #0096FF & #3/Z #C0C0C0; wait 50
    4645 
    4646 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    4647 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    4648 
    4649 > crossfade
    4650 
    4651 > color #3/Q #0096FF & color #3/Z #C0C0C0; wait 50
    4652 
    4653 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    4654 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    4655 
    4656 > crossfade
    4657 
    4658 > color #3/Q #0096FF #3/Z #9437FF; wait 50
    4659 
    4660 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    4661 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    4662 
    4663 > crossfade
    4664 
    4665 > color #3/Q #0096FF, #3/Z #9437FF; wait 50
    4666 
    4667 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    4668 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    4669 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    4670 
    4671 > crossfade
    4672 
    4673 > color #3/Q #0096FF & #3/Z #9437FF; wait 50
    4674 
    4675 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    4676 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    4677 
    4678 > crossfade
    4679 
    4680 > color #3/Q #0096FF
    4681 
    4682 > undo
    4683 
    4684 > crossfade
    4685 
    4686 > color #3/Q #0096FF
    4687 
    4688 > color #3/Z #9437FF
    4689 
    4690 > wait 50
    4691 
    4692 > undo
    4693 
    4694 [Repeated 1 time(s)]
    4695 
    4696 > crossfade
    4697 
    4698 > color #3/Q #0096FF
    4699 
    4700 > color #3/Z #9437FF
    4701 
    4702 > wait 50
    4703 
    4704 > wait 50
    4705 
    4706 > crossfade
    4707 
    4708 > color #3/Q dimgray
    4709 
    4710 > color #3/Z #C0C0C0
    4711 
    4712 > wait 50
    4713 
    4714 > crossfade
    4715 
    4716 > color #3/V #0096FF
    4717 
    4718 > color #3/I #9437FF
    4719 
    4720 > wait 50
    4721 
    4722 > wait 50
    4723 
    4724 > crossfade
    4725 
    4726 > color #3/V dimgray
    4727 
    4728 > color #3/I #C0C0C0
    4729 
    4730 > wait 50
    4731 
    4732 > crossfade
    4733 
    4734 > cartoon hide #6/O,L,A,C,B
    4735 
    4736 > wait 50
    4737 
    4738 > roll y 1 360
    4739 
    4740 > wait 390
    4741 
    4742 > roll x -1 90
    4743 
    4744 > crossfade
    4745 
    4746 > color #3/G,Q #0096FF
    4747 
    4748 > wait 50
    4749 
    4750 [Repeated 1 time(s)]
    4751 
    4752 > crossfade
    4753 
    4754 > color #3/G,Q dimgray
    4755 
    4756 > wait 50
    4757 
    4758 > crossfade
    4759 
    4760 > color #3/Y,Z #9437FF
    4761 
    4762 > wait 50
    4763 
    4764 [Repeated 1 time(s)]
    4765 
    4766 > crossfade
    4767 
    4768 > color #3/Y,Z #C0C0C0
    4769 
    4770 > wait 50
    4771 
    4772 > roll x 1 90
    4773 
    4774 > crossfade
    4775 
    4776 > cartoon hide #3/O,L,D,C,B
    4777 
    4778 > wait 50
    4779 
    4780 > crossfade
    4781 
    4782 > cartoon #6/O,L,A,C,B
    4783 
    4784 > wait 50
    4785 
    4786 > roll y 1 90
    4787 
    4788 > crossfade
    4789 
    4790 > color #3/Q #0096FF
    4791 
    4792 > color #3/Z #9437FF
    4793 
    4794 > wait 50
    4795 
    4796 > wait 50
    4797 
    4798 > crossfade
    4799 
    4800 > color #3/Q dimgray
    4801 
    4802 > color #3/Z #C0C0C0
    4803 
    4804 > wait 50
    4805 
    4806 > crossfade
    4807 
    4808 > color #3/V #0096FF
    4809 
    4810 > color #3/I #9437FF
    4811 
    4812 > wait 50
    4813 
    4814 > wait 50
    4815 
    4816 > crossfade
    4817 
    4818 > color #3/V dimgray
    4819 
    4820 > color #3/I #C0C0C0
    4821 
    4822 > wait 50
    4823 
    4824 > roll y 1 360
    4825 
    4826 > wait 390
    4827 
    4828 > roll x -1 90
    4829 
    4830 > crossfade
    4831 
    4832 > color #3/G,Q #0096FF
    4833 
    4834 > wait 50
    4835 
    4836 [Repeated 1 time(s)]
    4837 
    4838 > crossfade
    4839 
    4840 > color #3/G,Q dimgray
    4841 
    4842 > wait 50
    4843 
    4844 > crossfade
    4845 
    4846 > color #3/Y,Z #9437FF
    4847 
    4848 > wait 50
    4849 
    4850 [Repeated 1 time(s)]
    4851 
    4852 > crossfade
    4853 
    4854 > color #3/Y,Z #C0C0C0
    4855 
    4856 > wait 50
    4857 
    4858 > roll x 1 90
    4859 
    4860 > wait 50
    4861 
    4862 > crossfade
    4863 
    4864 > cartoon hide #3/O,L,D,C,B
    4865 
    4866 > wait 50
    4867 
    4868 > crossfade
    4869 
    4870 > cartoon #6/O,L,A,C,B
    4871 
    4872 > wait 50
    4873 
    4874 > roll y 1 90
    4875 
    4876 > wait 50
    4877 
    4878 > crossfade
    4879 
    4880 > color #3/Q #0096FF
    4881 
    4882 > color #3/Z #9437FF
    4883 
    4884 > wait 50
    4885 
    4886 > wait 50
    4887 
    4888 > crossfade
    4889 
    4890 > color #3/Q dimgray
    4891 
    4892 > color #3/Z #C0C0C0
    4893 
    4894 > wait 50
    4895 
    4896 > crossfade
    4897 
    4898 > color #3/V #0096FF
    4899 
    4900 > color #3/I #9437FF
    4901 
    4902 > wait 50
    4903 
    4904 > wait 50
    4905 
    4906 > crossfade
    4907 
    4908 > color #3/V dimgray
    4909 
    4910 > color #3/I #C0C0C0
    4911 
    4912 > wait 50
    4913 
    4914 > roll y 1 360
    4915 
    4916 > wait 390
    4917 
    4918 > roll x -1 90
    4919 
    4920 > wait 50
    4921 
    4922 > crossfade
    4923 
    4924 > color #3/G,Q #0096FF
    4925 
    4926 > wait 50
    4927 
    4928 [Repeated 1 time(s)]
    4929 
    4930 > crossfade
    4931 
    4932 > color #3/G,Q dimgray
    4933 
    4934 > wait 50
    4935 
    4936 > crossfade
    4937 
    4938 > color #3/Y,Z #9437FF
    4939 
    4940 > wait 50
    4941 
    4942 [Repeated 1 time(s)]
    4943 
    4944 > crossfade
    4945 
    4946 > color #3/Y,Z #C0C0C0
    4947 
    4948 > wait 50
    4949 
    4950 > roll x 1 90
    4951 
    4952 > wait 50
    4953 
    4954 > crossfade
    4955 
    4956 > cartoon hide #3/O,L,D,C,B
    4957 
    4958 > wait 50
    4959 
    4960 > crossfade
    4961 
    4962 > cartoon #6/O,L,A,C,B
    4963 
    4964 > wait 50
    4965 
    4966 > roll y 1 90
    4967 
    4968 > wait 50
    4969 
    4970 > crossfade
    4971 
    4972 > color #3/Q #0096FF
    4973 
    4974 > color #3/Z #9437FF
    4975 
    4976 > wait 50
    4977 
    4978 > wait 50
    4979 
    4980 > crossfade
    4981 
    4982 > color #3/Q dimgray
    4983 
    4984 > color #3/Z #C0C0C0
    4985 
    4986 > wait 50
    4987 
    4988 > crossfade
    4989 
    4990 > color #3/V #0096FF
    4991 
    4992 > color #3/I #9437FF
    4993 
    4994 > wait 50
    4995 
    4996 > wait 50
    4997 
    4998 > crossfade
    4999 
    5000 > color #3/V dimgray
    5001 
    5002 > color #3/I #C0C0C0
    5003 
    5004 > wait 50
    5005 
    5006 > roll y 1 360
    5007 
    5008 > wait 390
    5009 
    5010 > roll x -1 90
    5011 
    5012 > wait 100
    5013 
    5014 > crossfade
    5015 
    5016 > color #3/G,Q #0096FF
    5017 
    5018 > wait 50
    5019 
    5020 [Repeated 1 time(s)]
    5021 
    5022 > crossfade
    5023 
    5024 > color #3/G,Q dimgray
    5025 
    5026 > wait 50
    5027 
    5028 > crossfade
    5029 
    5030 > color #3/Y,Z #9437FF
    5031 
    5032 > wait 50
    5033 
    5034 [Repeated 1 time(s)]
    5035 
    5036 > crossfade
    5037 
    5038 > color #3/Y,Z #C0C0C0
    5039 
    5040 > wait 50
    5041 
    5042 > roll x 1 90
    5043 
    5044 > wait 100
    5045 
    5046 > crossfade
    5047 
    5048 > cartoon hide #3/O,L,D,C,B
    5049 
    5050 > wait 50
    5051 
    5052 > crossfade
    5053 
    5054 > cartoon #6/O,L,A,C,B
    5055 
    5056 > wait 50
    5057 
    5058 > roll y 1 90
    5059 
    5060 > wait 100
    5061 
    5062 > crossfade
    5063 
    5064 > color #3/Q #0096FF
    5065 
    5066 > color #3/Z #9437FF
    5067 
    5068 > wait 50
    5069 
    5070 > wait 50
    5071 
    5072 > crossfade
    5073 
    5074 > color #3/Q dimgray
    5075 
    5076 > color #3/Z #C0C0C0
    5077 
    5078 > wait 50
    5079 
    5080 > crossfade
    5081 
    5082 > color #3/V #0096FF
    5083 
    5084 > color #3/I #9437FF
    5085 
    5086 > wait 50
    5087 
    5088 > wait 50
    5089 
    5090 > crossfade
    5091 
    5092 > color #3/V dimgray
    5093 
    5094 > color #3/I #C0C0C0
    5095 
    5096 > wait 50
    5097 
    5098 > crossfade
    5099 
    5100 > cartoon hide #6/O,L,A,C,B
    5101 
    5102 > wait 50
    5103 
    5104 > crossfade
    5105 
    5106 > cartoon #3/O,L,D,C,B
    5107 
    5108 > wait 50
    5109 
    5110 > crossfade
    5111 
    5112 > color #3/V #0096FF
    5113 
    5114 > color #3/I dimgrey
    5115 
    5116 > wait 50
    5117 
    5118 > undo
    5119 
    5120 [Repeated 2 time(s)]
    5121 
    5122 > redo
    5123 
    5124 > roll y 1 360
    5125 
    5126 > wait 390
    5127 
    5128 > roll x -1 90
    5129 
    5130 > wait 100
    5131 
    5132 > crossfade
    5133 
    5134 > color #3/G,Q #0096FF
    5135 
    5136 > wait 50
    5137 
    5138 [Repeated 1 time(s)]
    5139 
    5140 > crossfade
    5141 
    5142 > color #3/G,Q dimgray
    5143 
    5144 > wait 50
    5145 
    5146 > crossfade
    5147 
    5148 > color #3/Y,Z #9437FF
    5149 
    5150 > wait 50
    5151 
    5152 [Repeated 1 time(s)]
    5153 
    5154 > crossfade
    5155 
    5156 > color #3/Y,Z #C0C0C0
    5157 
    5158 > wait 50
    5159 
    5160 > roll x 1 90
    5161 
    5162 > wait 80
    5163 
    5164 > crossfade
    5165 
    5166 > cartoon hide #3/O,L,D,C,B
    5167 
    5168 > wait 50
    5169 
    5170 > crossfade
    5171 
    5172 > cartoon #6/O,L,A,C,B
    5173 
    5174 > wait 50
    5175 
    5176 > roll y 1 90
    5177 
    5178 > wait 80
    5179 
    5180 > crossfade
    5181 
    5182 > color #3/Q #0096FF
    5183 
    5184 > color #3/Z #9437FF
    5185 
    5186 > wait 50
    5187 
    5188 > wait 50
    5189 
    5190 > crossfade
    5191 
    5192 > color #3/Q dimgray
    5193 
    5194 > color #3/Z #C0C0C0
    5195 
    5196 > wait 50
    5197 
    5198 > crossfade
    5199 
    5200 > color #3/V #0096FF
    5201 
    5202 > color #3/I #9437FF
    5203 
    5204 > wait 50
    5205 
    5206 > wait 50
    5207 
    5208 > crossfade
    5209 
    5210 > color #3/V dimgray
    5211 
    5212 > color #3/I dimgrey
    5213 
    5214 > wait 50
    5215 
    5216 > crossfade
    5217 
    5218 > cartoon #3/O,L,D,C,B
    5219 
    5220 > wait 50
    5221 
    5222 > crossfade
    5223 
    5224 > cartoon hide #6/O,L,A,C,B
    5225 
    5226 > wait 50
    5227 
    5228 > Movie record
    5229 
    5230 Unknown command: Movie record 
    5231 
    5232 > roll y 1 360
    5233 
    5234 > wait 390
    5235 
    5236 > roll x -1 90
    5237 
    5238 > wait 100
    5239 
    5240 > crossfade
    5241 
    5242 > color #3/G,Q #0096FF
    5243 
    5244 > wait 50
    5245 
    5246 [Repeated 1 time(s)]
    5247 
    5248 > crossfade
    5249 
    5250 > color #3/G,Q dimgray
    5251 
    5252 > wait 50
    5253 
    5254 > crossfade
    5255 
    5256 > color #3/Y,Z #9437FF
    5257 
    5258 > wait 50
    5259 
    5260 [Repeated 1 time(s)]
    5261 
    5262 > crossfade
    5263 
    5264 > color #3/Y,Z #C0C0C0
    5265 
    5266 > wait 50
    5267 
    5268 > roll x 1 90
    5269 
    5270 > wait 100
    5271 
    5272 > crossfade
    5273 
    5274 > cartoon hide #3/O,L,D,C,B
    5275 
    5276 > wait 50
    5277 
    5278 > crossfade
    5279 
    5280 > cartoon #6/O,L,A,C,B
    5281 
    5282 > wait 50
    5283 
    5284 > roll y 1 90
    5285 
    5286 > wait 100
    5287 
    5288 > crossfade
    5289 
    5290 > color #3/Q #0096FF
    5291 
    5292 > color #3/Z #9437FF
    5293 
    5294 > wait 50
    5295 
    5296 > wait 50
    5297 
    5298 > crossfade
    5299 
    5300 > color #3/Q dimgray
    5301 
    5302 > color #3/Z #C0C0C0
    5303 
    5304 > wait 50
    5305 
    5306 > crossfade
    5307 
    5308 > color #3/V #0096FF
    5309 
    5310 > color #3/I #9437FF
    5311 
    5312 > wait 50
    5313 
    5314 > wait 50
    5315 
    5316 > crossfade
    5317 
    5318 > color #3/V dimgray
    5319 
    5320 > color #3/I dimgrey
    5321 
    5322 > wait 50
    5323 
    5324 > crossfade
    5325 
    5326 > color #3/V C0C0C0; color #3/I dimgrey; wait 50
    5327 
    5328 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    5329 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    5330 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    5331 
    5332 > crossfade
    5333 
    5334 > color #3/V #C0C0C0
    5335 
    5336 > color #3/I dimgrey
    5337 
    5338 > wait 50
    5339 
    5340 > crossfade
    5341 
    5342 > cartoon #3/O,L,D,C,B
    5343 
    5344 > wait 50
    5345 
    5346 > crossfade
    5347 
    5348 > cartoon hide #6/O,L,A,C,B
    5349 
    5350 > wait 50
    5351 
    5352 > roll y 1 360
    5353 
    5354 > wait 390
    5355 
    5356 > roll x -1 90
    5357 
    5358 > wait 100
    5359 
    5360 > crossfade
    5361 
    5362 > color #3/G,Q #0096FF
    5363 
    5364 > wait 50
    5365 
    5366 [Repeated 1 time(s)]
    5367 
    5368 > crossfade
    5369 
    5370 > color #3/G,Q dimgray
    5371 
    5372 > wait 50
    5373 
    5374 > crossfade
    5375 
    5376 > color #3/Y,Z #9437FF
    5377 
    5378 > wait 50
    5379 
    5380 [Repeated 1 time(s)]
    5381 
    5382 > crossfade
    5383 
    5384 > color #3/Y,Z #C0C0C0
    5385 
    5386 > wait 50
    5387 
    5388 > roll x 1 90
    5389 
    5390 > wait 100
    5391 
    5392 > crossfade
    5393 
    5394 > cartoon hide #3/O,L,D,C,B
    5395 
    5396 > wait 50
    5397 
    5398 > crossfade
    5399 
    5400 > cartoon #6/O,L,A,C,B
    5401 
    5402 > wait 50
    5403 
    5404 > roll y 1 90
    5405 
    5406 > wait 100
    5407 
    5408 > crossfade
    5409 
    5410 > color #3/Q #0096FF
    5411 
    5412 > color #3/Z #9437FF
    5413 
    5414 > wait 50
    5415 
    5416 > wait 50
    5417 
    5418 > crossfade
    5419 
    5420 > color #3/Q dimgray
    5421 
    5422 > color #3/Z #C0C0C0
    5423 
    5424 > wait 50
    5425 
    5426 > crossfade
    5427 
    5428 > color #3/V #0096FF
    5429 
    5430 > color #3/I #9437FF
    5431 
    5432 > wait 50
    5433 
    5434 > wait 50
    5435 
    5436 > crossfade
    5437 
    5438 > color #3/V #C0C0C0
    5439 
    5440 > color #3/I dimgrey
    5441 
    5442 > wait 50
    5443 
    5444 > crossfade
    5445 
    5446 > cartoon #3/O,L,D,C,B
    5447 
    5448 > wait 50
    5449 
    5450 > crossfade
    5451 
    5452 > cartoon hide #6/O,L,A,C,B
    5453 
    5454 > wait 50
    5455 
    5456 > Movie record
    5457 
    5458 Unknown command: Movie record 
    5459 
    5460 > roll y 1 360
    5461 
    5462 > wait 390
    5463 
    5464 > roll x -1 90
    5465 
    5466 > wait 100
    5467 
    5468 > crossfade
    5469 
    5470 > color #3/G,Q #0096FF
    5471 
    5472 > wait 50
    5473 
    5474 [Repeated 1 time(s)]
    5475 
    5476 > crossfade
    5477 
    5478 > color #3/G,Q dimgray
    5479 
    5480 > wait 50
    5481 
    5482 > crossfade
    5483 
    5484 > color #3/Y,Z #9437FF
    5485 
    5486 > wait 50
    5487 
    5488 [Repeated 1 time(s)]
    5489 
    5490 > crossfade
    5491 
    5492 > color #3/Y,Z #C0C0C0
    5493 
    5494 > wait 50
    5495 
    5496 > roll x 1 90
    5497 
    5498 > wait 100
    5499 
    5500 > crossfade
    5501 
    5502 > cartoon hide #3/O,L,D,C,B
    5503 
    5504 > wait 50
    5505 
    5506 > crossfade
    5507 
    5508 > cartoon #6/O,L,A,C,B
    5509 
    5510 > wait 50
    5511 
    5512 > roll y 1 90
    5513 
    5514 > wait 100
    5515 
    5516 > crossfade
    5517 
    5518 > color #3/Q #0096FF
    5519 
    5520 > color #3/Z #9437FF
    5521 
    5522 > wait 50
    5523 
    5524 > wait 50
    5525 
    5526 > crossfade
    5527 
    5528 > color #3/Q dimgray
    5529 
    5530 > color #3/Z #C0C0C0
    5531 
    5532 > wait 50
    5533 
    5534 > crossfade
    5535 
    5536 > color #3/V #0096FF
    5537 
    5538 > color #3/I #9437FF
    5539 
    5540 > wait 50
    5541 
    5542 > wait 50
    5543 
    5544 > crossfade
    5545 
    5546 > color #3/V #C0C0C0
    5547 
    5548 > color #3/I dimgrey
    5549 
    5550 > wait 50
    5551 
    5552 > wait 100
    5553 
    5554 > movie encode
    5555 
    5556 No frames have been recorded 
    5557 
    5558 > crossfade
    5559 
    5560 > cartoon #3/O,L,D,C,B
    5561 
    5562 > wait 50
    5563 
    5564 > crossfade
    5565 
    5566 > cartoon hide #6/O,L,A,C,B
    5567 
    5568 > wait 50
    5569 
    5570 > Movie start
    5571 
    5572 Unknown command: Movie start 
    5573 
    5574 > roll y 1 360
    5575 
    5576 > wait 390
    5577 
    5578 > roll x -1 90
    5579 
    5580 > wait 100
    5581 
    5582 > crossfade
    5583 
    5584 > color #3/G,Q #0096FF
    5585 
    5586 > wait 50
    5587 
    5588 [Repeated 1 time(s)]
    5589 
    5590 > crossfade
    5591 
    5592 > color #3/G,Q dimgray
    5593 
    5594 > wait 50
    5595 
    5596 > crossfade
    5597 
    5598 > color #3/Y,Z #9437FF
    5599 
    5600 > wait 50
    5601 
    5602 [Repeated 1 time(s)]
    5603 
    5604 > crossfade
    5605 
    5606 > color #3/Y,Z #C0C0C0
    5607 
    5608 > wait 50
    5609 
    5610 > roll x 1 90
    5611 
    5612 > wait 100
    5613 
    5614 > crossfade
    5615 
    5616 > cartoon hide #3/O,L,D,C,B
    5617 
    5618 > wait 50
    5619 
    5620 > crossfade
    5621 
    5622 > cartoon #6/O,L,A,C,B
    5623 
    5624 > wait 50
    5625 
    5626 > roll y 1 90
    5627 
    5628 > wait 100
    5629 
    5630 > crossfade
    5631 
    5632 > color #3/Q #0096FF
    5633 
    5634 > color #3/Z #9437FF
    5635 
    5636 > wait 50
    5637 
    5638 > wait 50
    5639 
    5640 > crossfade
    5641 
    5642 > color #3/Q dimgray
    5643 
    5644 > color #3/Z #C0C0C0
    5645 
    5646 > wait 50
    5647 
    5648 > crossfade
    5649 
    5650 > color #3/V #0096FF
    5651 
    5652 > color #3/I #9437FF
    5653 
    5654 > wait 50
    5655 
    5656 > wait 50
    5657 
    5658 > crossfade
    5659 
    5660 > color #3/V #C0C0C0
    5661 
    5662 > color #3/I dimgrey
    5663 
    5664 > wait 50
    5665 
    5666 > wait 100
    5667 
    5668 > movie encode
    5669 
    5670 No frames have been recorded 
    5671 
    5672 > crossfade
    5673 
    5674 > cartoon #3/O,L,D,C,B
    5675 
    5676 > wait 50
    5677 
    5678 > crossfade
    5679 
    5680 > cartoon hide #6/O,L,A,C,B
    5681 
    5682 > wait 50
    5683 
    5684 > movie record
    5685 
    5686 > roll y 1 360
    5687 
    5688 > wait 390
    5689 
    5690 > roll x -1 90
    5691 
    5692 > wait 100
    5693 
    5694 > crossfade
    5695 
    5696 > color #3/G,Q #0096FF
    5697 
    5698 > wait 50
    5699 
    5700 [Repeated 1 time(s)]
    5701 
    5702 > crossfade
    5703 
    5704 > color #3/G,Q dimgray
    5705 
    5706 > wait 50
    5707 
    5708 > crossfade
    5709 
    5710 > color #3/Y,Z #9437FF
    5711 
    5712 > wait 50
    5713 
    5714 [Repeated 1 time(s)]
    5715 
    5716 > crossfade
    5717 
    5718 > color #3/Y,Z #C0C0C0
    5719 
    5720 > wait 50
    5721 
    5722 > roll x 1 90
    5723 
    5724 > wait 100
    5725 
    5726 > crossfade
    5727 
    5728 > cartoon hide #3/O,L,D,C,B
    5729 
    5730 > wait 50
    5731 
    5732 > crossfade
    5733 
    5734 > cartoon #6/O,L,A,C,B
    5735 
    5736 > wait 50
    5737 
    5738 > roll y 1 90
    5739 
    5740 > wait 100
    5741 
    5742 > crossfade
    5743 
    5744 > color #3/Q #0096FF
    5745 
    5746 > color #3/Z #9437FF
    5747 
    5748 > wait 50
    5749 
    5750 > wait 50
    5751 
    5752 > crossfade
    5753 
    5754 > color #3/Q dimgray
    5755 
    5756 > color #3/Z #C0C0C0
    5757 
    5758 > wait 50
    5759 
    5760 > crossfade
    5761 
    5762 > color #3/V #0096FF
    5763 
    5764 > color #3/I #9437FF
    5765 
    5766 > wait 50
    5767 
    5768 > wait 50
    5769 
    5770 > crossfade
    5771 
    5772 > color #3/V #C0C0C0
    5773 
    5774 > color #3/I dimgrey
    5775 
    5776 > wait 50
    5777 
    5778 > wait 100
    5779 
    5780 > movie encode
    5781 
    5782 Movie saved to /Users/zbxg977/Desktop/movie.mp4 
    5783  
    5784 
    5785 > save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    5786 > 2/Ub_states_movie.cxs" includeMaps true
    5787 
    5788 ——— End of log from Fri Nov 22 14:40:20 2024 ———
    5789 
    5790 opened ChimeraX session 
    5791 
    5792 > close #7
    5793 
    5794 > show #!5 models
    5795 
    5796 > show #!4 models
    5797 
    5798 > hide #!4 models
    5799 
    5800 > show #!4 models
    5801 
    5802 > hide #!4 models
    5803 
    5804 > show #!4 models
    5805 
    5806 > close #1-2
    5807 
    5808 > close #4-5
    5809 
    5810 > hide #!8 models
    5811 
    5812 > show #!8 models
    5813 
    5814 > hide #6 models
    5815 
    5816 > show #6 models
    5817 
    5818 > select add #3
    5819 
    5820 53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected 
    5821 
    5822 > show sel cartoons
    5823 
    5824 > hide #6 models
    5825 
    5826 > select subtract #3
    5827 
    5828 22 models selected 
    5829 
    5830 > show #6 models
    5831 
    5832 > hide #6 models
    5833 
    5834 > hide #!8 models
    5835 
    5836 > show #!8 models
    5837 
    5838 > select #8/L,T
    5839 
    5840 584 atoms, 590 bonds, 76 residues, 1 model selected 
    5841 
    5842 > select #8/L,C
    5843 
    5844 1186 atoms, 1198 bonds, 152 residues, 1 model selected 
    5845 
    5846 > hide sel cartoons
    5847 
    5848 > select add #8
    5849 
    5850 3424 atoms, 3454 bonds, 380 residues, 3 models selected 
    5851 
    5852 > select subtract #8
    5853 
    5854 5 models selected 
    5855 
    5856 > open "/Users/zbxg977/Desktop/BRISC_project/CryoSPARC processing
    5857 > Ub5/Composite_map_v1.mrc"
    5858 
    5859 Opened Composite_map_v1.mrc as #1, grid size 881,854,755, pixel
    5860 0.74,0.74,0.74, shown at step 1, values float32 
    5861 
    5862 > volume #1 level 0,0 level 0.01661,0.8 level 1.287,1
    5863 
    5864 > volume #1 level 0,1 level 0.01661,0.8 level 1.287,1
    5865 
    5866 > volume #1 region 0,0,0,880,853,754 step 4
    5867 
    5868 [Repeated 1 time(s)]
    5869 
    5870 > volume #1 step 1
    5871 
    5872 > hide #!1 models
    5873 
    5874 > show #!1 models
    5875 
    5876 > volume #1 level 0,1 level 0,0 level 1.287,1
    5877 
    5878 > volume #1 level 0,1 level 0,0 level 1.322,0
    5879 
    5880 > volume planes z style image imageMode "full region"
    5881 
    5882 > mousemode rightMode "move planes"
    5883 
    5884 > volume planes z style image imageMode "full region"
    5885 
    5886 > mousemode rightMode "move planes"
    5887 
    5888 > volume planes z style image imageMode "full region"
    5889 
    5890 > mousemode rightMode "move planes"
    5891 
    5892 > volume style surface
    5893 
    5894 > volume region all imageMode "full region"
    5895 
    5896 > volume unzone
    5897 
    5898 > mousemode rightMode "crop volume"
    5899 
    5900 Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
    5901 models, 1 maps. 
