The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202110110902 (2021-10-11 09:02:34 UTC)
Description
Model Loops should allow mismatches in unmodeled part
Example session attached with 2mnr structure associated with 3toy sequence, attempted to model active region "ADYDL" plus 2 adjacent flexible . I will also attach the pairwise sequence alignment as an aln file in case the session breaks.
Log:
> version
UCSF ChimeraX version: 1.3.dev202110110902 (2021-10-11)
© 2016-2021 Regents of the University of California. All rights reserved.
> ui tool show "Model Loops"
> modeller refine 1:2:237-241 numModels 3 fast false adjacentFlexible 2
> protocol standard
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service1633983975482-559494696
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1633983975482-559494696
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service1633983975482-559494696 finished
Modeller error output
Traceback (most recent call last):
File "/usr/local/opal-local/bin/modeller9v8.py", line 332, in <module>
main()
File "/usr/local/opal-local/bin/modeller9v8.py", line 24, in main
VersionMap[cf["version"]](cf)
File "/usr/local/opal-local/bin/modeller9v8.py", line 34, in v2_run
execfile(fn)
File "ModellerModelling.py", line 86, in <module>
a.make()
File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
**** IGNORE FOLLOWING LICENSE KEY MESSAGE ****
check_lice_E> Invalid license key: xxx
Go to https://salilab.org/modeller/ to get a license key,
and then set the 'license' variable to it in the file
/usr/lib/modeller10.1/modlib/modeller/config.py
**** END IGNORED MESSAGE ****
MODELLER 10.1, 2021/03/12, r12156
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2021 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu
3.10.0-1160.36.2.el7.x86_64 x86_64
Date and time of compilation : 2021/03/12 00:18:43
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2021/10/11 13:26:15
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v1}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v1}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL10v1}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL10v1}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v1}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v1}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
loopmodel__W> The class 'loopmodel' is deprecated; use 'LoopModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
0.270
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
0.299
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
0.387
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 528709 516.317
0.504
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 530981 518.536 0.506
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 533253 520.755 0.509
read_al_374_> Non-standard residue type,position,sequence: . 357 1
read_al_374_> Non-standard residue type,position,sequence: . 358 1
read_al_374_> Non-standard residue type,position,sequence: w 359 1
read_al_374_> Non-standard residue type,position,sequence: w 360 1
read_al_374_> Non-standard residue type,position,sequence: w 361 1
read_al_374_> Non-standard residue type,position,sequence: w 362 1
read_al_374_> Non-standard residue type,position,sequence: w 363 1
read_al_374_> Non-standard residue type,position,sequence: w 364 1
read_al_374_> Non-standard residue type,position,sequence: w 365 1
read_al_374_> Non-standard residue type,position,sequence: w 366 1
read_al_374_> Non-standard residue type,position,sequence: w 367 1
read_al_374_> Non-standard residue type,position,sequence: w 368 1
read_al_374_> Non-standard residue type,position,sequence: w 369 1
read_al_374_> Non-standard residue type,position,sequence: w 370 1
read_al_374_> Non-standard residue type,position,sequence: w 371 1
read_al_374_> Non-standard residue type,position,sequence: w 372 1
read_al_374_> Non-standard residue type,position,sequence: w 373 1
read_al_374_> Non-standard residue type,position,sequence: w 374 1
read_al_374_> Non-standard residue type,position,sequence: w 375 1
read_al_374_> Non-standard residue type,position,sequence: w 376 1
read_al_374_> Non-standard residue type,position,sequence: w 377 1
read_al_374_> Non-standard residue type,position,sequence: w 378 1
read_al_374_> Non-standard residue type,position,sequence: w 379 1
read_al_374_> Non-standard residue type,position,sequence: w 380 1
read_al_374_> Non-standard residue type,position,sequence: w 381 1
read_al_374_> Non-standard residue type,position,sequence: w 382 1