    5902 
    5903 > volume #1 orthoplanes xyz positionPlanes 440,427,377 style image region all
    5904 
    5905 > mousemode rightMode "move planes"
    5906 
    5907 > volume style surface
    5908 
    5909 > volume #1 level 0.04462
    5910 
    5911 > surface dust #1 size 7.4
    5912 
    5913 > ui tool show "Side View"
    5914 
    5915 > ui tool show "Fit in Map"
    5916 
    5917 > fitmap #3 inMap #1
    5918 
    5919 Fit molecule P64_J12_model-coot-56.pdb (#3) to map Composite_map_v1.mrc (#1)
    5920 using 53424 atoms 
    5921 average map value = 0.2036, steps = 252 
    5922 shifted from previous position = 23.8 
    5923 rotated from previous position = 6.84 degrees 
    5924 atoms outside contour = 19147, contour level = 0.044618 
    5925  
    5926 Position of P64_J12_model-coot-56.pdb (#3) relative to Composite_map_v1.mrc
    5927 (#1) coordinates: 
    5928 Matrix rotation and translation 
    5929 0.99999824 -0.00034178 0.00184313 -0.29642060 
    5930 0.00034053 0.99999971 0.00068229 -0.21302121 
    5931 -0.00184336 -0.00068166 0.99999807 0.51592373 
    5932 Axis -0.34188411 0.92404809 0.17102743 
    5933 Axis point 280.38615462 0.00000000 162.43947673 
    5934 Rotation angle (degrees) 0.11429067 
    5935 Shift along axis -0.00726324 
    5936  
    5937 
    5938 > fitmap #8 inMap #1
    5939 
    5940 Fit molecule penta_Ub_merged.pdb (#8) to map Composite_map_v1.mrc (#1) using
    5941 3424 atoms 
    5942 average map value = 0.144, steps = 232 
    5943 shifted from previous position = 18.2 
    5944 rotated from previous position = 20.5 degrees 
    5945 atoms outside contour = 1522, contour level = 0.044618 
    5946  
    5947 Position of penta_Ub_merged.pdb (#8) relative to Composite_map_v1.mrc (#1)
    5948 coordinates: 
    5949 Matrix rotation and translation 
    5950 -0.65356489 0.44939063 0.60901642 118.65823822 
    5951 0.44163674 -0.42703489 0.78904891 10.59241835 
    5952 0.61466245 0.78465869 0.08062760 -72.88467696 
    5953 Axis -0.41618722 -0.53523602 -0.73505823 
    5954 Axis point 79.98021623 31.62011254 0.00000000 
    5955 Rotation angle (degrees) 179.69780160 
    5956 Shift along axis -1.47900474 
    5957  
    5958 
    5959 > transparency 0
    5960 
    5961 > transparency 50
    5962 
    5963 > close #6
    5964 
    5965 > transparency 0
    5966 
    5967 > dssp
    5968 
    5969 > volume showOutlineBox false
    5970 
    5971 > hide #!1 models
    5972 
    5973 > select #8/O
    5974 
    5975 1034 atoms, 1040 bonds, 76 residues, 1 model selected 
    5976 
    5977 > hide sel cartoons
    5978 
    5979 > select add #8
    5980 
    5981 3424 atoms, 3454 bonds, 380 residues, 2 models selected 
    5982 
    5983 > select subtract #8
    5984 
    5985 5 models selected 
    5986 
    5987 > save "/Users/zbxg977/Desktop/BRISC_project/CryoSPARC processing
    5988 > Ub5/Map_model_Ub5_27Nov2024.cxs" includeMaps true
    5989 
    5990 ——— End of log from Wed Nov 27 09:59:35 2024 ———
    5991 
    5992 opened ChimeraX session 
    5993 
    5994 > save /Users/sxfp8838/Library/CloudStorage/OneDrive-
    5995 > UniversityofLeeds/BRISC/BRISC.cxs
    5996 
    5997 ——— End of log from Tue Feb 18 11:20:33 2025 ———
    5998 
    5999 opened ChimeraX session 
    6000 
    6001 > open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
    6002 > UniversityofLeeds/BRISC/Abraxas2 alphafold.pdb"
    6003 
    6004 Abraxas2 alphafold.pdb title: 
    6005 Alphafold monomer V2.0 prediction for brisc complex subunit abraxas 2 (Q15018)
    6006 [more info...] 
    6007  
    6008 Chain information for Abraxas2 alphafold.pdb #2 
    6009 --- 
    6010 Chain | Description | UniProt 
    6011 A | brisc complex subunit abraxas 2 | ABRX2_HUMAN 1-415 
    6012  
    6013 
    6014 > open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
    6015 > UniversityofLeeds/BRISC/Brcc36 alphafold.pdb"
    6016 
    6017 Brcc36 alphafold.pdb title: 
    6018 Alphafold monomer V2.0 prediction for lys-63-specific deubiquitinase BRCC36
    6019 (P46736) [more info...] 
    6020  
    6021 Chain information for Brcc36 alphafold.pdb #4 
    6022 --- 
    6023 Chain | Description | UniProt 
    6024 A | lys-63-specific deubiquitinase BRCC36 | BRCC3_HUMAN 1-316 
    6025  
    6026 
    6027 > open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
    6028 > UniversityofLeeds/BRISC/Brcc45 alphafold.pdb"
    6029 
    6030 Brcc45 alphafold.pdb title: 
    6031 Alphafold monomer V2.0 prediction for brisc and BRCA1-A complex member 2
    6032 (Q9NXR7) [more info...] 
    6033  
    6034 Chain information for Brcc45 alphafold.pdb #5 
    6035 --- 
    6036 Chain | Description | UniProt 
    6037 A | brisc and BRCA1-A complex member 2 | BABA2_HUMAN 1-383 
    6038  
    6039 Drag select of 4 residues 
    6040 
    6041 > ui mousemode right "move picked models"
    6042 
    6043 > view matrix models #2,1,0,0,49.333,0,1,0,-85.824,0,0,1,90.52
    6044 
    6045 > view matrix models #2,1,0,0,161.85,0,1,0,44.609,0,0,1,140.07
    6046 
    6047 > view matrix models #2,1,0,0,249.46,0,1,0,94.779,0,0,1,323.36
    6048 
    6049 > ui mousemode right translate
    6050 
    6051 > ui tool show Matchmaker
    6052 
    6053 > matchmaker #2/A to #3/M pairing ss
    6054 
    6055 Parameters 
    6056 --- 
    6057 Chain pairing | ss 
    6058 Alignment algorithm | Needleman-Wunsch 
    6059 Similarity matrix | BLOSUM-62 
    6060 SS fraction | 0.3 
    6061 Gap open (HH/SS/other) | 18/18/6 
    6062 Gap extend | 1 
    6063 SS matrix |  |  | H | S | O 
    6064 ---|---|---|--- 
    6065 H | 6 | -9 | -6 
    6066 S |  | 6 | -6 
    6067 O |  |  | 4 
    6068 Iteration cutoff | 2 
    6069  
    6070 Matchmaker P64_J12_model-coot-56.pdb, chain M (#3) with Abraxas2
    6071 alphafold.pdb, chain A (#2), sequence alignment score = 819.5 
    6072 RMSD between 169 pruned atom pairs is 1.047 angstroms; (across all 192 pairs:
    6073 2.148) 
    6074  
    6075 
    6076 > select #2/A:32-52
    6077 
    6078 172 atoms, 173 bonds, 21 residues, 1 model selected 
    6079 
    6080 > select up
    6081 
    6082 311 atoms, 317 bonds, 38 residues, 1 model selected 
    6083 
    6084 > select up
    6085 
    6086 3301 atoms, 3372 bonds, 415 residues, 1 model selected 
    6087 
    6088 > hide sel cartoons
    6089 
    6090 > select #2/A:32-52
    6091 
    6092 172 atoms, 173 bonds, 21 residues, 1 model selected 
    6093 
    6094 > show sel cartoons
    6095 
    6096 > color sel lime
    6097 
    6098 > select #2/A:32-54
    6099 
    6100 187 atoms, 188 bonds, 23 residues, 1 model selected 
    6101 
    6102 > show sel cartoons
    6103 
    6104 > color sel dim gray
    6105 
    6106 > select #2/A:37-50
    6107 
    6108 110 atoms, 111 bonds, 14 residues, 1 model selected 
    6109 
    6110 > color sel lime
    6111 
    6112 > ui mousemode right select
    6113 
    6114 > select clear
    6115 
    6116 > open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
    6117 > UniversityofLeeds/BRISC/Brcc36 alphafold.pdb"
    6118 
    6119 Brcc36 alphafold.pdb title: 
    6120 Alphafold monomer V2.0 prediction for lys-63-specific deubiquitinase BRCC36
    6121 (P46736) [more info...] 
    6122  
    6123 Chain information for Brcc36 alphafold.pdb #6 
    6124 --- 
    6125 Chain | Description | UniProt 
    6126 A | lys-63-specific deubiquitinase BRCC36 | BRCC3_HUMAN 1-316 
    6127  
    6128 
    6129 > select clear
    6130 
    6131 > ui mousemode right translate
    6132 
    6133 > ui mousemode right "move picked models"
    6134 
    6135 > view matrix models #4,1,0,0,-56.122,0,1,0,-84.255,0,0,1,51.498
    6136 
    6137 > view matrix models #6,1,0,0,68.2,0,1,0,52.979,0,0,1,4.8463
    6138 
    6139 > ui mousemode right select
    6140 
    6141 Drag select of 356 residues 
    6142 Drag select of 363 residues 
    6143 Drag select of 316 residues 
    6144 
    6145 > select clear
    6146 
    6147 Drag select of 316 residues 
    6148 
    6149 > delete
    6150 
    6151 Missing or invalid "atoms" argument: empty atom specifier 
    6152 
    6153 > select clear
    6154 
    6155 > ui mousemode right translate
    6156 
    6157 > ui mousemode right "translate selected models"
    6158 
    6159 > ui mousemode right "rotate selected models"
    6160 
    6161 > ui mousemode right "move picked models"
    6162 
    6163 > ui mousemode right translate
    6164 
    6165 > ui mousemode right select
    6166 
    6167 > ui mousemode right rotate
    6168 
    6169 > ui mousemode right translate
    6170 
    6171 > ui tool show Matchmaker
    6172 
    6173 > matchmaker #4/A to #3/G pairing ss
    6174 
    6175 Parameters 
    6176 --- 
    6177 Chain pairing | ss 
    6178 Alignment algorithm | Needleman-Wunsch 
    6179 Similarity matrix | BLOSUM-62 
    6180 SS fraction | 0.3 
    6181 Gap open (HH/SS/other) | 18/18/6 
    6182 Gap extend | 1 
    6183 SS matrix |  |  | H | S | O 
    6184 ---|---|---|--- 
    6185 H | 6 | -9 | -6 
    6186 S |  | 6 | -6 
    6187 O |  |  | 4 
    6188 Iteration cutoff | 2 
    6189  
    6190 Matchmaker P64_J12_model-coot-56.pdb, chain G (#3) with Brcc36 alphafold.pdb,
    6191 chain A (#4), sequence alignment score = 1180.5 
    6192 RMSD between 235 pruned atom pairs is 0.786 angstroms; (across all 250 pairs:
    6193 1.302) 
    6194  
    6195 
    6196 > select #4/A:184-208
    6197 
    6198 207 atoms, 212 bonds, 25 residues, 1 model selected 
    6199 
    6200 > color sel cyan
    6201 
    6202 > color sel light sea green
    6203 
    6204 > color sel cyan
    6205 
    6206 > select up
    6207 
    6208 251 atoms, 256 bonds, 31 residues, 1 model selected 
    6209 
    6210 > select up
    6211 
    6212 2529 atoms, 2575 bonds, 316 residues, 1 model selected 
    6213 
    6214 > hide sel cartoons
    6215 
    6216 > select #4/A:184-208
    6217 
    6218 207 atoms, 212 bonds, 25 residues, 1 model selected 
    6219 
    6220 > show sel cartoons
    6221 
    6222 > select #4/A:180-208
    6223 
    6224 237 atoms, 242 bonds, 29 residues, 1 model selected 
    6225 
    6226 > show sel cartoons
    6227 
    6228 > select #4/A:176-208
    6229 
    6230 268 atoms, 273 bonds, 33 residues, 1 model selected 
    6231 
    6232 > show sel cartoons
    6233 
    6234 > select #4/A:183
    6235 
    6236 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6237 
    6238 > select #4/A:182
    6239 
    6240 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6241 
    6242 > select #4/A:183
    6243 
    6244 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6245 
    6246 > select #4/A:182
    6247 
    6248 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6249 
    6250 > select #4/A:181
    6251 
    6252 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6253 
    6254 > select #4/A:176-183
    6255 
    6256 61 atoms, 60 bonds, 8 residues, 1 model selected 
    6257 
    6258 > color sel dim gray
    6259 
    6260 > ui mousemode right select
    6261 
    6262 > select clear
    6263 
    6264 > select #3/G:88
    6265 
    6266 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6267 
    6268 > show sel atoms
    6269 
    6270 > style sel ball
    6271 
    6272 Changed 7 atom styles 
    6273 
    6274 > color (#!3 & sel) cyan
    6275 
    6276 > select #3/G:145
    6277 
    6278 17 atoms, 16 bonds, 1 residue, 1 model selected 
    6279 
    6280 > show sel atoms
    6281 
    6282 > style sel ball
    6283 
    6284 Changed 17 atom styles 
    6285 
    6286 > color (#!3 & sel) cyan
    6287 
    6288 > ui tool show Matchmaker
    6289 
    6290 > matchmaker #5/A to #3/Y pairing ss
    6291 
    6292 Parameters 
    6293 --- 
    6294 Chain pairing | ss 
    6295 Alignment algorithm | Needleman-Wunsch 
    6296 Similarity matrix | BLOSUM-62 
    6297 SS fraction | 0.3 
    6298 Gap open (HH/SS/other) | 18/18/6 
    6299 Gap extend | 1 
    6300 SS matrix |  |  | H | S | O 
    6301 ---|---|---|--- 
    6302 H | 6 | -9 | -6 
    6303 S |  | 6 | -6 
    6304 O |  |  | 4 
    6305 Iteration cutoff | 2 
    6306  
    6307 Matchmaker P64_J12_model-coot-56.pdb, chain Y (#3) with Brcc45 alphafold.pdb,
    6308 chain A (#5), sequence alignment score = 1634.1 
    6309 RMSD between 209 pruned atom pairs is 1.153 angstroms; (across all 351 pairs:
    6310 2.724) 
    6311  
    6312 
    6313 > select #5/A:378
    6314 
    6315 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6316 
    6317 > select up
    6318 
    6319 79 atoms, 81 bonds, 10 residues, 1 model selected 
    6320 
    6321 > select up
    6322 
    6323 3078 atoms, 3169 bonds, 383 residues, 1 model selected 
    6324 
    6325 > ui mousemode right "move picked models"
    6326 
    6327 > view matrix models
    6328 > #5,0.82998,0.35439,0.43074,135.5,0.40064,-0.91606,-0.018284,95.563,0.3881,0.18775,-0.90229,157.7
    6329 
    6330 > view matrix models
    6331 > #5,0.82998,0.35439,0.43074,143.32,0.40064,-0.91606,-0.018284,35.228,0.3881,0.18775,-0.90229,66.629
    6332 
    6333 > show sel cartoons
    6334 
    6335 > hide sel cartoons
    6336 
    6337 > select #6/A:98
    6338 
    6339 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6340 
    6341 > select up
    6342 
    6343 133 atoms, 133 bonds, 18 residues, 1 model selected 
    6344 
    6345 > select up
    6346 
    6347 2529 atoms, 2575 bonds, 316 residues, 1 model selected 
    6348 
    6349 > hide sel cartoons
    6350 
    6351 > select #3/Y:263
    6352 
    6353 20 atoms, 20 bonds, 1 residue, 1 model selected 
    6354 
    6355 > show sel atoms
    6356 
    6357 > style sel sphere
    6358 
    6359 Changed 20 atom styles 
    6360 
    6361 > style sel ball
    6362 
    6363 Changed 20 atom styles 
    6364 
    6365 > color (#!3 & sel) purple
    6366 
    6367 > color (#!3 & sel) #b13dffff
    6368 
    6369 > select #3/Y:320
    6370 
    6371 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6372 
    6373 > style sel ball
    6374 
    6375 Changed 11 atom styles 
    6376 
    6377 > show sel atoms
    6378 
    6379 > color (#!3 & sel) #b13dffff
    6380 
    6381 > select #3/Y:140
    6382 
    6383 20 atoms, 20 bonds, 1 residue, 1 model selected 
    6384 
    6385 > show sel atoms
    6386 
    6387 > color (#!3 & sel) #b13dffff
    6388 
    6389 > style sel ball
    6390 
    6391 Changed 20 atom styles 
    6392 
    6393 > ui mousemode right select
    6394 
    6395 > select clear
    6396 
    6397 > save "/Users/sxfp8838/OneDrive - University of Leeds/BRISC/BRISC all
    6398 > mutations coloured.cxs"
    6399 
    6400 > select #3/Y:165
    6401 
    6402 Nothing selected 
    6403 
    6404 > select #3/Y:10
    6405 
    6406 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6407 
    6408 > select #3/Y:160
    6409 
    6410 Nothing selected 
    6411 
    6412 > view
    6413 
    6414 > select #3/Y:160
    6415 
    6416 Nothing selected 
    6417 
    6418 > select #3/Y:150
    6419 
    6420 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6421 
    6422 > select #3/M:21
    6423 
    6424 14 atoms, 13 bonds, 1 residue, 1 model selected 
    6425 
    6426 > select #3/M:72
    6427 
    6428 Nothing selected 
    6429 
    6430 > select #3/M:99
    6431 
    6432 24 atoms, 23 bonds, 1 residue, 1 model selected 
    6433 
    6434 > select #3/M:105
    6435 
    6436 17 atoms, 16 bonds, 1 residue, 1 model selected 
    6437 
    6438 > select #3/M:107
    6439 
    6440 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6441 
    6442 > select #3/M:117
    6443 
    6444 14 atoms, 13 bonds, 1 residue, 1 model selected 
    6445 
    6446 > select #3/M:121
    6447 
    6448 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6449 
    6450 > select #3/M:131
    6451 
    6452 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6453 
    6454 > select #3/M:161
    6455 
    6456 10 atoms, 9 bonds, 1 residue, 1 model selected 
    6457 
    6458 > select #3/M:208
    6459 
    6460 10 atoms, 9 bonds, 1 residue, 1 model selected 
    6461 
    6462 > select #3/M:219
    6463 
    6464 22 atoms, 21 bonds, 1 residue, 1 model selected 
    6465 
    6466 > select #3/M:223
    6467 
    6468 16 atoms, 15 bonds, 1 residue, 1 model selected 
    6469 
    6470 > select #3/M:240
    6471 
    6472 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6473 
    6474 > select #3/M:267
    6475 
    6476 Nothing selected 
    6477 
    6478 > select #3/M:406
    6479 
    6480 Nothing selected 
    6481 