read_al_374_> Non-standard residue type,position,sequence: w 383 1
read_al_374_> Non-standard residue type,position,sequence: w 384 1
read_al_374_> Non-standard residue type,position,sequence: w 385 1
read_al_374_> Non-standard residue type,position,sequence: w 386 1
read_al_374_> Non-standard residue type,position,sequence: w 387 1
read_al_374_> Non-standard residue type,position,sequence: w 388 1
read_al_374_> Non-standard residue type,position,sequence: w 389 1
read_al_374_> Non-standard residue type,position,sequence: w 390 1
read_al_374_> Non-standard residue type,position,sequence: w 391 1
read_al_374_> Non-standard residue type,position,sequence: w 392 1
read_al_374_> Non-standard residue type,position,sequence: w 393 1
read_al_374_> Non-standard residue type,position,sequence: w 394 1
read_al_374_> Non-standard residue type,position,sequence: w 395 1
read_al_374_> Non-standard residue type,position,sequence: w 396 1
read_al_374_> Non-standard residue type,position,sequence: w 397 1
read_al_374_> Non-standard residue type,position,sequence: w 398 1
read_al_374_> Non-standard residue type,position,sequence: w 399 1
read_al_374_> Non-standard residue type,position,sequence: w 400 1
read_al_374_> Non-standard residue type,position,sequence: w 401 1
read_al_374_> Non-standard residue type,position,sequence: w 402 1
read_al_374_> Non-standard residue type,position,sequence: w 403 1
read_al_374_> Non-standard residue type,position,sequence: w 404 1
read_al_374_> Non-standard residue type,position,sequence: w 405 1
read_al_374_> Non-standard residue type,position,sequence: w 406 1
read_al_374_> Non-standard residue type,position,sequence: w 407 1
read_al_374_> Non-standard residue type,position,sequence: w 408 1
read_al_374_> Non-standard residue type,position,sequence: w 409 1
read_al_374_> Non-standard residue type,position,sequence: w 410 1
read_al_374_> Non-standard residue type,position,sequence: w 411 1
read_al_374_> Non-standard residue type,position,sequence: w 412 1
read_al_374_> Non-standard residue type,position,sequence: w 413 1
read_al_374_> Non-standard residue type,position,sequence: w 414 1
read_al_374_> Non-standard residue type,position,sequence: w 415 1
read_al_374_> Non-standard residue type,position,sequence: w 416 1
read_al_374_> Non-standard residue type,position,sequence: w 417 1
read_al_374_> Non-standard residue type,position,sequence: w 418 1
read_al_374_> Non-standard residue type,position,sequence: w 419 1
read_al_374_> Non-standard residue type,position,sequence: w 420 1
read_al_374_> Non-standard residue type,position,sequence: w 421 1
read_al_374_> Non-standard residue type,position,sequence: w 422 1
read_al_374_> Non-standard residue type,position,sequence: w 423 1
read_al_374_> Non-standard residue type,position,sequence: w 424 1
read_al_374_> Non-standard residue type,position,sequence: w 425 1
read_al_374_> Non-standard residue type,position,sequence: w 426 1
read_al_374_> Non-standard residue type,position,sequence: w 427 1
read_al_374_> Non-standard residue type,position,sequence: w 428 1
read_al_374_> Non-standard residue type,position,sequence: w 429 1
read_al_374_> Non-standard residue type,position,sequence: w 430 1
read_al_374_> Non-standard residue type,position,sequence: w 431 1
read_al_374_> Non-standard residue type,position,sequence: w 432 1
read_al_374_> Non-standard residue type,position,sequence: w 433 1
read_al_374_> Non-standard residue type,position,sequence: w 434 1
read_al_374_> Non-standard residue type,position,sequence: w 435 1
read_al_374_> Non-standard residue type,position,sequence: w 436 1
read_al_374_> Non-standard residue type,position,sequence: w 437 1
read_al_374_> Non-standard residue type,position,sequence: w 438 1
read_al_374_> Non-standard residue type,position,sequence: w 439 1
read_al_374_> Non-standard residue type,position,sequence: w 440 1
read_al_374_> Non-standard residue type,position,sequence: w 441 1
read_al_374_> Non-standard residue type,position,sequence: w 442 1
read_al_374_> Non-standard residue type,position,sequence: w 443 1
read_al_374_> Non-standard residue type,position,sequence: w 444 1
read_al_374_> Non-standard residue type,position,sequence: w 445 1
read_al_374_> Non-standard residue type,position,sequence: w 446 1
read_al_374_> Non-standard residue type,position,sequence: w 447 1
read_al_374_> Non-standard residue type,position,sequence: w 448 1
read_al_374_> Non-standard residue type,position,sequence: w 449 1
read_al_374_> Non-standard residue type,position,sequence: w 450 1