    6482 > select #3/F:21
    6483 
    6484 14 atoms, 13 bonds, 1 residue, 1 model selected 
    6485 
    6486 > select #3/F:72
    6487 
    6488 10 atoms, 9 bonds, 1 residue, 1 model selected 
    6489 
    6490 > select #3/F:99
    6491 
    6492 24 atoms, 23 bonds, 1 residue, 1 model selected 
    6493 
    6494 > select #3/F:105
    6495 
    6496 17 atoms, 16 bonds, 1 residue, 1 model selected 
    6497 
    6498 > select #3/F:107
    6499 
    6500 21 atoms, 21 bonds, 1 residue, 1 model selected 
    6501 
    6502 > select #3/F:117
    6503 
    6504 14 atoms, 13 bonds, 1 residue, 1 model selected 
    6505 
    6506 > select #3/F:121
    6507 
    6508 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6509 
    6510 > select #3/F:122
    6511 
    6512 16 atoms, 15 bonds, 1 residue, 1 model selected 
    6513 
    6514 > select #3/F:131
    6515 
    6516 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6517 
    6518 > select #3/F:161
    6519 
    6520 10 atoms, 9 bonds, 1 residue, 1 model selected 
    6521 
    6522 > select #3/G:59
    6523 
    6524 Nothing selected 
    6525 
    6526 > select #3/G:60
    6527 
    6528 Nothing selected 
    6529 
    6530 > select #3/G:70
    6531 
    6532 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6533 
    6534 > select #3/G:187
    6535 
    6536 Nothing selected 
    6537 
    6538 > select #3/G:190
    6539 
    6540 Nothing selected 
    6541 
    6542 > select #3/G:191
    6543 
    6544 Nothing selected 
    6545 
    6546 > select #3/G:195
    6547 
    6548 Nothing selected 
    6549 
    6550 > select #3/G:200
    6551 
    6552 Nothing selected 
    6553 
    6554 > select #3/Y:5
    6555 
    6556 Nothing selected 
    6557 
    6558 > select #3/Y:10
    6559 
    6560 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6561 
    6562 > ui mousemode right translate
    6563 
    6564 > select #3/Y:50
    6565 
    6566 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6567 
    6568 > select #3/Y:60
    6569 
    6570 19 atoms, 18 bonds, 1 residue, 1 model selected 
    6571 
    6572 > select #3/Y:68
    6573 
    6574 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6575 
    6576 > select #3/Y:109
    6577 
    6578 14 atoms, 13 bonds, 1 residue, 1 model selected 
    6579 
    6580 > select #3/Y:133
    6581 
    6582 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6583 
    6584 > show sel atoms
    6585 
    6586 > hide sel atoms
    6587 
    6588 > select #3/Y:139
    6589 
    6590 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6591 
    6592 > show sel atoms
    6593 
    6594 > select #3/Y:203
    6595 
    6596 19 atoms, 18 bonds, 1 residue, 1 model selected 
    6597 
    6598 > show sel atoms
    6599 
    6600 > hide sel atoms
    6601 
    6602 > select #3/Y:157
    6603 
    6604 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6605 
    6606 > select #3/Y:162
    6607 
    6608 Nothing selected 
    6609 
    6610 > select #3/Y:172
    6611 
    6612 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6613 
    6614 > select #3/Y:186
    6615 
    6616 Nothing selected 
    6617 
    6618 > select #4/A:184
    6619 
    6620 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6621 
    6622 > select up
    6623 
    6624 251 atoms, 256 bonds, 31 residues, 1 model selected 
    6625 
    6626 > select up
    6627 
    6628 2529 atoms, 2575 bonds, 316 residues, 1 model selected 
    6629 
    6630 > select up
    6631 
    6632 68285 atoms, 69226 bonds, 5893 residues, 8 models selected 
    6633 
    6634 > select down
    6635 
    6636 2529 atoms, 2575 bonds, 316 residues, 28 models selected 
    6637 
    6638 > show sel cartoons
    6639 
    6640 > undo
    6641 
    6642 > ui mousemode right select
    6643 
    6644 > select clear
    6645 
    6646 > open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
    6647 > UniversityofLeeds/BRISC/Brcc45 alphafold.pdb"
    6648 
    6649 Brcc45 alphafold.pdb title: 
    6650 Alphafold monomer V2.0 prediction for brisc and BRCA1-A complex member 2
    6651 (Q9NXR7) [more info...] 
    6652  
    6653 Chain information for Brcc45 alphafold.pdb #7 
    6654 --- 
    6655 Chain | Description | UniProt 
    6656 A | brisc and BRCA1-A complex member 2 | BABA2_HUMAN 1-383 
    6657  
    6658 
    6659 > ui mousemode right "move picked models"
    6660 
    6661 > view matrix models #7,1,0,0,123.09,0,1,0,171.58,0,0,1,39.68
    6662 
    6663 > ui tool show Matchmaker
    6664 
    6665 > matchmaker #7/A to #3/Y pairing ss
    6666 
    6667 Parameters 
    6668 --- 
    6669 Chain pairing | ss 
    6670 Alignment algorithm | Needleman-Wunsch 
    6671 Similarity matrix | BLOSUM-62 
    6672 SS fraction | 0.3 
    6673 Gap open (HH/SS/other) | 18/18/6 
    6674 Gap extend | 1 
    6675 SS matrix |  |  | H | S | O 
    6676 ---|---|---|--- 
    6677 H | 6 | -9 | -6 
    6678 S |  | 6 | -6 
    6679 O |  |  | 4 
    6680 Iteration cutoff | 2 
    6681  
    6682 Matchmaker P64_J12_model-coot-56.pdb, chain Y (#3) with Brcc45 alphafold.pdb,
    6683 chain A (#7), sequence alignment score = 1634.1 
    6684 RMSD between 209 pruned atom pairs is 1.153 angstroms; (across all 351 pairs:
    6685 2.724) 
    6686  
    6687 
    6688 > select #3/Y:172
    6689 
    6690 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6691 
    6692 > select #3/Y:186
    6693 
    6694 Nothing selected 
    6695 
    6696 > select #3/Y:186
    6697 
    6698 Nothing selected 
    6699 
    6700 > select #3/Y:206
    6701 
    6702 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6703 
    6704 > select #3/Y:209
    6705 
    6706 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6707 
    6708 > select clear
    6709 
    6710 > select #7/A:167
    6711 
    6712 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6713 
    6714 > select up
    6715 
    6716 89 atoms, 91 bonds, 11 residues, 1 model selected 
    6717 
    6718 > select up
    6719 
    6720 3078 atoms, 3169 bonds, 383 residues, 1 model selected 
    6721 
    6722 > hide sel cartoons
    6723 
    6724 > select #3/Y:209
    6725 
    6726 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6727 
    6728 > show sel atoms
    6729 
    6730 > hide sel atoms
    6731 
    6732 > select #3/Y:220
    6733 
    6734 21 atoms, 21 bonds, 1 residue, 1 model selected 
    6735 
    6736 > select #3/Y:227
    6737 
    6738 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6739 
    6740 > select #3/Y:266
    6741 
    6742 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6743 
    6744 > view matrix models
    6745 > #3,1,-0.00034178,0.0018431,-11.971,0.00034053,1,0.00068229,19.772,-0.0018434,-0.00068166,1,-12.284
    6746 
    6747 > select #3/Y:287
    6748 
    6749 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6750 
    6751 > select #3/Y:2300
    6752 
    6753 Nothing selected 
    6754 
    6755 > select #3/Y:300
    6756 
    6757 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6758 
    6759 > select #3/Y:366
    6760 
    6761 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6762 
    6763 > select #3/Y:348
    6764 
    6765 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6766 
    6767 > show sel atoms
    6768 
    6769 > hide sel atoms
    6770 
    6771 > select #3/Y:330
    6772 
    6773 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6774 
    6775 Unsupported scale factor (0.000000) detected on Display0 
    6776 
    6777 Unsupported scale factor (0.000000) detected on Display1 
    6778 
    6779 Unsupported scale factor (0.000000) detected on Display0 
    6780 
    6781 Unsupported scale factor (0.000000) detected on Display1 
    6782 
    6783 QPainter::begin: Paint device returned engine == 0, type: 3 
    6784 
    6785 
    6786 ===== Log before crash end =====
    6787 
    6788 Log:
    6789 UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    6790 © 2016-2023 Regents of the University of California. All rights reserved. 
    6791 
    6792 > open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
    6793 > UniversityofLeeds/BRISC/BRISC coloured .cxs"
    6794 
    6795 Opened Composite_map_v1.mrc as #1, grid size 881,854,755, pixel
    6796 0.74,0.74,0.74, shown at level 0.0446, step 1, values float32 
    6797 Log from Tue Feb 25 14:10:22 2025UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    6798 © 2016-2023 Regents of the University of California. All rights reserved. 
    6799 
    6800 > open /Users/sxfp8838/Library/CloudStorage/OneDrive-
    6801 > UniversityofLeeds/BRISC/BRISC.cxs format session
    6802 
    6803 Opened Composite_map_v1.mrc as #1, grid size 881,854,755, pixel
    6804 0.74,0.74,0.74, shown at level 0.0446, step 1, values float32 
    6805 Log from Tue Feb 18 11:20:33 2025UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    6806 © 2016-2023 Regents of the University of California. All rights reserved. 
    6807 
    6808 > open "/Users/sxfp8838/Downloads/Map_model_Ub5_27Nov2024 copy.cxs" format
    6809 > session
    6810 
    6811 Opened Composite_map_v1.mrc as #1, grid size 881,854,755, pixel
    6812 0.74,0.74,0.74, shown at level 0.0446, step 1, values float32 
    6813 Log from Wed Nov 27 09:59:35 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    6814 © 2016-2023 Regents of the University of California. All rights reserved. 
    6815 
    6816 > open "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    6817 > 2/Ub_states_movie.cxs"
    6818 
    6819 Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
    6820 shown at level 0.04, step 1, values float32 
    6821 Opened P64_W2_J50_tightTarget.mrc as #1, grid size 512,512,512, pixel 0.74,
    6822 shown at level 0.0301, step 1, values float32 
    6823 Opened P64_W2_J50_tightTarget.mrc copy as #4, grid size 512,512,512, pixel
    6824 0.74, shown at level 0.0641, step 1, values float32 
    6825 Opened cryosparc_P1_DeepEmhancer_J202_highres.mrc as #5, grid size
    6826 512,512,512, pixel 0.74, shown at level 0.113, step 1, values float32 
    6827 Log from Fri Nov 22 14:40:20 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    6828 © 2016-2023 Regents of the University of California. All rights reserved. 
    6829 
    6830 > open "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    6831 > 2/Map_localref.cxs"
    6832 
    6833 Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
    6834 shown at level 0.04, step 1, values float32 
    6835 Opened P64_W2_J50_tightTarget.mrc as #1, grid size 512,512,512, pixel 0.74,
    6836 shown at level 0.0301, step 1, values float32 
    6837 Opened P64_W2_J50_tightTarget.mrc copy as #4, grid size 512,512,512, pixel
    6838 0.74, shown at level 0.0641, step 1, values float32 
    6839 Log from Thu Oct 31 16:48:37 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    6840 © 2016-2023 Regents of the University of California. All rights reserved. 
    6841 
    6842 > open /Users/zbxg977/Desktop/BRISC_Ub5_colouredbychain.cxs
    6843 
    6844 Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
    6845 shown at level 0.04, step 1, values float32 
    6846 Log from Tue Oct 8 13:02:45 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    6847 © 2016-2023 Regents of the University of California. All rights reserved. 
    6848 
    6849 > open "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    6850 > 2/Map_model_coloured_v4.cxs"
    6851 
    6852 Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
    6853 shown at level 0.04, step 1, values float32 
    6854 Opened P64_J12_deepemhancer.mrc copy as #4, grid size 512,512,512, pixel 0.74,
    6855 shown at level 0.04, step 1, values float32 
    6856 Opened cryosparc_P64_J40_020_volume_map (1).mrc as #6, grid size 512,512,512,
    6857 pixel 0.74, shown at level 0.154, step 1, values float32 
    6858 Log from Wed Oct 2 15:29:10 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    6859 © 2016-2023 Regents of the University of California. All rights reserved. 
    6860 
    6861 > open "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    6862 > 2/Map_model_coloured_v2.cxs"
    6863 
    6864 Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
    6865 shown at level 0.04, step 1, values float32 
    6866 Opened P64_J12_deepemhancer.mrc copy as #4, grid size 512,512,512, pixel 0.74,
    6867 shown at level 0.04, step 1, values float32 
    6868 Log from Tue Oct 1 13:16:34 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    6869 © 2016-2023 Regents of the University of California. All rights reserved. 
    6870 
    6871 > open "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    6872 > 2/Map_model_coloured.cxs"
    6873 
    6874 Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
    6875 shown at level 0.04, step 1, values float32 
    6876 Opened P64_J12_deepemhancer.mrc copy as #4, grid size 512,512,512, pixel 0.74,
    6877 shown at level 0.04, step 1, values float32 
    6878 Log from Wed Sep 4 11:11:03 2024 Startup Messages 
    6879 --- 
    6880 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
    6881 bundle with that from NMRSTAR bundle 
    6882  
    6883 UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    6884 © 2016-2023 Regents of the University of California. All rights reserved. 
    6885 How to cite UCSF ChimeraX 
    6886 
    6887 > open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_46/P64_J12_model-
    6888 > coot-48.pdb
    6889 
    6890 Chain information for P64_J12_model-coot-48.pdb #1 
    6891 --- 
    6892 Chain | Description 
    6893 A | No description available 
    6894 B | No description available 
    6895 D | No description available 
    6896 E K N P | No description available 
    6897 F | No description available 
    6898 G | No description available 
    6899 H | No description available 
    6900 I | No description available 
    6901 J | No description available 
    6902 L Q | No description available 
    6903 M | No description available 
    6904 O | No description available 
    6905 W | No description available 
    6906 X | No description available 
    6907 Y | No description available 
    6908  
    6909 
    6910 > open "/Users/zbxg977/Desktop/BRISC_project/CryoSPARC
    6911 > processing/P64_W1_J12/Deepemhancer/P64_J12_deepemhancer.mrc"
    6912 
    6913 Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
    6914 shown at level 0.00279, step 2, values float32 
    6915 
    6916 > set bgColor white
    6917 
    6918 > lighting soft
    6919 
    6920 > volume #2 step 1
    6921 
    6922 > hide atoms
    6923 
    6924 > show cartoons
    6925 
    6926 > dssp
    6927 
    6928 > volume #2 level 0.02757
    6929 
    6930 > surface dust #2 size 7.4
    6931 
    6932 > hide #!2 models
    6933 
    6934 > colour #1/B,G,X,M #0096FF
    6935 
    6936 > colour #1/A,F,J,W #00F900
    6937 
    6938 > colour #1/H,Y,D,I #9437FF
    6939 
    6940 > colour #1/L,O,Q #FF9300
    6941 
    6942 > colour #1/E,K,N,P #EF4E5D
    6943 
    6944 > show #!2 models
    6945 
    6946 > ui tool show "Surface Color"
    6947 
    6948 > ui tool show "Color Zone"
    6949 
    6950 > color zone #2 near #1 distance 4.44
    6951 
    6952 > color zone #2 near #1 distance 4.54
    6953 
    6954 > color zone #2 near #1 distance 4.64
    6955 
    6956 > color zone #2 near #1 distance 4.74
    6957 
    6958 > color zone #2 near #1 distance 4.84
    6959 
    6960 > hide #!1 models
    6961 
    6962 > color zone #2 near #1 distance 4.94
    6963 
    6964 > color zone #2 near #1 distance 5.04
    6965 
    6966 > color zone #2 near #1 distance 5.14
    6967 
    6968 > color zone #2 near #1 distance 5.24
    6969 
    6970 > color zone #2 near #1 distance 5.34
    6971 
    6972 > color zone #2 near #1 distance 5.44
    6973 
    6974 > color zone #2 near #1 distance 5.54
    6975 
    6976 > color zone #2 near #1 distance 5.64
    6977 
    6978 > color zone #2 near #1 distance 5.74
    6979 
    6980 > volume #2 level 0.03
    6981 
    6982 > volume #2 level 0.035
    6983 
    6984 > save "/Users/zbxg977/Desktop/BRISC_project/Main
    6985 > figures/Map_model_coloured.cxs" includeMaps true
    6986 
    6987 > volume #2 level 0.04
    6988 
    6989 > save /Users/zbxg977/Desktop/image2.png supersample 3
    6990 
    6991 > save /Users/zbxg977/Desktop/image3.png supersample 3
    6992 
    6993 > save /Users/zbxg977/Desktop/image4.png supersample 3
    6994 
    6995 > open 1ubq
    6996 
    6997 1ubq title: 