read_al_374_> Non-standard residue type,position,sequence: w 451 1
read_al_374_> Non-standard residue type,position,sequence: w 452 1
read_al_374_> Non-standard residue type,position,sequence: w 453 1
read_al_374_> Non-standard residue type,position,sequence: w 454 1
read_al_374_> Non-standard residue type,position,sequence: w 455 1
read_al_374_> Non-standard residue type,position,sequence: w 456 1
read_al_374_> Non-standard residue type,position,sequence: w 457 1
read_al_374_> Non-standard residue type,position,sequence: w 458 1
read_al_374_> Non-standard residue type,position,sequence: w 459 1
read_al_374_> Non-standard residue type,position,sequence: w 460 1
read_al_374_> Non-standard residue type,position,sequence: w 461 1
read_al_374_> Non-standard residue type,position,sequence: w 462 1
read_al_374_> Non-standard residue type,position,sequence: w 463 1
read_al_374_> Non-standard residue type,position,sequence: w 464 1
read_al_374_> Non-standard residue type,position,sequence: w 465 1
read_al_374_> Non-standard residue type,position,sequence: w 466 1
read_al_374_> Non-standard residue type,position,sequence: w 467 1
read_al_374_> Non-standard residue type,position,sequence: w 468 1
read_al_374_> Non-standard residue type,position,sequence: w 469 1
read_al_374_> Non-standard residue type,position,sequence: w 470 1
read_al_374_> Non-standard residue type,position,sequence: w 471 1
read_al_374_> Non-standard residue type,position,sequence: w 472 1
read_al_374_> Non-standard residue type,position,sequence: w 473 1
read_al_374_> Non-standard residue type,position,sequence: w 474 1
read_al_374_> Non-standard residue type,position,sequence: w 475 1
read_al_374_> Non-standard residue type,position,sequence: w 476 1
read_al_374_> Non-standard residue type,position,sequence: w 477 1
read_al_374_> Non-standard residue type,position,sequence: w 478 1
read_al_374_> Non-standard residue type,position,sequence: w 479 1
read_al_374_> Non-standard residue type,position,sequence: w 480 1
read_al_374_> Non-standard residue type,position,sequence: w 481 1
read_al_374_> Non-standard residue type,position,sequence: w 482 1
read_al_374_> Non-standard residue type,position,sequence: w 483 1
read_al_374_> Non-standard residue type,position,sequence: w 484 1
read_al_374_> Non-standard residue type,position,sequence: w 485 1
read_al_374_> Non-standard residue type,position,sequence: w 486 1
read_al_374_> Non-standard residue type,position,sequence: w 487 1
read_al_374_> Non-standard residue type,position,sequence: w 488 1
read_al_374_> Non-standard residue type,position,sequence: w 489 1
read_al_374_> Non-standard residue type,position,sequence: w 490 1
read_al_374_> Non-standard residue type,position,sequence: w 491 1
read_al_374_> Non-standard residue type,position,sequence: w 492 1
read_al_374_> Non-standard residue type,position,sequence: w 493 1
read_al_374_> Non-standard residue type,position,sequence: w 494 1
read_al_374_> Non-standard residue type,position,sequence: w 495 1
read_al_374_> Non-standard residue type,position,sequence: w 496 1
read_al_374_> Non-standard residue type,position,sequence: w 497 1
read_al_374_> Non-standard residue type,position,sequence: w 498 1
read_al_374_> Non-standard residue type,position,sequence: w 499 1
read_al_374_> Non-standard residue type,position,sequence: w 500 1
read_al_374_> Non-standard residue type,position,sequence: w 501 1
read_al_374_> Non-standard residue type,position,sequence: w 502 1
read_al_374_> Non-standard residue type,position,sequence: w 503 1
read_al_374_> Non-standard residue type,position,sequence: w 504 1
read_al_374_> Non-standard residue type,position,sequence: w 505 1
read_al_374_> Non-standard residue type,position,sequence: w 506 1
read_al_374_> Non-standard residue type,position,sequence: w 507 1
read_al_374_> Non-standard residue type,position,sequence: w 508 1
read_al_374_> Non-standard residue type,position,sequence: w 509 1
read_al_374_> Non-standard residue type,position,sequence: w 510 1
read_al_374_> Non-standard residue type,position,sequence: w 511 1
read_al_374_> Non-standard residue type,position,sequence: w 512 1
read_al_374_> Non-standard residue type,position,sequence: w 513 1
read_al_374_> Non-standard residue type,position,sequence: w 514 1
read_al_374_> Non-standard residue type,position,sequence: w 515 1
read_al_374_> Non-standard residue type,position,sequence: w 516 1
read_al_374_> Non-standard residue type,position,sequence: w 517 1
read_al_374_> Non-standard residue type,position,sequence: w 518 1