    6998 Structure of ubiquitin refined At 1.8 angstroms resolution [more info...] 
    6999  
    7000 Chain information for 1ubq #3 
    7001 --- 
    7002 Chain | Description | UniProt 
    7003 A | UBIQUITIN | UBIQ_HUMAN 1-76 
    7004  
    7005 
    7006 > select add #3
    7007 
    7008 660 atoms, 608 bonds, 134 residues, 1 model selected 
    7009 
    7010 > ui mousemode right "translate selected models"
    7011 
    7012 > view matrix models #3,1,0,0,22.142,0,1,0,146.55,0,0,1,177.99
    7013 
    7014 > view matrix models #3,1,0,0,85.901,0,1,0,77.699,0,0,1,152.28
    7015 
    7016 > view matrix models #3,1,0,0,106,0,1,0,120.98,0,0,1,189.39
    7017 
    7018 > view matrix models #3,1,0,0,108.09,0,1,0,99.383,0,0,1,182.46
    7019 
    7020 > close #3
    7021 
    7022 > show #!1 models
    7023 
    7024 > hide #!2 models
    7025 
    7026 > select #1/O
    7027 
    7028 1034 atoms, 1040 bonds, 76 residues, 1 model selected 
    7029 
    7030 > show sel atoms
    7031 
    7032 > save /Users/zbxg977/4Ub.pdb selectedOnly true relModel #2
    7033 
    7034 > open /Users/zbxg977/Desktop/4Ub.pdb
    7035 
    7036 Summary of feedback from opening /Users/zbxg977/Desktop/4Ub.pdb 
    7037 --- 
    7038 warnings | Start residue of secondary structure not found: HELIX 1 1 GLU E 104
    7039 SER E 106 1 3 
    7040 Start residue of secondary structure not found: HELIX 2 2 ALA E 120 VAL E 132
    7041 1 13 
    7042 Start residue of secondary structure not found: HELIX 3 3 ARG E 133 HIS E 136
    7043 1 4 
    7044 Start residue of secondary structure not found: HELIX 4 4 PRO E 163 SER E 168
    7045 1 6 
    7046 Start residue of secondary structure not found: HELIX 5 5 GLU E 184 LYS E 193
    7047 1 10 
    7048 230 messages similar to the above omitted 
    7049  
    7050 Chain information for 4Ub.pdb #3 
    7051 --- 
    7052 Chain | Description 
    7053 O | No description available 
    7054  
    7055 
    7056 > hide #!1 models
    7057 
    7058 > select add #1
    7059 
    7060 45135 atoms, 45847 bonds, 43 pseudobonds, 4183 residues, 2 models selected 
    7061 
    7062 > select subtract #1
    7063 
    7064 Nothing selected 
    7065 
    7066 > show #!2 models
    7067 
    7068 > select add #3
    7069 
    7070 1034 atoms, 1040 bonds, 76 residues, 1 model selected 
    7071 
    7072 > view matrix models #3,1,0,0,-45.77,0,1,0,-55.623,0,0,1,60.278
    7073 
    7074 > ui mousemode right "rotate selected models"
    7075 
    7076 > view matrix models
    7077 > #3,-0.64657,0.76019,0.063756,122.26,-0.11869,-0.1828,0.97596,39.647,0.75356,0.62346,0.20842,-81.893
    7078 
    7079 > ui mousemode right "translate selected models"
    7080 
    7081 > view matrix models
    7082 > #3,-0.64657,0.76019,0.063756,133.01,-0.11869,-0.1828,0.97596,51.544,0.75356,0.62346,0.20842,-92.026
    7083 
    7084 > volume #2 level 0.02
    7085 
    7086 > view matrix models
    7087 > #3,-0.64657,0.76019,0.063756,131.7,-0.11869,-0.1828,0.97596,48.688,0.75356,0.62346,0.20842,-91.418
    7088 
    7089 > ui mousemode right "rotate selected models"
    7090 
    7091 > view matrix models
    7092 > #3,-0.92486,0.37158,0.081038,254.86,-0.0046565,-0.22413,0.97455,34.504,0.38029,0.90094,0.20902,-70.711
    7093 
    7094 > view matrix models
    7095 > #3,-0.99669,0.0074678,0.080982,336.17,0.077958,-0.19583,0.97753,12.84,0.023158,0.98061,0.1946,-14.243
    7096 
    7097 > ui tool show "Fit in Map"
    7098 
    7099 > fitmap #3 inMap #2
    7100 
    7101 Fit molecule 4Ub.pdb (#3) to map P64_J12_deepemhancer.mrc (#2) using 1034
    7102 atoms 
    7103 average map value = 0.02144, steps = 152 
    7104 shifted from previous position = 3.73 
    7105 rotated from previous position = 9.35 degrees 
    7106 atoms outside contour = 820, contour level = 0.02 
    7107  
    7108 Position of 4Ub.pdb (#3) relative to P64_J12_deepemhancer.mrc (#2)
    7109 coordinates: 
    7110 Matrix rotation and translation 
    7111 -0.98830394 -0.01606640 0.15164823 329.56486754 
    7112 0.14821753 -0.33513041 0.93044031 28.20456991 
    7113 0.03587311 0.94203475 0.33359202 -29.19789796 
    7114 Axis 0.05759369 0.57509586 0.81605620 
    7115 Axis point 165.14304010 34.55878631 0.00000000 
    7116 Rotation angle (degrees) 174.22298154 
    7117 Shift along axis 11.37406101 
    7118  
    7119 
    7120 > hide #!2 models
    7121 
    7122 > show #!1 models
    7123 
    7124 > show #!2 models
    7125 
    7126 > ui mousemode right "translate selected models"
    7127 
    7128 > view matrix models
    7129 > #3,-0.9883,-0.016066,0.15165,335.85,0.14822,-0.33513,0.93044,32.137,0.035873,0.94203,0.33359,-27.52
    7130 
    7131 > ui mousemode right "rotate selected models"
    7132 
    7133 > view matrix models
    7134 > #3,-0.78284,-0.58586,-0.20959,455.92,-0.24052,-0.025733,0.9703,44.024,-0.57386,0.81,-0.12077,183.11
    7135 
    7136 > view matrix models
    7137 > #3,-0.80058,-0.5206,0.29672,371.17,0.27623,0.11879,0.95372,-80.16,-0.53176,0.84549,0.048707,142.93
    7138 
    7139 > ui mousemode right "translate selected models"
    7140 
    7141 > ui mousemode right "rotate selected models"
    7142 
    7143 > view matrix models
    7144 > #3,-0.87819,-0.058049,0.47478,273.77,0.44528,0.26324,0.85582,-124.88,-0.17466,0.96298,-0.20532,90.305
    7145 
    7146 > fitmap #3 inMap #2
    7147 
    7148 Fit molecule 4Ub.pdb (#3) to map P64_J12_deepemhancer.mrc (#2) using 1034
    7149 atoms 
    7150 average map value = 0.02942, steps = 84 
    7151 shifted from previous position = 2.76 
    7152 rotated from previous position = 7.03 degrees 
    7153 atoms outside contour = 753, contour level = 0.02 
    7154  
    7155 Position of 4Ub.pdb (#3) relative to P64_J12_deepemhancer.mrc (#2)
    7156 coordinates: 
    7157 Matrix rotation and translation 
    7158 -0.86861384 0.06310794 0.49145435 247.47541190 
    7159 0.48957680 0.26208308 0.83164116 -131.75136294 
    7160 -0.07631871 0.96297967 -0.25854517 77.15930390 
    7161 Axis 0.18187306 0.78623263 0.59055943 
    7162 Axis point 149.05714988 0.00000000 58.37470019 
    7163 Rotation angle (degrees) 158.83395882 
    7164 Shift along axis -13.01095516 
    7165  
    7166 
    7167 > volume #2 level 0.015
    7168 
    7169 > hide #!2 models
    7170 
    7171 > show #!2 models
    7172 
    7173 > ui mousemode right "translate selected models"
    7174 
    7175 > view matrix models
    7176 > #3,-0.86861,0.063108,0.49145,245.67,0.48958,0.26208,0.83164,-132.49,-0.076319,0.96298,-0.25855,78.734
    7177 
    7178 > fitmap #3 inMap #2
    7179 
    7180 Fit molecule 4Ub.pdb (#3) to map P64_J12_deepemhancer.mrc (#2) using 1034
    7181 atoms 
    7182 average map value = 0.04094, steps = 272 
    7183 shifted from previous position = 3.53 
    7184 rotated from previous position = 24.2 degrees 
    7185 atoms outside contour = 675, contour level = 0.015 
    7186  
    7187 Position of 4Ub.pdb (#3) relative to P64_J12_deepemhancer.mrc (#2)
    7188 coordinates: 
    7189 Matrix rotation and translation 
    7190 -0.66115790 0.32526680 0.67607081 131.95953052 
    7191 0.72210154 0.03138215 0.69107490 -114.53308250 
    7192 0.20356717 0.94510141 -0.25562421 24.27981973 
    7193 Axis 0.38068765 0.70810053 0.59470207 
    7194 Axis point 100.89632926 0.00000000 43.47460178 
    7195 Rotation angle (degrees) 160.51004202 
    7196 Shift along axis -16.42631342 
    7197  
    7198 
    7199 > hide #!2 models
    7200 
    7201 > show #!2 models
    7202 
    7203 > view matrix models
    7204 > #3,-0.66116,0.32527,0.67607,129.56,0.7221,0.031382,0.69107,-115.04,0.20357,0.9451,-0.25562,25.841
    7205 
    7206 > ui mousemode right "rotate selected models"
    7207 
    7208 > view matrix models
    7209 > #3,-0.81701,0.17495,0.54944,206.56,0.56462,0.43612,0.70072,-160.98,-0.11703,0.88272,-0.4551,129.36
    7210 
    7211 > hide #!2 models
    7212 
    7213 > hide sel atoms
    7214 
    7215 > show sel cartoons
    7216 
    7217 > select subtract #3
    7218 
    7219 Nothing selected 
    7220 
    7221 > hide atoms
    7222 
    7223 > show #!2 models
    7224 
    7225 > select add #3
    7226 
    7227 1034 atoms, 1040 bonds, 76 residues, 1 model selected 
    7228 
    7229 > ui mousemode right "translate selected models"
    7230 
    7231 > view matrix models
    7232 > #3,-0.81701,0.17495,0.54944,208.56,0.56462,0.43612,0.70072,-159.01,-0.11703,0.88272,-0.4551,130.17
    7233 
    7234 > view matrix models
    7235 > #3,-0.81701,0.17495,0.54944,207.37,0.56462,0.43612,0.70072,-159.4,-0.11703,0.88272,-0.4551,131.11
    7236 
    7237 > view matrix models
    7238 > #3,-0.81701,0.17495,0.54944,206.51,0.56462,0.43612,0.70072,-159.88,-0.11703,0.88272,-0.4551,131.78
    7239 
    7240 > hide #!2 models
    7241 
    7242 > ui mousemode right "rotate selected models"
    7243 
    7244 > view matrix models
    7245 > #3,-0.93722,0.21306,0.27609,263.78,0.3343,0.3234,0.88524,-122.21,0.099324,0.92196,-0.37432,70.546
    7246 
    7247 > show #!2 models
    7248 
    7249 > view matrix models
    7250 > #3,-0.9119,0.33361,0.23904,242.14,0.32086,0.21634,0.92209,-105.33,0.2559,0.91755,-0.30432,30.568
    7251 
    7252 > hide #!2 models
    7253 
    7254 > show #!2 models
    7255 
    7256 > ui mousemode right "translate selected models"
    7257 
    7258 > view matrix models
    7259 > #3,-0.9119,0.33361,0.23904,241.56,0.32086,0.21634,0.92209,-103.63,0.2559,0.91755,-0.30432,28.63
    7260 
    7261 > view matrix models
    7262 > #3,-0.9119,0.33361,0.23904,242.51,0.32086,0.21634,0.92209,-102.98,0.2559,0.91755,-0.30432,29.306
    7263 
    7264 > view matrix models
    7265 > #3,-0.9119,0.33361,0.23904,242.12,0.32086,0.21634,0.92209,-103.19,0.2559,0.91755,-0.30432,29.625
    7266 
    7267 > ui mousemode right "rotate selected models"
    7268 
    7269 > view matrix models
    7270 > #3,-0.87355,0.41506,0.25422,217.34,0.3549,0.18575,0.91626,-103.23,0.33309,0.89063,-0.30957,20.475
    7271 
    7272 > fitmap #3 inMap #2
    7273 
    7274 Fit molecule 4Ub.pdb (#3) to map P64_J12_deepemhancer.mrc (#2) using 1034
    7275 atoms 
    7276 average map value = 0.04273, steps = 188 
    7277 shifted from previous position = 6.11 
    7278 rotated from previous position = 27.6 degrees 
    7279 atoms outside contour = 691, contour level = 0.015 
    7280  
    7281 Position of 4Ub.pdb (#3) relative to P64_J12_deepemhancer.mrc (#2)
    7282 coordinates: 
    7283 Matrix rotation and translation 
    7284 -0.68181384 0.30235068 0.66611857 146.23416859 
    7285 0.68338301 -0.06162106 0.72745481 -90.64295049 
    7286 0.26099339 0.95120287 -0.16460723 3.10516441 
    7287 Axis 0.37323744 0.67579529 0.63560565 
    7288 Axis point 98.83947470 0.00000000 27.38301406 
    7289 Rotation angle (degrees) 162.55803812 
    7290 Shift along axis -4.70235247 
    7291  
    7292 
    7293 > undo
    7294 
    7295 > hide #!2 models
    7296 
    7297 > view matrix models
    7298 > #3,-0.71118,0.70096,-0.053665,179.29,0.064186,0.14076,0.98796,-49.463,0.70007,0.69917,-0.1451,-39.754
    7299 
    7300 > view matrix models
    7301 > #3,-0.70029,0.71301,-0.034876,172.12,0.066121,0.11343,0.99134,-45.286,0.71079,0.69192,-0.12658,-43.266
    7302 
    7303 > view matrix models
    7304 > #3,-0.52247,0.83371,0.17875,83.286,-0.01801,-0.22038,0.97525,35.207,0.85247,0.50632,0.13015,-74.88
    7305 
    7306 > view matrix models
    7307 > #3,-0.93075,-0.10152,-0.35128,415.05,-0.13281,0.98894,0.066087,-29.866,0.34068,0.10816,-0.93394,257.72
    7308 
    7309 > view matrix models
    7310 > #3,-0.64634,0.57103,0.50613,106.67,0.56883,-0.081552,0.8184,-80.391,0.50861,0.81687,-0.27211,-5.4368
    7311 
    7312 > show #!2 models
    7313 
    7314 > ui mousemode right "translate selected models"
    7315 
    7316 > view matrix models
    7317 > #3,-0.64634,0.57103,0.50613,107.8,0.56883,-0.081552,0.8184,-80.999,0.50861,0.81687,-0.27211,-7.3342
    7318 
    7319 > view matrix models
    7320 > #3,-0.64634,0.57103,0.50613,108.34,0.56883,-0.081552,0.8184,-80.397,0.50861,0.81687,-0.27211,-7.3389
    7321 
    7322 > fitmap #3 inMap #2
    7323 
    7324 Fit molecule 4Ub.pdb (#3) to map P64_J12_deepemhancer.mrc (#2) using 1034
    7325 atoms 
    7326 average map value = 0.04552, steps = 96 
    7327 shifted from previous position = 1.7 
    7328 rotated from previous position = 22.8 degrees 
    7329 atoms outside contour = 528, contour level = 0.015 
    7330  
    7331 Position of 4Ub.pdb (#3) relative to P64_J12_deepemhancer.mrc (#2)
    7332 coordinates: 
    7333 Matrix rotation and translation 
    7334 -0.60159277 0.47587877 0.64158049 97.54037792 
    7335 0.45805470 -0.45249689 0.76513558 15.82248234 
    7336 0.65442496 0.75417900 0.05424035 -70.47054678 
    7337 Axis -0.44628855 -0.52318661 -0.72601811 
    7338 Axis point 70.49501793 32.89156096 0.00000000 
    7339 Rotation angle (degrees) 179.29666393 
    7340 Shift along axis -0.64637166 
    7341  
    7342 
    7343 > hide #!2 models
    7344 
    7345 > show #!2 models
    7346 
    7347 > hide #!2 models
    7348 
    7349 > select subtract #3
    7350 
    7351 Nothing selected 
    7352 
    7353 > select add #3
    7354 
    7355 1034 atoms, 1040 bonds, 76 residues, 1 model selected 
    7356 
    7357 > show sel atoms
    7358 
    7359 > save /Users/zbxg977/Desktop/4Ub.pdb models #3 selectedOnly true relModel #2
    7360 
    7361 > close #3
    7362 
    7363 > open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_46/P64_J12_model-
    7364 > coot-49.pdb
    7365 
    7366 Chain information for P64_J12_model-coot-49.pdb #3 
    7367 --- 
    7368 Chain | Description 
    7369 A | No description available 
    7370 B | No description available 
    7371 D | No description available 
    7372 E K N P | No description available 
    7373 F | No description available 
    7374 G | No description available 
    7375 H | No description available 
    7376 I | No description available 
    7377 J | No description available 
    7378 L Q | No description available 
    7379 M | No description available 
    7380 O R | No description available 
    7381 W | No description available 
    7382 X | No description available 
    7383 Y | No description available 
    7384  
    7385 
    7386 > hide #!1 models
    7387 
    7388 > hide #!3 atoms
    7389 
    7390 > show #!3 cartoons
    7391 
    7392 > dssp
    7393 
    7394 > colour #3/B,G,X,M #0096FF
    7395 
    7396 > colour #3/A,F,J,W #00F900
    7397 
    7398 > colour #3/H,Y,D,I #9437FF
    7399 
    7400 > colour #3/L,O,Q,R #FF9300
    7401 
    7402 > colour #3/E,K,N,P #EF4E5D
    7403 
    7404 > show #!2 models
    7405 
    7406 > ui tool show "Color Zone"
    7407 
    7408 > color zone #2 near #3 distance 5.74
    7409 
    7410 > hide #!3 models
    7411 
    7412 > volume #2 level 0.035
    7413 
    7414 > hide #!2 models
    7415 
    7416 > show #!3 models
    7417 
    7418 > select #3/O,L,Q
    7419 
    7420 2220 atoms, 2238 bonds, 228 residues, 1 model selected 
    7421 
    7422 > show sel atoms
    7423 
    7424 > save /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_46/Ub3.pdb models
    7425 > #3 selectedOnly true relModel #2
    7426 
    7427 > open /Users/zbxg977/Desktop/Ub3.pdb
    7428 
    7429 Summary of feedback from opening /Users/zbxg977/Desktop/Ub3.pdb 
    7430 --- 
    7431 warnings | Start residue of secondary structure not found: HELIX 1 1 GLU E 104
    7432 SER E 106 1 3 
    7433 Start residue of secondary structure not found: HELIX 2 2 ALA E 120 VAL E 132
    7434 1 13 
    7435 Start residue of secondary structure not found: HELIX 3 3 ARG E 133 HIS E 136
    7436 1 4 
    7437 Start residue of secondary structure not found: HELIX 4 4 PRO E 163 SER E 168
    7438 1 6 
    7439 Start residue of secondary structure not found: HELIX 5 5 GLU E 184 LYS E 193
    7440 1 10 
    7441 221 messages similar to the above omitted 
    7442  
    7443 Chain information for Ub3.pdb #4 
    7444 --- 
    7445 Chain | Description 
    7446 L Q | No description available 
    7447 O | No description available 
    7448  
    7449 
    7450 > ui tool show Matchmaker
    7451 
    7452 > matchmaker #4 to #3/R pairing bs
    7453 
    7454 Parameters 
    7455 --- 
    7456 Chain pairing | bs 
    7457 Alignment algorithm | Needleman-Wunsch 
    7458 Similarity matrix | BLOSUM-62 
    7459 SS fraction | 0.3 
    7460 Gap open (HH/SS/other) | 18/18/6 
    7461 Gap extend | 1 
    7462 SS matrix |  |  | H | S | O 
    7463 ---|---|---|--- 
    7464 H | 6 | -9 | -6 
    7465 S |  | 6 | -6 
    7466 O |  |  | 4 
    7467 Iteration cutoff | 2 
    7468  
    7469 Matchmaker P64_J12_model-coot-49.pdb, chain R (#3) with Ub3.pdb, chain O (#4),
    7470 sequence alignment score = 374 
    7471 RMSD between 76 pruned atom pairs is 0.000 angstroms; (across all 76 pairs:
    7472 0.000) 
    7473  
    7474 
    7475 > select add #3
    7476 
    7477 46169 atoms, 46887 bonds, 43 pseudobonds, 4259 residues, 2 models selected 
    7478 
    7479 > select subtract #3
    7480 
    7481 Nothing selected 
    7482 
    7483 > select add #3
    7484 
    7485 46169 atoms, 46887 bonds, 43 pseudobonds, 4259 residues, 2 models selected 
    7486 
    7487 > hide sel atoms
    7488 
    7489 > select subtract #3
    7490 
    7491 Nothing selected 
    7492 
    7493 > show #!2 models
    7494 
    7495 > color #2 #b2b2b2dd models
    7496 
    7497 > select add #4
    7498 
    7499 2220 atoms, 2238 bonds, 228 residues, 1 model selected 
    7500 
    7501 > lighting simple
    7502 
    7503 > view matrix models
    7504 > #4,-0.60159,0.47588,0.64158,93.534,0.45806,-0.45249,0.76514,14.188,0.65442,0.75418,0.054236,-72.225
    7505 
    7506 > view matrix models
    7507 > #4,-0.60159,0.47588,0.64158,92.645,0.45806,-0.45249,0.76514,15.149,0.65442,0.75418,0.054236,-71.708
    7508 
    7509 > view matrix models
    7510 > #4,-0.60159,0.47588,0.64158,93.136,0.45806,-0.45249,0.76514,15.699,0.65442,0.75418,0.054236,-73.795
    7511 
    7512 > view matrix models
    7513 > #4,-0.60159,0.47588,0.64158,94.386,0.45806,-0.45249,0.76514,15.328,0.65442,0.75418,0.054236,-74.44
    7514 
    7515 > hide #!2 models
    7516 
    7517 > select subtract #4
    7518 
    7519 Nothing selected 
    7520 
    7521 > select #4/L,Q
    7522 
    7523 1186 atoms, 1198 bonds, 152 residues, 1 model selected 
    7524 
    7525 > show sel atoms
    7526 
    7527 > save /Users/zbxg977/Desktop/Ub5_6.pdb models #4 selectedOnly true relModel
    7528 > #2
    7529 
    7530 > close #4
    7531 
    7532 > close #1
    7533 
    7534 > close #3
    7535 
    7536 > open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_46/P64_J12_model-
    7537 > coot-50.pdb
    7538 
    7539 Chain information for P64_J12_model-coot-50.pdb #1 
    7540 --- 
    7541 Chain | Description 
    7542 A | No description available 
    7543 B | No description available 
    7544 D | No description available 
    7545 E K N P | No description available 
    7546 F | No description available 
    7547 G | No description available 
    7548 H | No description available 
    7549 I | No description available 
    7550 J | No description available 
    7551 L Q S T | No description available 
    7552 M | No description available 
    7553 O R | No description available 
    7554 W | No description available 
    7555 X | No description available 
    7556 Y | No description available 
    7557  
    7558 
    7559 > hide atoms
    7560 
    7561 > show cartoons
    7562 
    7563 > colour #1/B,G,X,M #0096FF
    7564 
    7565 > colour #1/A,F,J,W #00F900
    7566 
    7567 > colour #1/H,Y,D,I #9437FF
    7568 
    7569 > colour #1/L,O,Q,R,S,T #FF9300
    7570 
    7571 > colour #1/E,K,N,P #EF4E5D
    7572 
    7573 > dssp
    7574 
    7575 > show #!2 models
    7576 
    7577 > color zone #2 near #1 distance 5.74
    7578 
    7579 > lighting soft
    7580 
    7581 > hide #!1 models
    7582 
    7583 > volume #2 level 0.04
    7584 
    7585 > ui tool show "Map Eraser"
    7586 
    7587 > select add #3
    7588 
    7589 1 model selected 
    7590 
    7591 > ui mousemode right "translate selected models"
    7592 
    7593 > view matrix models #3,1,0,0,251.41,0,1,0,177.58,0,0,1,180.61
    7594 
    7595 > view matrix models #3,1,0,0,255.51,0,1,0,182.96,0,0,1,177.37
    7596 
    7597 > view matrix models #3,1,0,0,256.04,0,1,0,181.46,0,0,1,179.8
    7598 
    7599 > volume erase #2 center 256.04,181.46,179.8 radius 13.074
    7600 
    7601 Opened P64_J12_deepemhancer.mrc copy as #4, grid size 512,512,512, pixel 0.74,
    7602 shown at step 1, values float32 
    7603 
    7604 > color #4 #b2b2b2ff models
    7605 
    7606 > view matrix models #3,1,0,0,246.66,0,1,0,183.58,0,0,1,182.44
    7607 
    7608 > volume erase #4 center 246.66,183.58,182.44 radius 12.882
    7609 
    7610 > surface dust #4 size 7.4
    7611 
    7612 > view matrix models #3,1,0,0,287.73,0,1,0,151.7,0,0,1,186.47
    7613 
    7614 > view matrix models #3,1,0,0,131.22,0,1,0,184.9,0,0,1,227.76
    7615 
    7616 > view matrix models #3,1,0,0,128.37,0,1,0,188.93,0,0,1,233.07
    7617 
    7618 > volume erase #4 center 128.37,188.93,233.07 radius 12.882
    7619 
    7620 > view matrix models #3,1,0,0,130.5,0,1,0,187.1,0,0,1,229.29
    7621 
    7622 > volume erase #4 center 130.5,187.1,229.29 radius 12.882
    7623 
    7624 > color zone #4 near #1 distance 4.44
    7625 
    7626 > view matrix models #3,1,0,0,157.62,0,1,0,181.5,0,0,1,79.409
    7627 
    7628 > view matrix models #3,1,0,0,162,0,1,0,207.4,0,0,1,79.905
    7629 
    7630 > view matrix models #3,1,0,0,195.48,0,1,0,203.89,0,0,1,88.793
    7631 
    7632 > volume erase #4 center 195.48,203.89,88.793 radius 12.882
    7633 
    7634 > color zone #4 near #1 distance 4.28
    7635 
    7636 > color zone #4 near #1 distance 9.51
    7637 
    7638 [Repeated 1 time(s)]
    7639 
    7640 > view matrix models #3,1,0,0,118.5,0,1,0,217.26,0,0,1,155.6
    7641 
    7642 > view matrix models #3,1,0,0,119.32,0,1,0,224.9,0,0,1,156.18
    7643 
    7644 > view matrix models #3,1,0,0,120.41,0,1,0,224.7,0,0,1,154.87
    7645 
    7646 > volume erase #4 center 120.41,224.7,154.87 radius 12.882
    7647 
    7648 > view matrix models #3,1,0,0,132.73,0,1,0,234.58,0,0,1,160.81
    7649 
    7650 > view matrix models #3,1,0,0,132.69,0,1,0,234.45,0,0,1,160.79
    7651 
    7652 > view matrix models #3,1,0,0,132.7,0,1,0,233.37,0,0,1,158.05
    7653 
    7654 > volume erase #4 center 132.7,233.37,158.05 radius 12.882
    7655 
    7656 > view matrix models #3,1,0,0,199.12,0,1,0,91.549,0,0,1,168.91
    7657 
    7658 > view matrix models #3,1,0,0,225.06,0,1,0,103.46,0,0,1,184.2
    7659 
    7660 > view matrix models #3,1,0,0,225.89,0,1,0,100,0,0,1,191.46
    7661 
    7662 > view matrix models #3,1,0,0,225.33,0,1,0,99.137,0,0,1,194.08
    7663 
    7664 > view matrix models #3,1,0,0,225.33,0,1,0,97.404,0,0,1,193.65
    7665 
    7666 > volume erase #4 center 225.33,97.404,193.65 radius 12.882
    7667 
    7668 > view matrix models #3,1,0,0,224.86,0,1,0,149.52,0,0,1,283.13
    7669 
    7670 > view matrix models #3,1,0,0,211.04,0,1,0,137.18,0,0,1,287.39
    7671 
    7672 > view matrix models #3,1,0,0,209.5,0,1,0,136.2,0,0,1,276.75
    7673 
    7674 > view matrix models #3,1,0,0,211.99,0,1,0,133.21,0,0,1,273.61
    7675 
    7676 > volume erase #4 center 211.99,133.21,273.61 radius 12.882
    7677 
    7678 > view matrix models #3,1,0,0,204.87,0,1,0,143.03,0,0,1,282
    7679 
    7680 > volume erase #4 center 204.87,143.03,282 radius 12.882
    7681 
    7682 > view matrix models #3,1,0,0,225.79,0,1,0,222.83,0,0,1,236.03
    7683 
    7684 > view matrix models #3,1,0,0,206.22,0,1,0,265.74,0,0,1,169.52
    7685 
    7686 > view matrix models #3,1,0,0,206.01,0,1,0,267.32,0,0,1,166.4
    7687 
    7688 > volume erase #4 center 206.01,267.32,166.4 radius 12.882
    7689 
    7690 > view matrix models #3,1,0,0,211.1,0,1,0,201.51,0,0,1,232.99
    7691 
    7692 > view matrix models #3,1,0,0,249.46,0,1,0,178.84,0,0,1,255.3
    7693 
    7694 > view matrix models #3,1,0,0,252.28,0,1,0,177.38,0,0,1,211.75
    7695 
    7696 > color zone #4 near #1 distance 9.66
    7697 
    7698 > color zone #4 near #1 distance 21.47
    7699 
    7700 > hide #3 models
    7701 
    7702 > select subtract #3
    7703 
    7704 Nothing selected 
    7705 
    7706 > save "/Users/zbxg977/Desktop/BRISC_project/Main
    7707 > figures/Map_model_coloured.cxs" includeMaps true
    7708 
    7709 ——— End of log from Wed Sep 4 11:11:03 2024 ———
    7710 
    7711 opened ChimeraX session 
    7712 
    7713 > open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_55/P64_J12_model-
    7714 > coot-51_modified.pdb
    7715 
    7716 Chain information for P64_J12_model-coot-51_modified.pdb #3 
    7717 --- 
    7718 Chain | Description 
    7719 A | No description available 
    7720 B | No description available 
    7721 D | No description available 
    7722 E K N P | No description available 
    7723 F | No description available 
    7724 G | No description available 
    7725 H | No description available 
    7726 I | No description available 
    7727 J | No description available 
    7728 L Q S T | No description available 
    7729 M | No description available 
    7730 O R | No description available 
    7731 W | No description available 
    7732 X | No description available 
    7733 Y | No description available 
    7734  
    7735 
    7736 > show #!1 models
    7737 
    7738 > hide #!4 models
    7739 
    7740 > select add #3
    7741 
    7742 63902 atoms, 64635 bonds, 43 pseudobonds, 4411 residues, 2 models selected 
    7743 
    7744 > hide sel atoms
    7745 
    7746 > show sel cartoons
    7747 
    7748 > select subtract #3
    7749 
    7750 Nothing selected 
    7751 
    7752 > dssp
    7753 
    7754 > color #3 by #1
    7755 
    7756 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    7757 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    7758 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    7759 
    7760 > color #3 bychain #1
    7761 
    7762 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    7763 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    7764 
    7765 > hide #!1 models
    7766 
    7767 > colour #3/B,G,X,M #0096FF
    7768 
    7769 > colour #3/A,F,J,W #00F900
    7770 
    7771 > colour #3/H,Y,D,I #9437FF
    7772 
    7773 > colour #3/L,O,Q,R,S,T #FF9300
    7774 
    7775 > colour #3/E,K,N,P #EF4E5D
    7776 
    7777 > save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    7778 > 2/Map_model_coloured_v2.cxs" includeMaps true
    7779 
    7780 ——— End of log from Tue Oct 1 13:16:34 2024 ———
    7781 
    7782 opened ChimeraX session 
    7783 
    7784 > open /Users/zbxg977/Desktop/penta_Ub_merged.pdb
    7785 
    7786 Chain information for penta_Ub_merged.pdb #5 
    7787 --- 
    7788 Chain | Description 
    7789 A B C L | No description available 
    7790 O | No description available 
    7791  
    7792 
    7793 > select add #5
    7794 
    7795 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    7796 
    7797 > hide sel atoms
    7798 
    7799 > show sel cartoons
    7800 
    7801 > color sel orange
    7802 
    7803 > ui mousemode right select
    7804 
    7805 > select clear
    7806 
    7807 > ui tool show Matchmaker
    7808 
    7809 > matchmaker #5 to #3
    7810 
    7811 Parameters 
    7812 --- 
    7813 Chain pairing | bb 
    7814 Alignment algorithm | Needleman-Wunsch 
    7815 Similarity matrix | BLOSUM-62 
    7816 SS fraction | 0.3 
    7817 Gap open (HH/SS/other) | 18/18/6 
    7818 Gap extend | 1 
    7819 SS matrix |  |  | H | S | O 
    7820 ---|---|---|--- 
    7821 H | 6 | -9 | -6 
    7822 S |  | 6 | -6 
    7823 O |  |  | 4 
    7824 Iteration cutoff | 2 
    7825  
    7826 Matchmaker P64_J12_model-coot-51_modified.pdb, chain Q (#3) with
    7827 penta_Ub_merged.pdb, chain A (#5), sequence alignment score = 381.3 
    7828 RMSD between 76 pruned atom pairs is 0.252 angstroms; (across all 76 pairs:
    7829 0.252) 
    7830  
    7831 
    7832 > undo
    7833 
    7834 [Repeated 3 time(s)]
    7835 
    7836 > select subtract #5
    7837 
    7838 Nothing selected 
    7839 
    7840 > hide #5 models
    7841 
    7842 > show #5 models
    7843 
    7844 > close #5
    7845 
    7846 > open /Users/zbxg977/Desktop/penta_Ub_merged.pdb
    7847 
    7848 Chain information for penta_Ub_merged.pdb #5 
    7849 --- 
    7850 Chain | Description 
    7851 A B C L | No description available 
    7852 O | No description available 
    7853  
    7854 
    7855 > hide #5#!3 atoms
    7856 
    7857 > show #5#!3 cartoons
    7858 
    7859 > ui tool show Matchmaker
    7860 
    7861 > matchmaker #5 to #3/O pairing bs
    7862 
    7863 Parameters 
    7864 --- 
    7865 Chain pairing | bs 
    7866 Alignment algorithm | Needleman-Wunsch 
    7867 Similarity matrix | BLOSUM-62 
    7868 SS fraction | 0.3 
    7869 Gap open (HH/SS/other) | 18/18/6 
    7870 Gap extend | 1 
    7871 SS matrix |  |  | H | S | O 
    7872 ---|---|---|--- 
    7873 H | 6 | -9 | -6 
    7874 S |  | 6 | -6 
    7875 O |  |  | 4 
    7876 Iteration cutoff | 2 
    7877  
    7878 Matchmaker P64_J12_model-coot-51_modified.pdb, chain O (#3) with
    7879 penta_Ub_merged.pdb, chain O (#5), sequence alignment score = 374 
    7880 RMSD between 76 pruned atom pairs is 0.115 angstroms; (across all 76 pairs:
    7881 0.115) 
    7882  
    7883 
    7884 > show #!4 models
    7885 
    7886 > open "/Users/zbxg977/Desktop/cryosparc_P64_J40_020_volume_map (1).mrc"
    7887 
    7888 Opened cryosparc_P64_J40_020_volume_map (1).mrc as #6, grid size 512,512,512,
    7889 pixel 0.74, shown at level 0.00718, step 2, values float32 
    7890 
    7891 > volume #6 step 1
    7892 
    7893 > volume #6 level 0.1541
    7894 
    7895 > ui tool show "Fit in Map"
    7896 
    7897 > fitmap #6 inMap #4
    7898 
    7899 Fit map cryosparc_P64_J40_020_volume_map (1).mrc in map
    7900 P64_J12_deepemhancer.mrc copy using 129829 points 
    7901 correlation = 0.5054, correlation about mean = 0.1598, overlap = 3273 
    7902 steps = 68, shift = 1.22, angle = 0.929 degrees 
    7903  
    7904 Position of cryosparc_P64_J40_020_volume_map (1).mrc (#6) relative to
    7905 P64_J12_deepemhancer.mrc copy (#4) coordinates: 
    7906 Matrix rotation and translation 
    7907 0.99997912 -0.00487300 -0.00424498 0.66325650 
    7908 0.00493555 0.99987753 0.01485147 -2.81150978 
    7909 0.00417209 -0.01487211 0.99988070 2.51382637 
    7910 Axis -0.91705127 -0.25968865 0.30261984 
    7911 Axis point 0.00000000 149.66536670 175.10960512 
    7912 Rotation angle (degrees) 0.92857977 
    7913 Shift along axis 0.88261072 
    7914  
    7915 
    7916 > fitmap #5 inMap #6
    7917 
    7918 Fit molecule penta_Ub_merged.pdb (#5) to map cryosparc_P64_J40_020_volume_map
    7919 (1).mrc (#6) using 3424 atoms 
    7920 average map value = 0.1626, steps = 124 
    7921 shifted from previous position = 5.16 
    7922 rotated from previous position = 14.8 degrees 
    7923 atoms outside contour = 1623, contour level = 0.15407 
    7924  
    7925 Position of penta_Ub_merged.pdb (#5) relative to
    7926 cryosparc_P64_J40_020_volume_map (1).mrc (#6) coordinates: 
    7927 Matrix rotation and translation 
    7928 0.99999913 0.00110329 0.00072892 -0.22178002 
    7929 -0.00110201 0.99999785 -0.00175506 0.47587376 
    7930 -0.00073085 0.00175425 0.99999819 -0.26439380 
    7931 Axis 0.79861150 0.33219833 -0.50186048 
    7932 Axis point 0.00000000 118.45743317 249.48623484 
    7933 Rotation angle (degrees) 0.12588650 
    7934 Shift along axis 0.11365719 
    7935  
    7936 
    7937 > hide #!6 models
    7938 
    7939 > hide #!4 models
    7940 
    7941 > select #5/O
    7942 
    7943 1034 atoms, 1040 bonds, 76 residues, 1 model selected 
    7944 
    7945 > hide sel cartoons
    7946 
    7947 > select clear
    7948 
    7949 > select #3/L,Q
    7950 
    7951 2394 atoms, 2406 bonds, 152 residues, 1 model selected 
    7952 
    7953 > hide sel cartoons
    7954 
    7955 > select clear
    7956 
    7957 > select #5/A:63
    7958 
    7959 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7960 
    7961 > show sel atoms
    7962 
    7963 > color sel byhetero
    7964 
    7965 > style sel stick
    7966 
    7967 Changed 9 atom styles 
    7968 
    7969 > select clear
    7970 
    7971 > select #5
    7972 
    7973 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    7974 
    7975 > color sel orange
    7976 
    7977 > select #5:63
    7978 
    7979 47 atoms, 42 bonds, 5 residues, 1 model selected 
    7980 
    7981 > show sel atoms
    7982 
    7983 > style sel stick
    7984 
    7985 Changed 47 atom styles 
    7986 
    7987 > select up
    7988 
    7989 464 atoms, 461 bonds, 45 residues, 1 model selected 
    7990 
    7991 > select up
    7992 
    7993 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    7994 
    7995 > select up
    7996 
    7997 114681 atoms, 116174 bonds, 9202 residues, 9 models selected 
    7998 
    7999 > select up
    8000 
    8001 114681 atoms, 116174 bonds, 9202 residues, 9 models selected 
    8002 
    8003 > select down
    8004 
    8005 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    8006 
    8007 > select down
    8008 
    8009 464 atoms, 461 bonds, 45 residues, 1 model selected 
    8010 
    8011 > select down
    8012 
    8013 47 atoms, 42 bonds, 5 residues, 1 model selected 
    8014 
    8015 > select down
    8016 
    8017 47 atoms, 42 bonds, 5 residues, 1 model selected 
    8018 
    8019 > select clear
    8020 
    8021 > select #5/O
    8022 
    8023 1034 atoms, 1040 bonds, 76 residues, 1 model selected 
    8024 
    8025 > hide sel atoms
    8026 
    8027 > select clear
    8028 
    8029 > color #3,5 byhetero
    8030 
    8031 > select #3/O
    8032 
    8033 1070 atoms, 1076 bonds, 76 residues, 1 model selected 
    8034 
    8035 > select #3/O:63
    8036 
    8037 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8038 
    8039 > show sel atoms
    8040 
    8041 > style sel stick
    8042 
    8043 Changed 22 atom styles 
    8044 
    8045 > select clear
    8046 
    8047 > delete H
    8048 
    8049 > save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    8050 > 2/Map_model_coloured_v3.cxs" includeMaps true
    8051 
    8052 > ui tool show "Side View"
    8053 
    8054 > cartoon style width 1
    8055 
    8056 > cartoon style width 1.5
    8057 
    8058 > select add #5
    8059 
    8060 2929 atoms, 2959 bonds, 380 residues, 1 model selected 
    8061 
    8062 > show sel surfaces
    8063 
    8064 > select clear
    8065 
    8066 > lighting soft
    8067 
    8068 > select #5/O
    8069 
    8070 539 atoms, 545 bonds, 76 residues, 1 model selected 
    8071 
    8072 > hide sel surfaces
    8073 
    8074 > select #3/O
    8075 
    8076 539 atoms, 545 bonds, 76 residues, 1 model selected 
    8077 
    8078 > show sel surfaces
    8079 
    8080 > select clear
    8081 
    8082 > save /Users/zbxg977/Desktop/image1.png supersample 3
    8083 
    8084 > cartoon style thickness 1
    8085 
    8086 > cartoon style thickness 0.8
    8087 
    8088 > cartoon style thickness 0.7
    8089 
    8090 > cartoon style width 2 0.7
    8091 
    8092 Expected a keyword 
    8093 
    8094 > cartoon style width 2
    8095 
    8096 > lighting soft
    8097 
    8098 > lighting full
    8099 
    8100 > lighting simple
    8101 
    8102 > lighting soft
    8103 
    8104 > save /Users/zbxg977/Desktop/image2.png supersample 3
    8105 
    8106 > select add #5
    8107 
    8108 2929 atoms, 2959 bonds, 380 residues, 1 model selected 
    8109 
    8110 > hide sel surfaces
    8111 
    8112 > select #3/O
    8113 
    8114 539 atoms, 545 bonds, 76 residues, 1 model selected 
    8115 
    8116 > hide sel surfaces
    8117 
    8118 > select clear
    8119 
    8120 > save /Users/zbxg977/Desktop/image3.png supersample 3
    8121 
    8122 > open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_55/P64_J12_model-
    8123 > coot-52.pdb
    8124 
    8125 Summary of feedback from opening
    8126 /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_55/P64_J12_model-
    8127 coot-52.pdb 
    8128 --- 
    8129 warnings | Start residue of secondary structure not found: HELIX 46 46 ILE L
    8130 23 GLU L 34 1 12 
    8131 Start residue of secondary structure not found: HELIX 47 47 PRO L 38 GLN L 40
    8132 5 3 
    8133 Start residue of secondary structure not found: HELIX 48 48 SER L 57 TYR L 59
    8134 5 3 
    8135 Start residue of secondary structure not found: HELIX 49 49 ILE Q 23 GLU Q 34
    8136 1 12 
    8137 Start residue of secondary structure not found: HELIX 50 50 PRO Q 38 GLN Q 40
    8138 5 3 
    8139 9 messages similar to the above omitted 
    8140  
    8141 Chain information for P64_J12_model-coot-52.pdb #7 
    8142 --- 
    8143 Chain | Description 
    8144 A | No description available 
    8145 B | No description available 
    8146 D | No description available 
    8147 E K N P | No description available 
    8148 F | No description available 
    8149 G | No description available 
    8150 H | No description available 
    8151 I | No description available 
    8152 J | No description available 
    8153 M | No description available 
    8154 O R | No description available 
    8155 S T | No description available 
    8156 W | No description available 
    8157 X | No description available 
    8158 Y | No description available 
    8159  
    8160 
    8161 > select add #7
    8162 
    8163 61508 atoms, 62229 bonds, 43 pseudobonds, 4259 residues, 2 models selected 
    8164 
    8165 > select subtract #7
    8166 
    8167 Nothing selected 
    8168 
    8169 > hide #!5 models
    8170 
    8171 > select add #7
    8172 
    8173 61508 atoms, 62229 bonds, 43 pseudobonds, 4259 residues, 2 models selected 
    8174 
    8175 > show sel atoms
    8176 
    8177 > close #7
    8178 
    8179 > show #!6 models
    8180 
    8181 > hide #!6 models
    8182 
    8183 > show #!5 models
    8184 
    8185 > open /Users/zbxg977/Desktop/penta_Ub.pdb
    8186 
    8187 Summary of feedback from opening /Users/zbxg977/Desktop/penta_Ub.pdb 
    8188 --- 
    8189 warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 23
    8190 LYS A 33 1 11 
    8191 Start residue of secondary structure not found: HELIX 2 2 PRO A 38 GLN A 40 1
    8192 3 
    8193 Start residue of secondary structure not found: HELIX 3 3 SER A 57 TYR A 59 1
    8194 3 
    8195 Start residue of secondary structure not found: SHEET 1 1 1 GLN A 2 THR A 7 0 
    8196 Start residue of secondary structure not found: SHEET 2 2 1 THR A 12 GLU A 16
    8197 0 
    8198 7 messages similar to the above omitted 
    8199  
    8200 Chain information for penta_Ub.pdb 
    8201 --- 
    8202 Chain | Description 
    8203 7.1/A 7.2/A 7.3/A 7.4/A 7.6/L | No description available 
    8204 7.5/O | No description available 
    8205  
    8206 
    8207 > close #7
    8208 
    8209 > open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_55/P64_J12_model-
    8210 > coot-52.pdb
    8211 
    8212 Chain information for P64_J12_model-coot-52.pdb #7 
    8213 --- 
    8214 Chain | Description 
    8215 A B C L S T | No description available 
    8216 E K N P | No description available 
    8217 F | No description available 
    8218 G | No description available 
    8219 H | No description available 
    8220 I | No description available 
    8221 J | No description available 
    8222 M | No description available 
    8223 O R | No description available 
    8224 Q | No description available 
    8225 U | No description available 
    8226 V | No description available 
    8227 W | No description available 
    8228 X | No description available 
    8229 Y | No description available 
    8230  
    8231 
    8232 > hide #!5 models
    8233 
    8234 > hide #!3 models
    8235 
    8236 > select add #7
    8237 
    8238 63898 atoms, 64643 bonds, 43 pseudobonds, 4563 residues, 2 models selected 
    8239 
    8240 > hide sel atoms
    8241 
    8242 > show sel cartoons
    8243 
    8244 > select clear
    8245 
    8246 > dssp
    8247 
    8248 > save /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_55/P64_J12_model-
    8249 > coot-52.pdb models #7
    8250 
    8251 > colour #7/B,G,X,M #0096FF
    8252 
    8253 > colour #7/A,F,J,W #00F900
    8254 
    8255 > colour #7/H,Y,D,I #9437FF
    8256 
    8257 > colour #7/L,O,Q,R,S,T #FF9300
    8258 
    8259 > colour #7/E,K,N,P #EF4E5D
    8260 
    8261 > colour #7/G,X,M,U #0096FF
    8262 
    8263 > colour #7/Q,F,J,W #00F900
    8264 
    8265 > colour #7/H,Y,D,I,V #9437FF
    8266 
    8267 > colour #7/L,O,R,S,T,C,B,A #FF9300
    8268 
    8269 > colour #7/E,K,N,P #EF4E5D
    8270 
    8271 > cartoon style width 1
    8272 
    8273 > cartoon style width 2
    8274 
    8275 > cartoon style width 1.5
    8276 
    8277 > cartoon style width 2
    8278 
    8279 > open /Users/zbxg977/Desktop/penta_Ub_merged.pdb
    8280 
    8281 Chain information for penta_Ub_merged.pdb #8 
    8282 --- 
    8283 Chain | Description 
    8284 A B C L | No description available 
    8285 O | No description available 
    8286  
    8287 
    8288 > select add #8
    8289 
    8290 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    8291 
    8292 > hide sel atoms
    8293 
    8294 > show sel cartoons
    8295 
    8296 > ui tool show Matchmaker
    8297 
    8298 > matchmaker #8 to #7/S pairing bs
    8299 
    8300 Parameters 
    8301 --- 
    8302 Chain pairing | bs 
    8303 Alignment algorithm | Needleman-Wunsch 
    8304 Similarity matrix | BLOSUM-62 
    8305 SS fraction | 0.3 
    8306 Gap open (HH/SS/other) | 18/18/6 
    8307 Gap extend | 1 
    8308 SS matrix |  |  | H | S | O 
    8309 ---|---|---|--- 
    8310 H | 6 | -9 | -6 
    8311 S |  | 6 | -6 
    8312 O |  |  | 4 
    8313 Iteration cutoff | 2 
    8314  
    8315 Matchmaker P64_J12_model-coot-52.pdb, chain S (#7) with penta_Ub_merged.pdb,
    8316 chain L (#8), sequence alignment score = 373.5 
    8317 RMSD between 76 pruned atom pairs is 0.190 angstroms; (across all 76 pairs:
    8318 0.190) 
    8319  
    8320 
    8321 > select clear
    8322 
    8323 > select #8/O
    8324 
    8325 1034 atoms, 1040 bonds, 76 residues, 1 model selected 
    8326 
    8327 > hide sel atoms
    8328 
    8329 > hide sel cartoons
    8330 
    8331 > select #7/S,T
    8332 
    8333 2394 atoms, 2406 bonds, 152 residues, 1 model selected 
    8334 
    8335 > hide sel cartoons
    8336 
    8337 > color #8 #ff9300ff
    8338 
    8339 > select clear
    8340 
    8341 > save /Users/zbxg977/Desktop/image4.png supersample 3
    8342 
    8343 > hide #8 models
    8344 
    8345 > show #8 models
    8346 
    8347 > save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    8348 > 2/Map_model_coloured_v4.cxs" includeMaps true
    8349 
    8350 ——— End of log from Wed Oct 2 15:29:10 2024 ———
    8351 
    8352 opened ChimeraX session 
    8353 
    8354 > lighting simple
    8355 
    8356 > hide #8 models
    8357 
    8358 > show #8 models
    8359 
    8360 > show #!6 models
    8361 
    8362 > hide #!6 models
    8363 
    8364 > show #!1 models
    8365 
    8366 > hide #!1 models
    8367 
    8368 > close #1
    8369 
    8370 > show #!2 models
    8371 
    8372 > hide #!2 models
    8373 
    8374 > close #3
    8375 
    8376 > show #!4 models
    8377 
    8378 > hide #!4 models
    8379 
    8380 > close #4
    8381 
    8382 > show #!5 models
    8383 
    8384 > hide #!5 models
    8385 
    8386 > close #5
    8387 
    8388 > show #!6 models
    8389 
    8390 > hide #!6 models
    8391 
    8392 > show #!6 models
    8393 
    8394 > hide #!6 models
    8395 
    8396 > close #6
    8397 
    8398 > hide #8 models
    8399 
    8400 > show #8 models
    8401 
    8402 > save /Users/zbxg977/Desktop/BRISC_Ub5_colouredbychain.cxs includeMaps true
    8403 
    8404 ——— End of log from Tue Oct 8 13:02:45 2024 ———
    8405 
    8406 opened ChimeraX session 
    8407 
    8408 > open "/Users/zbxg977/Desktop/BRISC_project/CryoSPARC processing
    8409 > Ub5/P64_W2_J50/P64_W2_J50_tightTarget.mrc"
    8410 
    8411 Opened P64_W2_J50_tightTarget.mrc as #1, grid size 512,512,512, pixel 0.74,
    8412 shown at level 9.17e-05, step 2, values float32 
    8413 
    8414 > hide #8 models
    8415 
    8416 > hide #!7 models
    8417 
    8418 > show #!2 models
    8419 
    8420 > volume #1 step 1
    8421 
    8422 > volume #1 level 0.03755
    8423 
    8424 > volume #1 level 0.04504
    8425 
    8426 > ui tool show "Fit in Map"
    8427 
    8428 > fitmap #1 inMap #2
    8429 
    8430 Fit map P64_W2_J50_tightTarget.mrc in map P64_J12_deepemhancer.mrc using
    8431 199202 points 
    8432 correlation = 0.5686, correlation about mean = 0.3003, overlap = 8709 
    8433 steps = 48, shift = 0.318, angle = 0.391 degrees 
    8434  
    8435 Position of P64_W2_J50_tightTarget.mrc (#1) relative to
    8436 P64_J12_deepemhancer.mrc (#2) coordinates: 
    8437 Matrix rotation and translation 
    8438 0.99997687 -0.00507535 -0.00452680 1.41739114 
    8439 0.00507771 0.99998698 0.00051083 -1.00298621 
    8440 0.00452415 -0.00053381 0.99998962 -0.85475381 
    8441 Axis -0.07657733 -0.66347764 0.74426698 
    8442 Axis point 208.59266405 277.12373612 0.00000000 
    8443 Rotation angle (degrees) 0.39080851 
    8444 Shift along axis -0.07924613 
    8445  
    8446 
    8447 > volume #1 level 0.1462
    8448 
    8449 > hide #!1 models
    8450 
    8451 > ui tool show "Map Eraser"
    8452 
    8453 > select add #3
    8454 
    8455 1 model selected 
    8456 
    8457 > ui mousemode right "translate selected models"
    8458 
    8459 > view matrix models #3,1,0,0,177.62,0,1,0,221.79,0,0,1,116.11
    8460 
    8461 > volume erase #2 center 177.62,221.79,116.11 radius 32.12
    8462 
    8463 > view matrix models #3,1,0,0,188.72,0,1,0,194.5,0,0,1,112.11
    8464 
    8465 > view matrix models #3,1,0,0,212.28,0,1,0,201.47,0,0,1,106.94
    8466 
    8467 > volume erase #2 center 212.28,201.47,106.94 radius 32.12
    8468 
    8469 > view matrix models #3,1,0,0,220.92,0,1,0,166.89,0,0,1,106.53
    8470 
    8471 > view matrix models #3,1,0,0,227.3,0,1,0,168.78,0,0,1,111.01
    8472 
    8473 > volume erase #2 center 227.3,168.78,111.01 radius 32.12
    8474 
    8475 > view matrix models #3,1,0,0,241.37,0,1,0,186.51,0,0,1,178.42
    8476 
    8477 > view matrix models #3,1,0,0,265.96,0,1,0,195.56,0,0,1,150.36
    8478 
    8479 > view matrix models #3,1,0,0,267.41,0,1,0,191.95,0,0,1,151.06
    8480 
    8481 > view matrix models #3,1,0,0,267.98,0,1,0,191.29,0,0,1,150.88
    8482 
    8483 > volume erase #2 center 267.98,191.29,150.88 radius 32.12
    8484 
    8485 > view matrix models #3,1,0,0,249.24,0,1,0,183.14,0,0,1,169.43
    8486 
    8487 > view matrix models #3,1,0,0,247.96,0,1,0,180.13,0,0,1,176.94
    8488 
    8489 > view matrix models #3,1,0,0,247.62,0,1,0,180.93,0,0,1,175.55
    8490 
    8491 > volume erase #2 center 247.62,180.93,175.55 radius 14.85
    8492 
    8493 > view matrix models #3,1,0,0,230.85,0,1,0,183.35,0,0,1,140.43
    8494 
    8495 > view matrix models #3,1,0,0,227.29,0,1,0,181.05,0,0,1,132.78
    8496 
    8497 > volume erase #2 center 227.29,181.05,132.78 radius 14.85
    8498 
    8499 > hide #3 models
    8500 
    8501 > select subtract #3
    8502 
    8503 Nothing selected 
    8504 
    8505 > show #!1 models
    8506 
    8507 > volume #1 level 0.03006
    8508 
    8509 > hide #!2 models
    8510 
    8511 > ui tool show "Map Eraser"
    8512 
    8513 > select add #3
    8514 
    8515 1 model selected 
    8516 
    8517 > volume erase #1 center 139.02,180.94,179.91 radius 22.182
    8518 
    8519 Opened P64_W2_J50_tightTarget.mrc copy as #4, grid size 512,512,512, pixel
    8520 0.74, shown at step 1, values float32 
    8521 
    8522 > volume erase #4 center 135.12,201.97,197.24 radius 22.164
    8523 
    8524 > volume erase #4 center 153.11,212.48,222.77 radius 22.164
    8525 
    8526 > volume erase #4 center 189.01,222.98,218.1 radius 22.164
    8527 
    8528 > volume erase #4 center 207.63,218.66,207.51 radius 22.164
    8529 
    8530 > volume erase #4 center 205.67,233.05,195.36 radius 22.164
    8531 
    8532 > volume erase #4 center 240.61,226.55,200.09 radius 22.164
    8533 
    8534 > volume erase #4 center 234.06,210.34,215.07 radius 22.164
    8535 
    8536 > volume erase #4 center 165.06,178.19,208.63 radius 22.164
    8537 
    8538 > volume erase #4 center 147.44,141.75,161.18 radius 22.164
    8539 
    8540 > volume erase #4 center 168.46,130.94,174.07 radius 22.164
    8541 
    8542 > volume erase #4 center 170.77,147.86,164.7 radius 22.164
    8543 
    8544 > volume erase #4 center 150.68,174.81,163.92 radius 22.164
    8545 
    8546 > volume erase #4 center 158.83,159.78,197.76 radius 22.164
    8547 
    8548 > hide #3 models
    8549 
    8550 > select subtract #3
    8551 
    8552 Nothing selected 
    8553 
    8554 > show #!2 models
    8555 
    8556 > hide #!4 models
    8557 
    8558 > show #!4 models
    8559 
    8560 > hide #!4 models
    8561 
    8562 > show #!4 models
    8563 
    8564 > hide #!2 models
    8565 
    8566 > show #3 models
    8567 
    8568 > select add #3
    8569 
    8570 1 model selected 
    8571 
    8572 > volume erase #4 center 163.24,190.1,158.8 radius 22.164
    8573 
    8574 > volume erase #4 center 165.54,184.04,168.19 radius 22.164
    8575 
    8576 > volume erase #4 center 171.2,201.05,166.92 radius 22.164
    8577 
    8578 > undo
    8579 
    8580 [Repeated 2 time(s)]
    8581 
    8582 > show #!1 models
    8583 
    8584 > hide #!1 models
    8585 
    8586 > hide #!2 models
    8587 
    8588 > show #!2 models
    8589 
    8590 > hide #!2 models
    8591 
    8592 > show #!2 models
    8593 
    8594 > show #!1 models
    8595 
    8596 > hide #!1 models
    8597 
    8598 > show #!1 models
    8599 
    8600 > hide #!1 models
    8601 
    8602 > hide #!2 models
    8603 
    8604 > show #!1 models
    8605 
    8606 > hide #!1 models
    8607 
    8608 > hide #!4 models
    8609 
    8610 > show #!4 models
    8611 
    8612 > ui tool show "Side View"
    8613 
    8614 > show #!1 models
    8615 
    8616 > hide #!1 models
    8617 
    8618 > show #!2 models
    8619 
    8620 > show #!1 models
    8621 
    8622 > hide #!2 models
    8623 
    8624 > hide #!4 models
    8625 
    8626 > hide #!1 models
    8627 
    8628 > show #!4 models
    8629 
    8630 > show #!2 models
    8631 
    8632 > hide #!4 models
    8633 
    8634 > show #!4 models
    8635 
    8636 > hide #!2 models
    8637 
    8638 > ui tool show "Map Eraser"
    8639 
    8640 > select add #3
    8641 
    8642 1 model selected 
    8643 
    8644 > volume erase #4 center 223.42,218.19,178.35 radius 17.475
    8645 
    8646 > volume erase #4 center 211.53,221.7,173.87 radius 17.475
    8647 
    8648 > show #!1 models
    8649 
    8650 > hide #!1 models
    8651 
    8652 > show #!2 models
    8653 
    8654 > show #!1 models
    8655 
    8656 > hide #!1 models
    8657 
    8658 > show #!1 models
    8659 
    8660 > hide #!1 models
    8661 
    8662 > hide #3 models
    8663 
    8664 > select subtract #3
    8665 
    8666 Nothing selected 
    8667 
    8668 > lighting soft
    8669 
    8670 > ui tool show "Color Zone"
    8671 
    8672 > color zone #4 near #7 distance 4.44
    8673 
    8674 > color zone #4 near #7 distance 4.6
    8675 
    8676 > color zone #4 near #7 distance 72.5
    8677 
    8678 > lighting simple
    8679 
    8680 > lighting soft
    8681 
    8682 > surface dust #2 size 7.4
    8683 
    8684 > surface dust #4 size 7.4
    8685 
    8686 > color zone #4 near #7 distance 74.79
    8687 
    8688 > color zone #4 near #7 distance 58.36
    8689 
    8690 > lighting simple
    8691 
    8692 > lighting soft
    8693 
    8694 > volume #4 level 0.04729
    8695 
    8696 > lighting simple
    8697 
    8698 > volume #4 level 0.06407
    8699 
    8700 > lighting soft
    8701 
    8702 > save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
    8703 > 2/Map_localref.cxs" includeMaps true
    8704 
    8705 ——— End of log from Thu Oct 31 16:48:37 2024 ———
    8706 
    8707 opened ChimeraX session 
    8708 
    8709 > lighting simple
    8710 
    8711 > hide #!2 models
    8712 
    8713 > show #!2 models
    8714 
    8715 > hide #!4 models
    8716 
    8717 > show #!4 models
    8718 
    8719 > open
    8720 > /Users/zbxg977/Desktop/BRISC_project/Phenix/RealSpaceRefine_51/P64_J12_model-
    8721 > coot-56.pdb
    8722 
    8723 Summary of feedback from opening
    8724 /Users/zbxg977/Desktop/BRISC_project/Phenix/RealSpaceRefine_51/P64_J12_model-
    8725 coot-56.pdb 
    8726 --- 
    8727 warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 3
    8728 ALA A 6 1 4 
    8729 Start residue of secondary structure not found: HELIX 2 2 LEU A 7 ARG A 9 1 3 
    8730 Start residue of secondary structure not found: HELIX 3 3 SER A 15 ASN A 24 1
    8731 10 
    8732 Start residue of secondary structure not found: HELIX 4 4 PRO A 96 ALA A 98 1
    8733 3 
    8734 Start residue of secondary structure not found: HELIX 5 5 GLN A 100 ALA A 103
    8735 1 4 
    8736 24 messages similar to the above omitted 
    8737  
    8738 P64_J12_model-coot-56.pdb title: 
    8739 Alphafold monomer V2.0 prediction for brisc and BRCA1-A complex member 2
    8740 (Q9NXR7) [more info...] 
    8741  
    8742 Chain information for P64_J12_model-coot-56.pdb #3 
    8743 --- 
    8744 Chain | Description 
    8745 A | brisc and BRCA1-A complex member 2 
    8746 B C D L S T | No description available 
    8747 F | No description available 
    8748 G | No description available 
    8749 I | No description available 
    8750 J | No description available 
    8751 M | No description available 
    8752 N | No description available 
    8753 O R | No description available 
    8754 Q | No description available 
    8755 U | No description available 
    8756 V | No description available 
    8757 W | No description available 
    8758 X | No description available 
    8759 Y | No description available 
    8760 Z | No description available 
    8761  
    8762 Non-standard residues in P64_J12_model-coot-56.pdb #3 
    8763 --- 
    8764 ZN — (ZN) 
    8765  
    8766 
    8767 > select add #3
    8768 
    8769 53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected 
    8770 
    8771 > hide sel atoms
    8772 
    8773 > show sel cartoons
    8774 
    8775 > hide #!2 models
    8776 
    8777 > hide #!4 models
    8778 
    8779 > select subtract #3
    8780 
    8781 Nothing selected 
    8782 
    8783 > colour #3/G,X,M,U #0096FF
    8784 
    8785 > colour #3/Q,F,J,W #00F900
    8786 
    8787 > colour #3/H,Y,D,I,V #9437FF
    8788 
    8789 > colour #3/L,O,R,S,T,C,B,A #FF9300
    8790 
    8791 > colour #3/E,K,N,P #EF4E5D
    8792 
    8793 > select #3/D
    8794 
    8795 602 atoms, 608 bonds, 76 residues, 1 model selected 
    8796 
    8797 > color sel orange
    8798 
    8799 > select #3/A
    8800 
    8801 1839 atoms, 1884 bonds, 231 residues, 1 model selected 
    8802 
    8803 > color sel #ff7e79ff
    8804 
    8805 > color sel byelement
    8806 
    8807 > color sel #ff2600ff
    8808 
    8809 > color sel #ff7e79ff
    8810 
    8811 > select #3/Z
    8812 
    8813 4866 atoms, 4939 bonds, 3 pseudobonds, 340 residues, 2 models selected 
    8814 
    8815 > color (#!3 & sel) #9437ffff
    8816 
    8817 > select #3/V
    8818 
    8819 1998 atoms, 2019 bonds, 5 pseudobonds, 153 residues, 2 models selected 
    8820 
    8821 > color (#!3 & sel) lime
    8822 
    8823 > ui mousemode right select
    8824 
    8825 > select clear
    8826 
    8827 > select #3/J
    8828 
    8829 4726 atoms, 4795 bonds, 6 pseudobonds, 322 residues, 2 models selected 
    8830 
    8831 > color (#!3 & sel) #ff40ffff
    8832 
    8833 > color (#!3 & sel) #9437ffff
    8834 
    8835 > select clear
    8836 
    8837 > dssp
    8838 
    8839 > show #8 models
    8840 
    8841 > hide #8 models
    8842 
    8843 > select #3/S,T
    8844 
    8845 2394 atoms, 2406 bonds, 152 residues, 1 model selected 
    8846 
    8847 > hide sel cartoons
    8848 
    8849 > show #8 models
    8850 
    8851 > select add #3
    8852 
    8853 53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected 
    8854 
    8855 > select subtract #3
    8856 
    8857 Nothing selected 
    8858 
    8859 > select #3/SQ
    8860 
    8861 Nothing selected 
    8862 
    8863 > select #3/Q
    8864 
    8865 2420 atoms, 2446 bonds, 3 pseudobonds, 183 residues, 2 models selected 
    8866 
    8867 > color (#!3 & sel) #0096ffff
    8868 
    8869 > select #3/M
    8870 
    8871 2382 atoms, 2408 bonds, 4 pseudobonds, 192 residues, 2 models selected 
    8872 
    8873 > color (#!3 & sel) #00f900ff
    8874 
    8875 > select clear
    8876 
    8877 > cartoon style width 1
    8878 
    8879 > cartoon style width 5
    8880 
    8881 > cartoon style width 2
    8882 
    8883 > cartoon style thickness 2
    8884 
    8885 > cartoon style thickness 1
    8886 
    8887 > cartoon style thickness 0.9
    8888 
    8889 > cartoon style width 2
    8890 
    8891 > cartoon style width 3
    8892 
    8893 > lighting soft
    8894 
    8895 > cartoon style width 2
    8896 
    8897 > cartoon style thickness 0.8
    8898 
    8899 > cartoon style thickness 0.7
    8900 
    8901 > lighting full
    8902 
    8903 > lighting soft
    8904 
    8905 > lighting simple
    8906 
    8907 > select #3/N
    8908 
    8909 3760 atoms, 3805 bonds, 237 residues, 1 model selected 
    8910 
    8911 > color sel #ff7e79ff
    8912 
    8913 > select clear
    8914 
    8915 > select #3/X,U
    8916 
    8917 5022 atoms, 5072 bonds, 10 pseudobonds, 378 residues, 2 models selected 
    8918 
    8919 > color (#!3 & sel) #0433ffff
    8920 
    8921 > color (#!3 & sel) #7a81ffff
    8922 
    8923 > color (#!3 & sel) #0433ffff
    8924 
    8925 > color (#!3 & sel) #0096ffff
    8926 
    8927 > color (#!3 & sel) #00fdffff
    8928 
    8929 > color (#!3 & sel) #005493ff
    8930 
    8931 [Repeated 1 time(s)]
    8932 
    8933 > color (#!3 & sel) #005493a3
    8934 
    8935 > color (#!3 & sel) #00549385
    8936 
    8937 > color (#!3 & sel) #00549380
    8938 
    8939 > color (#!3 & sel) #0096ffff
    8940 
    8941 > select clear
    8942 
    8943 > select #3/B:63
    8944 
    8945 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8946 
    8947 > show sel atoms
    8948 
    8949 > style sel stick
    8950 
    8951 Changed 9 atom styles 
    8952 
    8953 > color sel byhetero
    8954 
    8955 > select #3/O:76
    8956 
    8957 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8958 
    8959 > select clear
    8960 
    8961 > select #3/B:63
    8962 
    8963 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8964 
    8965 > hide sel atoms
    8966 
    8967 > select clear
    8968 
    8969 > style #8#!3 stick
    8970 
    8971 Changed 56848 atom styles 
    8972 
    8973 > show #8#!3 surfaces
    8974 
    8975 > surface transparency 50
    8976 
    8977 > surface transparency 80
    8978 
    8979 > hide #!3,8 surfaces
    8980 
    8981 > hide #!8 models
    8982 
    8983 > show #!8 models
    8984 
    8985 > hide #!3 models
    8986 
    8987 > show #!3 models
    8988 
    8989 > hide #!3 models
    8990 
    8991 > show #!3 models
    8992 
    8993 > select #A,Y,W
    8994 
    8995 Expected an objects specifier or a keyword 
    8996 
    8997 > select #3A,Y,W
    8998 
    8999 Expected an objects specifier or a keyword 
    9000 
    9001 > select #3/A,Y,W
    9002 
    9003 9248 atoms, 9394 bonds, 8 pseudobonds, 805 residues, 2 models selected 
    9004 
    9005 > color (#!3 & sel) light gray
    9006 
    9007 [Repeated 1 time(s)]
    9008 
    9009 > color (#!3 & sel) #c0c0c0ff
    9010 
    9011 > select #3/X,U,V
    9012 
    9013 7020 atoms, 7091 bonds, 15 pseudobonds, 531 residues, 2 models selected 
    9014 
    9015 > color (#!3 & sel) #d6d6d6ff
    9016 
    9017 > color (#!3 & sel) #c0c0c0ff
    9018 
    9019 > select #3/Z,N
    9020 
    9021 8626 atoms, 8744 bonds, 3 pseudobonds, 577 residues, 2 models selected 
    9022 
    9023 > color (#!3 & sel) #a9a9a9ff
    9024 
    9025 > color (#!3 & sel) #c0c0c0ff
    9026 
    9027 > select clear
    9028 
    9029 > select #3/I,M,Q
    9030 
    9031 9765 atoms, 9908 bonds, 7 pseudobonds, 758 residues, 2 models selected 
    9032 
    9033 > color (#!3 & sel) dim gray
    9034 
    9035 > select #3/G,F
    9036 
    9037 7112 atoms, 7179 bonds, 4 pseudobonds, 479 residues, 2 models selected 
    9038 
    9039 > select #3/G,F,J
    9040 
    9041 11838 atoms, 11974 bonds, 10 pseudobonds, 801 residues, 2 models selected 
    9042 
    9043 > color (#!3 & sel) dim gray
    9044 
    9045 > select clear
    9046 
    9047 > ui tool show "Side View"
    9048 
    9049 > spin 360
    9050 
    9051 Unknown command: spin 360 
    9052 
    9053 > roll 360
    9054 
    9055 Expected an axis vector or a keyword 
    9056 
    9057 > roll x 360
    9058 
    9059 [Repeated 2 time(s)]
    9060 
    9061 > roll x 1 360
    9062 
    9063 > roll y 1 360
    9064 
    9065 > roll x 1 90
    9066 
    9067 > roll x 2 90
    9068 
    9069 > roll x -1 90
    9070 
    9071 > roll y 1 360
    9072 
    9073 > roll x -1 90
    9074 
    9075 > roll y 1 360
    9076 
    9077 > wait 20
    9078 
    9079 > roll x -1 90
    9080 
    9081 > roll y 1 360
    9082 
    9083 > wait 150
    9084 
    9085 > roll x -1 90
    9086 
    9087 > roll y 1 360
    9088 
    9089 > wait 250
    9090 
    9091 > roll x -1 90
    9092 
    9093 > roll y 1 360
    9094 
    9095 > wait 500
    9096 
    9097 > roll x -1 90
    9098 
    9099 > roll y 1 360
    9100 
    9101 > wait 450
    9102 
    9103 > roll x -1 90
    9104 
    9105 > roll y 1 360
    9106 
    9107 > wait 420
    9108 
    9109 > roll x -1 90
    9110 
    9111 > roll y 1 360
    9112 
    9113 > wait 400
    9114 
    9115 > roll x -1 90
    9116 
    9117 > color #3,8 #0096ffff
    9118 
    9119 [Repeated 1 time(s)]
    9120 
    9121 > undo
    9122 
    9123 [Repeated 1 time(s)]
    9124 
    9125 > Color #3/G,Q #0096FF
    9126 
    9127 Unknown command: Color #3/G,Q #0096FF 
    9128 
    9129 > Sel #3/G,Q color sel #0096FF
    9130 
    9131 Unknown command: Sel #3/G,Q color sel #0096FF 
    9132 
    9133 > Sel #3/G,Q
    9134 
    9135 Unknown command: Sel #3/G,Q 
    9136 
    9137 > select #3/G,Q
    9138 
    9139 6163 atoms, 6223 bonds, 5 pseudobonds, 433 residues, 2 models selected 
    9140 
    9141 > select #3/G,Q color sel #0096FF
    9142 
    9143 Expected a keyword 
    9144 
    9145 > select #3/G,Q
    9146 
    9147 6163 atoms, 6223 bonds, 5 pseudobonds, 433 residues, 2 models selected 
    9148 
    9149 > color sel #0096FF
    9150 
    9151 > select clear
    9152 
    9153 > color #3/G,Q #0096FF
    9154 
    9155 > color #3,8 #797979ff
    9156 
    9157 > color #3,8 #919191ff
    9158 
    9159 > undo
    9160 
    9161 [Repeated 1 time(s)]
    9162 
    9163 > color #3,8 dim gray
    9164 
    9165 > undo
    9166 
    9167 [Repeated 4 time(s)]
    9168 
    9169 > select clear
    9170 
    9171 > color #3/G,Q #0096FF
    9172 
    9173 > wait 150
    9174 
    9175 > color #3/G,Q dimgray
    9176 
    9177 > color #3/G,Q #0096FF
    9178 
    9179 > wait 50
    9180 
    9181 > color #3/G,Q dimgray
    9182 
    9183 > color fade #3/G,Q #0096FF
    9184 
    9185 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    9186 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    9187 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    9188 
    9189 > wait 50
    9190 
    9191 > color #3/G,Q dimgray
    9192 
    9193 > Crossfade color #3/G,Q #0096FF
    9194 
    9195 Unknown command: Crossfade color #3/G,Q #0096FF 
    9196 
    9197 > wait 50
    9198 
    9199 > color #3/G,Q dimgray
    9200 
    9201 > color #3/G,Q #0096FF
    9202 
    9203 > wait 50
    9204 
    9205 > color #3/G,Q dimgray
    9206 
    9207 > Crossfade; color #3/G,Q #0096FF; wait 50
    9208 
    9209 Unknown command: Crossfade; color #3/G,Q #0096FF; wait 50 
    9210 
    9211 > crossfade
    9212 
    9213 > color #3/G,Q #0096FF
    9214 
    9215 > wait 50
    9216 
    9217 > crossfade
    9218 
    9219 > color #3/G,Q #0096FF
    9220 
    9221 > wait 50
    9222 
    9223 > undo
    9224 
    9225 [Repeated 1 time(s)]
    9226 
    9227 > crossfade
    9228 
    9229 > color #3/G,Q #0096FF
    9230 
    9231 > wait 50
    9232 
    9233 [Repeated 1 time(s)]
    9234 
    9235 > crossfade
    9236 
    9237 > color #3/G,Q dimgray
    9238 
    9239 > wait 50
    9240 
    9241 > select #3/Z:275
    9242 
    9243 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9244 
    9245 > color (#!3 & sel) #9437ffff
    9246 
    9247 [Repeated 1 time(s)]
    9248 
    9249 > undo
    9250 
    9251 [Repeated 1 time(s)]
    9252 
    9253 > select clear
    9254 
    9255 > select #3/Z:274
    9256 
    9257 21 atoms, 21 bonds, 1 residue, 1 model selected 
    9258 
    9259 > color (#!3 & sel) light gray
    9260 
    9261 > select clear
    9262 
    9263 > undo
    9264 
    9265 > color (#!3 & sel) #d6d6d6ff
    9266 
    9267 > color (#!3 & sel) #c0c0c0ff
    9268 
    9269 [Repeated 1 time(s)]
    9270 
    9271 > crossfade
    9272 
    9273 > color #3/Y,Z #9437FF
    9274 
    9275 > wait 50
    9276 
    9277 [Repeated 1 time(s)]
    9278 
    9279 > crossfade
    9280 
    9281 > color #3/Y,Z #C0C0C0
    9282 
    9283 > wait 50
    9284 
    9285 > select clear
    9286 
    9287 > roll x -1 90
    9288 
    9289 > roll x 1 90
    9290 
    9291 > open
    9292 > /Users/zbxg977/Desktop/BRISC_project/BRISC_pentaUb_structure_Dan/cryosparc_P1_DeepEmhancer_J202_highres.mrc
    9293 
    9294 Opened cryosparc_P1_DeepEmhancer_J202_highres.mrc as #5, grid size
    9295 512,512,512, pixel 0.74, shown at level 0.00204, step 2, values float32 
    9296 
    9297 > select add #3
    9298 
    9299 53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected 
    9300 
    9301 > volume #5 step 1
    9302 
    9303 > volume #5 level 0.1134
    9304 
    9305 > ui mousemode right "rotate selected models"
    9306 
    9307 > view matrix models
    9308 > #3,0.95422,-0.27698,-0.11292,74.797,0.20162,0.87447,-0.44119,60.309,0.22095,0.39822,0.89028,-89.115
    9309 
    9310 > undo
    9311 
    9312 > select subtract #3
    9313 
    9314 22 models selected 
    9315 
    9316 > select add #5
    9317 
    9318 4 models selected 
    9319 
    9320 > view matrix models
    9321 > #5,0.89102,-0.11592,0.43892,-23.542,0.30523,0.86866,-0.39021,37.491,-0.33604,0.48165,0.80938,-20.252
    9322 
    9323 > view matrix models
    9324 > #5,0.42416,-0.27299,0.86346,9.9416,0.79723,0.56483,-0.21305,5.4897,-0.42955,0.77875,0.45721,-15.846
    9325 
    9326 > ui mousemode right "translate selected models"
    9327 
    9328 > view matrix models
    9329 > #5,0.42416,-0.27299,0.86346,6.061,0.79723,0.56483,-0.21305,-17.432,-0.42955,0.77875,0.45721,24.788
    9330 
    9331 > ui mousemode right "rotate selected models"
    9332 
    9333 > view matrix models
    9334 > #5,0.81844,-0.43282,0.37791,50.121,0.50998,0.24418,-0.8248,164.2,0.26471,0.86778,0.42057,-78.781
    9335 
    9336 > ui mousemode right "translate selected models"
    9337 
    9338 > view matrix models
    9339 > #5,0.81844,-0.43282,0.37791,40.926,0.50998,0.24418,-0.8248,160.85,0.26471,0.86778,0.42057,-105.12
    9340 
    9341 > view matrix models
    9342 > #5,0.81844,-0.43282,0.37791,56.133,0.50998,0.24418,-0.8248,169.15,0.26471,0.86778,0.42057,-100.7
    9343 
    9344 > ui mousemode right "rotate selected models"
    9345 
    9346 > view matrix models
    9347 > #5,-0.79885,-0.084636,0.59554,174.83,-0.6013,0.13968,-0.78672,330.58,-0.016603,-0.98657,-0.16248,364.87
    9348 
    9349 > view matrix models
    9350 > #5,-0.70691,-0.21333,0.67436,176.16,-0.70654,0.25721,-0.65928,305.02,-0.032808,-0.94251,-0.33255,381.88
    9351 
    9352 > view matrix models
    9353 > #5,-0.86037,-0.37738,0.34257,272.5,-0.34072,-0.074004,-0.93725,356.83,0.37905,-0.9231,-0.06491,287.32
    9354 
    9355 > view matrix models
    9356 > #5,0.27598,-0.92698,0.25405,237.73,-0.926,-0.32726,-0.18819,379.89,0.25759,-0.18332,-0.94871,284.51
    9357 
    9358 > ui mousemode right "translate selected models"
    9359 
    9360 > view matrix models
    9361 > #5,0.27598,-0.92698,0.25405,261.38,-0.926,-0.32726,-0.18819,442.24,0.25759,-0.18332,-0.94871,329.72
    9362 
    9363 > view matrix models
    9364 > #5,0.27598,-0.92698,0.25405,270.85,-0.926,-0.32726,-0.18819,441.82,0.25759,-0.18332,-0.94871,354.73
    9365 
    9366 > ui mousemode right "rotate selected models"
    9367 
    9368 > view matrix models
    9369 > #5,-0.76194,0.56796,0.31124,118.96,-0.39996,-0.034665,-0.91588,416.29,-0.5094,-0.82232,0.25357,412.69
    9370 
    9371 > ui mousemode right "translate selected models"
    9372 
    9373 > view matrix models
    9374 > #5,-0.76194,0.56796,0.31124,167.06,-0.39996,-0.034665,-0.91588,433.46,-0.5094,-0.82232,0.25357,417.86
    9375 
    9376 > ui tool show "Fit in Map"
    9377 
    9378 > fitmap #3 inMap #5
    9379 
    9380 Fit molecule P64_J12_model-coot-56.pdb (#3) to map
    9381 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 53424 atoms 
    9382 average map value = 0.07452, steps = 284 
    9383 shifted from previous position = 23.8 
    9384 rotated from previous position = 6.83 degrees 
    9385 atoms outside contour = 43940, contour level = 0.1134 
    9386  
    9387 Position of P64_J12_model-coot-56.pdb (#3) relative to
    9388 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates: 
    9389 Matrix rotation and translation 
    9390 -0.76336194 -0.42876028 -0.48315957 509.75254988 
    9391 0.58594633 -0.14473464 -0.79731974 262.25309824 
    9392 0.27192911 -0.89174912 0.36171543 201.03833376 
    9393 Axis -0.07445072 -0.59533266 0.80002257 
    9394 Axis point 210.03507452 319.31513667 0.00000000 
    9395 Rotation angle (degrees) 140.64127053 
    9396 Shift along axis -33.24407263 
    9397  
    9398 
    9399 > select subtract #5
    9400 
    9401 Nothing selected 
    9402 
    9403 > open /Users/zbxg977/Desktop/penta_Ub_merged.pdb
    9404 
    9405 Chain information for penta_Ub_merged.pdb #6 
    9406 --- 
    9407 Chain | Description 
    9408 A B C L | No description available 
    9409 O | No description available 
    9410  
    9411 
    9412 > select add #6
    9413 
    9414 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    9415 
    9416 > view matrix models #6,1,0,0,14.12,0,1,0,22.571,0,0,1,27.031
    9417 
    9418 > view matrix models #6,1,0,0,15.745,0,1,0,4.9213,0,0,1,39.269
    9419 
    9420 > fitmap #6 inMap #5
    9421 
    9422 Fit molecule penta_Ub_merged.pdb (#6) to map
    9423 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms 
    9424 average map value = 0.03084, steps = 240 
    9425 shifted from previous position = 5.63 
    9426 rotated from previous position = 11.6 degrees 
    9427 atoms outside contour = 3177, contour level = 0.1134 
    9428  
    9429 Position of penta_Ub_merged.pdb (#6) relative to
    9430 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates: 
    9431 Matrix rotation and translation 
    9432 -0.81522555 -0.25341032 -0.52075956 465.22557231 
    9433 0.51830802 0.08193703 -0.85125972 235.13444893 
    9434 0.25838749 -0.96388253 0.06454744 304.69339704 
    9435 Axis -0.10216074 -0.70676837 0.70002975 
    9436 Axis point 150.78544864 0.00000000 367.68057814 
    9437 Rotation angle (degrees) 146.55035104 
    9438 Shift along axis -0.41893617 
    9439  
    9440 
    9441 > hide sel atoms
    9442 
    9443 > show sel cartoons
    9444 
    9445 > hide #!3 models
    9446 
    9447 > ui mousemode right "rotate selected models"
    9448 
    9449 > view matrix models
    9450 > #6,0.9837,-0.11362,0.13936,21.477,0.056651,0.93143,0.35949,-55.449,-0.17065,-0.34573,0.92269,154.42
    9451 
    9452 > view matrix models
    9453 > #6,0.37349,-0.79347,0.48053,230.48,-0.0081346,0.5152,0.85703,-41.298,-0.9276,-0.324,0.18597,433.9
    9454 
    9455 > view matrix models
    9456 > #6,0.30923,-0.43531,0.8455,121.42,-0.36441,0.76697,0.52816,42.616,-0.8784,-0.47144,0.078541,467.05
    9457 
    9458 > ui mousemode right "translate selected models"
    9459 
    9460 > view matrix models
    9461 > #6,0.30923,-0.43531,0.8455,102.31,-0.36441,0.76697,0.52816,47.152,-0.8784,-0.47144,0.078541,461.46
    9462 
    9463 > ui mousemode right "rotate selected models"
    9464 
    9465 > view matrix models
    9466 > #6,0.92947,-0.26671,-0.25485,104.32,-0.27908,-0.96018,-0.012978,433.1,-0.24124,0.083187,-0.96689,379.48
    9467 
    9468 > ui mousemode right "translate selected models"
    9469 
    9470 > view matrix models
    9471 > #6,0.92947,-0.26671,-0.25485,106.56,-0.27908,-0.96018,-0.012978,437.85,-0.24124,0.083187,-0.96689,383.68
    9472 
    9473 > ui mousemode right "rotate selected models"
    9474 
    9475 > view matrix models
    9476 > #6,0.92611,0.0034423,-0.37724,76.233,-0.10302,-0.95964,-0.26168,437.28,-0.36292,0.28121,-0.88838,361.8
    9477 
    9478 > ui mousemode right "translate selected models"
    9479 
    9480 > ui mousemode right "rotate selected models"
    9481 
    9482 > view matrix models
    9483 > #6,0.58955,0.42781,-0.68513,120.44,-0.084315,-0.81099,-0.57896,454.97,-0.80332,0.39909,-0.44205,368.48
    9484 
    9485 > view matrix models
    9486 > #6,0.43235,-0.37451,-0.82026,325.47,-0.65274,-0.75758,0.0018353,481.19,-0.6221,0.53463,-0.57199,323.19
    9487 
    9488 > view matrix models
    9489 > #6,0.66075,-0.25513,-0.70591,234.59,-0.3588,-0.93341,0.0015123,448.38,-0.65929,0.25228,-0.7083,405.14
    9490 
    9491 > view matrix models
    9492 > #6,0.53137,-0.26167,-0.80572,280.2,-0.12418,-0.96488,0.23147,366.1,-0.83799,-0.022937,-0.5452,470.63
    9493 
    9494 > fitmap #6 inMap #5
    9495 
    9496 Fit molecule penta_Ub_merged.pdb (#6) to map
    9497 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms 
    9498 average map value = 0.04473, steps = 216 
    9499 shifted from previous position = 8.49 
    9500 rotated from previous position = 8.17 degrees 
    9501 atoms outside contour = 3016, contour level = 0.1134 
    9502  
    9503 Position of penta_Ub_merged.pdb (#6) relative to
    9504 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates: 
    9505 Matrix rotation and translation 
    9506 0.07651590 0.64458117 0.76069733 -87.66333612 
    9507 0.99486624 0.00132160 -0.10119000 11.31246327 
    9508 -0.06623051 0.76453474 -0.64117092 155.61742874 
    9509 Axis 0.69402741 0.66292501 0.28081378 
    9510 Axis point 0.00000000 7.59449819 100.00864003 
    9511 Rotation angle (degrees) 141.41343192 
    9512 Shift along axis -9.64192415 
    9513  
    9514 
    9515 > view matrix models
    9516 > #6,0.27731,-0.24257,-0.92965,347.92,-0.0086426,-0.96819,0.25005,334.1,-0.96074,-0.061309,-0.27059,467.65
    9517 
    9518 > ui mousemode right "translate selected models"
    9519 
    9520 > view matrix models
    9521 > #6,0.27731,-0.24257,-0.92965,352.22,-0.0086426,-0.96819,0.25005,333.08,-0.96074,-0.061309,-0.27059,463.08
    9522 
    9523 > view matrix models
    9524 > #6,0.27731,-0.24257,-0.92965,355.74,-0.0086426,-0.96819,0.25005,333.93,-0.96074,-0.061309,-0.27059,466.06
    9525 
    9526 > ui mousemode right "rotate selected models"
    9527 
    9528 > view matrix models
    9529 > #6,0.29679,-0.35595,-0.88612,365.66,0.10608,-0.9099,0.40103,274.01,-0.94903,-0.21303,-0.23229,485.65
    9530 
    9531 > ui mousemode right "translate selected models"
    9532 
    9533 > view matrix models
    9534 > #6,0.29679,-0.35595,-0.88612,367.16,0.10608,-0.9099,0.40103,280.02,-0.94903,-0.21303,-0.23229,486.54
    9535 
    9536 > fitmap #6 inMap #5
    9537 
    9538 Fit molecule penta_Ub_merged.pdb (#6) to map
    9539 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms 
    9540 average map value = 0.04044, steps = 88 
    9541 shifted from previous position = 2.76 
    9542 rotated from previous position = 5.25 degrees 
    9543 atoms outside contour = 3054, contour level = 0.1134 
    9544  
    9545 Position of penta_Ub_merged.pdb (#6) relative to
    9546 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates: 
    9547 Matrix rotation and translation 
    9548 0.15609642 0.72235882 0.67367027 -116.00954017 
    9549 0.96951994 0.01835015 -0.24432426 42.58067044 
    9550 -0.18885174 0.69127491 -0.69747689 205.63722394 
    9551 Axis 0.72174910 0.66537520 0.19066746 
    9552 Axis point 0.00000000 21.56062234 131.74159871 
    9553 Rotation angle (degrees) 139.59795370 
    9554 Shift along axis -16.18933184 
    9555  
    9556 
    9557 > view matrix models
    9558 > #6,0.37294,-0.32482,-0.86914,348.3,0.076925,-0.92267,0.37783,289.83,-0.92466,-0.20777,-0.31911,493.61
    9559 
    9560 > fitmap #6 inMap #5
    9561 
    9562 Fit molecule penta_Ub_merged.pdb (#6) to map
    9563 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms 
    9564 average map value = 0.06226, steps = 212 
    9565 shifted from previous position = 3.45 
    9566 rotated from previous position = 19.4 degrees 
    9567 atoms outside contour = 2811, contour level = 0.1134 
    9568  
    9569 Position of penta_Ub_merged.pdb (#6) relative to
    9570 cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates: 
    9571 Matrix rotation and translation 
    9572 0.00314523 0.52331352 0.85213441 -73.49266478 
    9573 0.95223623 0.25863119 -0.16234552 -8.10699426 
    9574 -0.30534615 0.81194388 -0.49750464 178.68162582 
    9575 Axis 0.61955240 0.73604400 0.27275273 
    9576 Axis point 25.90526356 0.00000000 114.54079787 
    9577 Rotation angle (degrees) 128.16032758 
    9578 Shift along axis -2.76376043 
    9579  
    9580 
    9581 > select subtract #6
    9582 
    9583 Nothing selected 
    9584 
    9585 > hide #!5 models
    9586 
    9587 > show #!3 models
    9588 
    9589 > color #6 #ff9300ff
    9590 
    9591 > ui tool show "Side View"
    9592 
    9593 > select #6
    9594 
    9595 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    9596 
    9597 > hide #6
    9598 
    9599 > view matrix models
    9600 > #6,0.4434,0.00086618,-0.89632,274.04,0.24539,-0.96191,0.12046,299.3,-0.86208,-0.27336,-0.42673,507.15
    9601 
    9602 > hide cartoons #6
    9603 
    9604 Expected ',' or a keyword 
    9605 
    9606 > view matrix models
    9607 > #6,0.4434,0.00086618,-0.89632,274.06,0.24539,-0.96191,0.12046,299.25,-0.86208,-0.27336,-0.42673,507.17
    9608 
    9609 > ui mousemode right select
    9610 
    9611 > select clear
    9612 
    9613 > crossfade #6
    9614 
    9615 Expected an integer >= 1 or a keyword 
    9616 
    9617 > hide #6 models
    9618 
    9619 > crossfade
    9620 
    9621 > hide #3/O,L,D,C,B
    9622 
    9623 > wait 50
    9624 
    9625 > crossfade
    9626 
    9627 > hide cartoons #3/O,L,D,C,B; wait 50
    9628 
    9629 Expected ',' or a keyword 
    9630 
    9631 > crossfade
    9632 
    9633 > cartoon hide #3/O,L,D,C,B
    9634 
    9635 > wait 50
    9636 
    9637 > undo
    9638 
    9639 > show #6 models
    9640 
    9641 > hide #6 models
    9642 
    9643 > show #6 models
    9644 
    9645 > crossfade
    9646 
    9647 > cartoon hide #3/O,L,D,C,B
    9648 
    9649 > wait 50
    9650 
    9651 > undo
    9652 
    9653 > hide #6 models
    9654 
    9655 > crossfade
    9656 
    9657 > cartoon hide #3/O,L,D,C,B
    9658 
    9659 > wait 50
    9660 
    9661 > crossfade
    9662 
    9663 > cartoon show #3/O,L,A,C,B; wait 50
    9664 
    9665 Expected an atoms specifier or a keyword 
    9666 
    9667 > show #6 models
    9668 
    9669 > crossfade
    9670 
    9671 > cartoon hide #3/O,L,A,C,B
    9672 
    9673 > wait 50
    9674 
    9675 > undo
    9676 
    9677 > crossfade
    9678 
    9679 > cartoon hide #6/O,L,A,C,B
    9680 
    9681 > wait 50
    9682 
    9683 > crossfade
    9684 
    9685 > cartoon hide #3/O,L,D,C,B
    9686 
    9687 > wait 50
    9688 
    9689 > crossfade
    9690 
    9691 > cartoon show #6/O,L,A,C,B; wait 50
    9692 
    9693 Expected an atoms specifier or a keyword 
    9694 
    9695 > undo
    9696 
    9697 > crossfade
    9698 
    9699 > cartoon #6/O,L,A,C,B
    9700 
    9701 > wait 50
    9702 
    9703 > crossfade
    9704 
    9705 > cartoon hide #3/O,L,D,C,B
    9706 
    9707 > wait 50
    9708 
    9709 > crossfade
    9710 
    9711 > cartoon #6/O,L,A,C,B
    9712 
    9713 > wait 50
    9714 
    9715 > roll y 1 90
    9716 
    9717 > hide #!8 models
    9718 
    9719 > show #!8 models
    9720 
    9721 > undo
    9722 
    9723 [Repeated 9 time(s)]
    9724 
    9725 > show #!1 models
    9726 
    9727 > hide #!1 models
    9728 
    9729 > show #!2 models
    9730 
    9731 > hide #!2 models
    9732 
    9733 > show #6 models
    9734 
    9735 > show #!2 models
    9736 
    9737 > hide #!2 models
    9738 
    9739 > hide #6 models
    9740 
    9741 > show #!5 models
    9742 
    9743 > hide #!5 models
    9744 
    9745 > show #6 models
    9746 
    9747 > hide #6 models
    9748 
    9749 > hide #!8 models
    9750 
    9751 > show #!8 models
    9752 
    9753 > hide #!8 models
    9754 
    9755 > show #!8 models
    9756 
    9757 > select add #8
    9758 
    9759 3424 atoms, 3454 bonds, 380 residues, 1 model selected 
    9760 
    9761 > show sel cartoons
    9762 
    9763 > ui tool show Matchmaker
    9764 
    9765 [Repeated 1 time(s)]
    9766 
    9767 > matchmaker #8/O to #3/R pairing ss
    9768 
    9769 Parameters 
    9770 --- 
    9771 Chain pairing | ss 
    9772 Alignment algorithm | Needleman-Wunsch 
    9773 Similarity matrix | BLOSUM-62 
    9774 SS fraction | 0.3 
    9775 Gap open (HH/SS/other) | 18/18/6 
    9776 Gap extend | 1 
    9777 SS matrix |  |  | H | S | O 
    9778 ---|---|---|--- 
    9779 H | 6 | -9 | -6 
    9780 S |  | 6 | -6 
    9781 O |  |  | 4 
    9782 Iteration cutoff | 2 
    9783  
    9784 Matchmaker P64_J12_model-coot-56.pdb, chain R (#3) with penta_Ub_merged.pdb,
    9785 chain O (#8), sequence alignment score = 374 
    9786 RMSD between 76 pruned atom pairs is 0.217 angstroms; (across all 76 pairs:
    9787 0.217) 
    9788  
    9789 
    9790 > select clear
    9791 
    9792 > show #6 models
    9793 
    9794 > hide #!8 models
    9795 
    9796 > show #!8 models
    9797 
    9798 > hide #6 models
    9799 
    9800 > show #6 models
    9801 
    9802 > crossfade
    9803 
    9804 > color #3/Q #0096FF, color #3/Z #C0C0C0; wait 50
    9805 
    9806 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    9807 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    9808 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    9809 
    9810 > wait 50
    9811 
    9812 > crossfade
    9813 
    9814 > color #3/Q #0096FF
    9815 
    9816 > color #3/Z #C0C0C0
    9817 
    9818 > wait 50
    9819 
    9820 > select clear
    9821 
    9822 > undo
    9823 
    9824 [Repeated 3 time(s)]
    9825 
    9826 > crossfade
    9827 
    9828 > color #3/Q #0096FF, #3/Z #C0C0C0; wait 50
    9829 
    9830 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    9831 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    9832 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    9833 
    9834 > crossfade
    9835 
    9836 > color #3/Q #0096FF & #3/Z #C0C0C0; wait 50
    9837 
    9838 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    9839 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    9840 
    9841 > crossfade
    9842 
    9843 > color #3/Q #0096FF & color #3/Z #C0C0C0; wait 50
    9844 
    9845 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    9846 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    9847 
    9848 > crossfade
    9849 
    9850 > color #3/Q #0096FF #3/Z #9437FF; wait 50
    9851 
    9852 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    9853 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    9854 
    9855 > crossfade
    9856 
    9857 > color #3/Q #0096FF, #3/Z #9437FF; wait 50
    9858 
    9859 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    9860 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    9861 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    9862 
    9863 > crossfade
    9864 
    9865 > color #3/Q #0096FF & #3/Z #9437FF; wait 50
    9866 
    9867 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    9868 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    9869 
    9870 > crossfade
    9871 
    9872 > color #3/Q #0096FF
    9873 
    9874 > undo
    9875 
    9876 > crossfade
    9877 
    9878 > color #3/Q #0096FF
    9879 
    9880 > color #3/Z #9437FF
    9881 
    9882 > wait 50
    9883 
    9884 > undo
    9885 
    9886 [Repeated 1 time(s)]
    9887 
    9888 > crossfade
    9889 
    9890 > color #3/Q #0096FF
    9891 
    9892 > color #3/Z #9437FF
    9893 
    9894 > wait 50
    9895 
    9896 > wait 50
    9897 
    9898 > crossfade
    9899 
    9900 > color #3/Q dimgray
    9901 
    9902 > color #3/Z #C0C0C0
    9903 
    9904 > wait 50
    9905 
    9906 > crossfade
    9907 
    9908 > color #3/V #0096FF
    9909 
    9910 > color #3/I #9437FF
    9911 
    9912 > wait 50
    9913 
    9914 > wait 50
    9915 
    9916 > crossfade
    9917 
    9918 > color #3/V dimgray
    9919 
    9920 > color #3/I #C0C0C0
    9921 
    9922 > wait 50
    9923 
    9924 > crossfade
    9925 
    9926 > cartoon hide #6/O,L,A,C,B
    9927 
    9928 > wait 50
    9929 
    9930 > roll y 1 360
    9931 
    9932 > wait 390
    9933 
    9934 > roll x -1 90
    9935 
    9936 > crossfade
    9937 
    9938 > color #3/G,Q #0096FF
    9939 
    9940 > wait 50
    9941 
    9942 [Repeated 1 time(s)]
    9943 
    9944 > crossfade
    9945 
    9946 > color #3/G,Q dimgray
    9947 
    9948 > wait 50
    9949 
    9950 > crossfade
    9951 
    9952 > color #3/Y,Z #9437FF
    9953 
    9954 > wait 50
    9955 
    9956 [Repeated 1 time(s)]
    9957 
    9958 > crossfade
    9959 
    9960 > color #3/Y,Z #C0C0C0
    9961 
    9962 > wait 50
    9963 
    9964 > roll x 1 90
    9965 
    9966 > crossfade
    9967 
    9968 > cartoon hide #3/O,L,D,C,B
    9969 
    9970 > wait 50
    9971 
    9972 > crossfade
    9973 
    9974 > cartoon #6/O,L,A,C,B
    9975 
    9976 > wait 50
    9977 
    9978 > roll y 1 90
    9979 
    9980 > crossfade
    9981 
    9982 > color #3/Q #0096FF
    9983 
    9984 > color #3/Z #9437FF
    9985 
    9986 > wait 50
    9987 
    9988 > wait 50
    9989 
    9990 > crossfade
    9991 
    9992 > color #3/Q dimgray
    9993 
    9994 > color #3/Z #C0C0C0
    9995 
    9996 > wait 50
    9997 
    9998 > crossfade
    9999 
    10000 > color #3/V #0096FF
    10001 
    10002 > color #3/I #9437FF
    10003 
    10004 > wait 50
    10005 
    10006 > wait 50
    10007 
    10008 > crossfade
    10009 
    10010 > color #3/V dimgray
    10011 
    10012 > color #3/I #C0C0C0
    10013 
    10014 > wait 50
    10015 
    10016 > roll y 1 360
    10017 
    10018 > wait 390
    10019 
    10020 > roll x -1 90
    10021 
    10022 > crossfade
    10023 
    10024 > color #3/G,Q #0096FF
    10025 
    10026 > wait 50
    10027 
    10028 [Repeated 1 time(s)]
    10029 
    10030 > crossfade
    10031 
    10032 > color #3/G,Q dimgray
    10033 
    10034 > wait 50
    10035 
    10036 > crossfade
    10037 
    10038 > color #3/Y,Z #9437FF
    10039 
    10040 > wait 50
    10041 
    10042 [Repeated 1 time(s)]
    10043 
    10044 > crossfade
    10045 
    10046 > color #3/Y,Z #C0C0C0
    10047 
    10048 > wait 50
    10049 
    10050 > roll x 1 90
    10051 
    10052 > wait 50
    10053 
    10054 > crossfade
    10055 
    10056 > cartoon hide #3/O,L,D,C,B
    10057 
    10058 > wait 50
    10059 
    10060 > crossfade
    10061 
    10062 > cartoon #6/O,L,A,C,B
    10063 
    10064 > wait 50
    10065 
    10066 > roll y 1 90
    10067 
    10068 > wait 50
    10069 
    10070 > crossfade
    10071 
    10072 > color #3/Q #0096FF
    10073 
    10074 > color #3/Z #9437FF
    10075 
    10076 > wait 50
    10077 
    10078 > wait 50
    10079 
    10080 > crossfade
    10081 
    10082 > color #3/Q dimgray
    10083 
    10084 > color #3/Z #C0C0C0
    10085 
    10086 > wait 50
    10087 
    10088 > crossfade
    10089 
    10090 > color #3/V #0096FF
    10091 
    10092 > color #3/I #9437FF
    10093 
    10094 > wait 50
    10095 
    10096 > wait 50
    10097 
    10098 > crossfade
    10099 
    10100 > color #3/V dimgray
    10101 
    10102 > color #3/I #C0C0C0
    10103 
    10104 > wait 50
    10105 
    10106 > roll y 1 360
    10107 
    10108 > wait 390
    10109 
    10110 > roll x -1 90
    10111 
    10112 > wait 50
    10113 
    10114 > crossfade
    10115 
    10116 > color #3/G,Q #0096FF
    10117 
    10118 > wait 50
    10119 
    10120 [Repeated 1 time(s)]
    10121 
    10122 > crossfade
    10123 
    10124 > color #3/G,Q dimgray
    10125 
    10126 > wait 50
    10127 
    10128 > crossfade
    10129 
    10130 > color #3/Y,Z #9437FF
    10131 
    10132 > wait 50
    10133 
    10134 [Repeated 1 time(s)]
    10135 
    10136 > crossfade
    10137 
    10138 > color #3/Y,Z #C0C0C0
    10139 
    10140 > wait 50
    10141 
    10142 > roll x 1 90
    10143 
    10144 > wait 50
    10145 
    10146 > crossfade
    10147 
    10148 > cartoon hide #3/O,L,D,C,B
    10149 
    10150 > wait 50
    10151 
    10152 > crossfade
    10153 
    10154 > cartoon #6/O,L,A,C,B
    10155 
    10156 > wait 50
    10157 
    10158 > roll y 1 90
    10159 
    10160 > wait 50
    10161 
    10162 > crossfade
    10163 
    10164 > color #3/Q #0096FF
    10165 
    10166 > color #3/Z #9437FF
    10167 
    10168 > wait 50
    10169 
    10170 > wait 50
    10171 
    10172 > crossfade
    10173 
    10174 > color #3/Q dimgray
    10175 
    10176 > color #3/Z #C0C0C0
    10177 
    10178 > wait 50
    10179 
    10180 > crossfade
    10181 
    10182 > color #3/V #0096FF
    10183 
    10184 > color #3/I #9437FF
    10185 
    10186 > wait 50
    10187 
    10188 > wait 50
    10189 
    10190 > crossfade
    10191 
    10192 > color #3/V dimgray
    10193 
    10194 > color #3/I #C0C0C0
    10195 
    10196 > wait 50
    10197 
    10198 > roll y 1 360
    10199 
    10200 > wait 390
    10201 
    10202 > roll x -1 90
    10203 
    10204 > wait 100
    10205 
    10206 > crossfade
    10207 
    10208 > color #3/G,Q #0096FF
    10209 
    10210 > wait 50
    10211 
    10212 [Repeated 1 time(s)]
    10213 
    10214 > crossfade
    10215 
    10216 > color #3/G,Q dimgray
    10217 
    10218 > wait 50
    10219 
    10220 > crossfade
    10221 
    10222 > color #3/Y,Z #9437FF
    10223 
    10224 > wait 50
    10225 
    10226 [Repeated 1 time(s)]
    10227 
    10228 > crossfade
    10229 
    10230 > color #3/Y,Z #C0C0C0
    10231 
    10232 > wait 50
    10233 
    10234 > roll x 1 90
    10235 
    10236 > wait 100
    10237 
    10238 > crossfade
    10239 
    10240 > cartoon hide #3/O,L,D,C,B
    10241 
    10242 > wait 50
    10243 
    10244 > crossfade
    10245 
    10246 > cartoon #6/O,L,A,C,B
    10247 
    10248 > wait 50
    10249 
    10250 > roll y 1 90
    10251 
    10252 > wait 100
    10253 
    10254 > crossfade
    10255 
    10256 > color #3/Q #0096FF
    10257 
    10258 > color #3/Z #9437FF
    10259 
    10260 > wait 50
    10261 
    10262 > wait 50
    10263 
    10264 > crossfade
    10265 
    10266 > color #3/Q dimgray
    10267 
    10268 > color #3/Z #C0C0C0
    10269 
    10270 > wait 50
    10271 
    10272 > crossfade
    10273 
    10274 > color #3/V #0096FF
    10275 
    10276 > color #3/I #9437FF
    10277 
    10278 > wait 50
    10279 
    10280 > wait 50
    10281 
    10282 > crossfade
    10283 
    10284 > color #3/V dimgray
    10285 
    10286 > color #3/I #C0C0C0
    10287 
    10288 > wait 50
    10289 
    10290 > crossfade
    10291 
    10292 > cartoon hide #6/O,L,A,C,B
    10293 
    10294 > wait 50
    10295 
    10296 > crossfade
    10297 
    10298 > cartoon #3/O,L,D,C,B
    10299 
    10300 > wait 50
    10301 
    10302 > crossfade
    10303 
    10304 > color #3/V #0096FF
    10305 
    10306 > color #3/I dimgrey
    10307 
    10308 > wait 50
    10309 
    10310 > undo
    10311 
    10312 [Repeated 2 time(s)]
    10313 
    10314 > redo
    10315 
    10316 > roll y 1 360
    10317 
    10318 > wait 390
    10319 
    10320 > roll x -1 90
    10321 
    10322 > wait 100
    10323 
    10324 > crossfade
    10325 
    10326 > color #3/G,Q #0096FF
    10327 
    10328 > wait 50
    10329 
    10330 [Repeated 1 time(s)]
    10331 
    10332 > crossfade
    10333 
    10334 > color #3/G,Q dimgray
    10335 
    10336 > wait 50
    10337 
    10338 > crossfade
    10339 
    10340 > color #3/Y,Z #9437FF
    10341 
    10342 > wait 50
    10343 
    10344 [Repeated 1 time(s)]
    10345 
    10346 > crossfade
    10347 
    10348 > color #3/Y,Z #C0C0C0
    10349 
    10350 > wait 50
    10351 
    10352 > roll x 1 90
    10353 
    10354 > wait 80
    10355 
    10356 > crossfade
    10357 
    10358 > cartoon hide #3/O,L,D,C,B
    10359 
    10360 > wait 50
    10361 
    10362 > crossfade
    10363 
    10364 > cartoon #6/O,L,A,C,B
    10365 
    10366 > wait 50
    10367 
    10368 > roll y 1 90
    10369 
    10370 > wait 80
    10371 
    10372 > crossfade
    10373 
    10374 > color #3/Q #0096FF
    10375 
    10376 > color #3/Z #9437FF
    10377 
    10378 > wait 50
    10379 
    10380 > wait 50
    10381 
    10382 > crossfade
    10383 
    10384 > color #3/Q dimgray
    10385 
    10386 > color #3/Z #C0C0C0
    10387 
    10388 > wait 50
    10389 
    10390 > crossfade
    10391 
    10392 > color #3/V #0096FF
    10393 
    10394 > color #3/I #9437FF
    10395 
    10396 > wait 50
    10397 
    10398 > wait 50
    10399 
    10400 > crossfade
    10401 
    10402 > color #3/V dimgray
    10403 
    10404 > color #3/I dimgrey
    10405 
    10406 > wait 50
    10407 
    10408 > crossfade
    10409 
    10410 > cartoon #3/O,L,D,C,B
    10411 
    10412 > wait 50
    10413 
    10414 > crossfade
    10415 
    10416 > cartoon hide #6/O,L,A,C,B
    10417 
    10418 > wait 50
    10419 
    10420 > Movie record
    10421 
    10422 Unknown command: Movie record 
    10423 
    10424 > roll y 1 360
    10425 
    10426 > wait 390
    10427 
    10428 > roll x -1 90
    10429 
    10430 > wait 100
    10431 
    10432 > crossfade
    10433 
    10434 > color #3/G,Q #0096FF
    10435 
    10436 > wait 50
    10437 
    10438 [Repeated 1 time(s)]
    10439 
    10440 > crossfade
    10441 
    10442 > color #3/G,Q dimgray
    10443 
    10444 > wait 50
    10445 
    10446 > crossfade
    10447 
    10448 > color #3/Y,Z #9437FF
    10449 
    10450 > wait 50
    10451 
    10452 [Repeated 1 time(s)]
    10453 
    10454 > crossfade
    10455 
    10456 > color #3/Y,Z #C0C0C0
    10457 
    10458 > wait 50
    10459 
    10460 > roll x 1 90
    10461 
    10462 > wait 100
    10463 
    10464 > crossfade
    10465 
    10466 > cartoon hide #3/O,L,D,C,B
    10467 
    10468 > wait 50
    10469 
    10470 > crossfade
    10471 
    10472 > cartoon #6/O,L,A,C,B
    10473 
    10474 > wait 50
    10475 
    10476 > roll y 1 90
    10477 
    10478 > wait 100
    10479 
    10480 > crossfade
    10481 
    10482 > color #3/Q #0096FF
    10483 
    10484 > color #3/Z #9437FF
    10485 
    10486 > wait 50
    10487 
    10488 > wait 50
    10489 
    10490 > crossfade
    10491 
    10492 > color #3/Q dimgray
    10493 
    10494 > color #3/Z #C0C0C0
    10495 
    10496 > wait 50
    10497 
    10498 > crossfade
    10499 
    10500 > color #3/V #0096FF
    10501 
    10502 > color #3/I #9437FF
    10503 
    10504 > wait 50
    10505 
    10506 > wait 50
    10507 
    10508 > crossfade
    10509 
    10510 > color #3/V dimgray
    10511 
    10512 > color #3/I dimgrey
    10513 
    10514 > wait 50
    10515 
    10516 > crossfade
    10517 
    10518 > color #3/V C0C0C0; color #3/I dimgrey; wait 50
    10519 
    10520 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    10521 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    10522 'fromcartoons', 'fromribbons', or 'random' or a keyword 
     1759[deleted to fit within ticket limits]
     1760
    105231761
    105241762> crossfade