read_al_374_> Non-standard residue type,position,sequence: w 519 1
read_al_374_> Non-standard residue type,position,sequence: w 520 1
read_al_374_> Non-standard residue type,position,sequence: w 521 1
read_al_374_> Non-standard residue type,position,sequence: w 522 1
read_al_374_> Non-standard residue type,position,sequence: w 523 1
read_al_374_> Non-standard residue type,position,sequence: w 524 1
read_al_374_> Non-standard residue type,position,sequence: w 525 1
read_al_374_> Non-standard residue type,position,sequence: w 526 1
read_al_374_> Non-standard residue type,position,sequence: w 527 1
read_al_374_> Non-standard residue type,position,sequence: w 528 1
read_al_374_> Non-standard residue type,position,sequence: w 529 1
read_al_374_> Non-standard residue type,position,sequence: w 530 1
read_al_374_> Non-standard residue type,position,sequence: w 531 1
read_al_374_> Non-standard residue type,position,sequence: w 532 1
read_al_374_> Non-standard residue type,position,sequence: w 533 1
read_al_374_> Non-standard residue type,position,sequence: w 534 1
read_al_374_> Non-standard residue type,position,sequence: w 535 1
read_al_374_> Non-standard residue type,position,sequence: w 536 1
read_al_374_> Non-standard residue type,position,sequence: w 537 1
read_al_374_> Non-standard residue type,position,sequence: w 538 1
read_al_374_> Non-standard residue type,position,sequence: w 539 1
read_al_374_> Non-standard residue type,position,sequence: w 540 1
read_al_374_> Non-standard residue type,position,sequence: w 541 1
read_al_374_> Non-standard residue type,position,sequence: w 542 1
read_al_374_> Non-standard residue type,position,sequence: w 543 1
read_al_374_> Non-standard residue type,position,sequence: w 544 1
read_al_374_> Non-standard residue type,position,sequence: w 545 1
read_al_374_> Non-standard residue type,position,sequence: w 546 1
read_al_374_> Non-standard residue type,position,sequence: w 547 1
read_al_374_> Non-standard residue type,position,sequence: w 548 1
read_al_374_> Non-standard residue type,position,sequence: w 549 1
read_al_374_> Non-standard residue type,position,sequence: w 550 1
read_al_374_> Non-standard residue type,position,sequence: w 551 1
read_al_374_> Non-standard residue type,position,sequence: w 552 1
read_al_374_> Non-standard residue type,position,sequence: w 553 1
read_al_374_> Non-standard residue type,position,sequence: w 554 1
read_al_374_> Non-standard residue type,position,sequence: w 555 1
read_al_374_> Non-standard residue type,position,sequence: w 556 1
read_al_374_> Non-standard residue type,position,sequence: w 557 1
read_al_374_> Non-standard residue type,position,sequence: w 558 1
read_al_374_> Non-standard residue type,position,sequence: w 559 1
read_al_374_> Non-standard residue type,position,sequence: w 560 1
read_al_374_> Non-standard residue type,position,sequence: w 561 1
read_al_374_> Non-standard residue type,position,sequence: w 562 1
read_al_374_> Non-standard residue type,position,sequence: w 563 1
read_al_374_> Non-standard residue type,position,sequence: w 564 1
read_al_374_> Non-standard residue type,position,sequence: w 565 1
read_al_374_> Non-standard residue type,position,sequence: w 566 1
read_al_374_> Non-standard residue type,position,sequence: w 567 1
read_al_374_> Non-standard residue type,position,sequence: w 568 1
read_al_374_> Non-standard residue type,position,sequence: w 569 1
read_al_374_> Non-standard residue type,position,sequence: . 357 2
read_al_374_> Non-standard residue type,position,sequence: . 358 2
read_al_374_> Non-standard residue type,position,sequence: w 359 2
read_al_374_> Non-standard residue type,position,sequence: w 360 2
read_al_374_> Non-standard residue type,position,sequence: w 361 2
read_al_374_> Non-standard residue type,position,sequence: w 362 2
read_al_374_> Non-standard residue type,position,sequence: w 363 2
read_al_374_> Non-standard residue type,position,sequence: w 364 2
read_al_374_> Non-standard residue type,position,sequence: w 365 2
read_al_374_> Non-standard residue type,position,sequence: w 366 2
read_al_374_> Non-standard residue type,position,sequence: w 367 2
read_al_374_> Non-standard residue type,position,sequence: w 368 2
read_al_374_> Non-standard residue type,position,sequence: w 369 2
read_al_374_> Non-standard residue type,position,sequence: w 370 2
read_al_374_> Non-standard residue type,position,sequence: w 371 2
read_al_374_> Non-standard residue type,position,sequence: w 372 2
read_al_374_> Non-standard residue type,position,sequence: w 373 2
read_al_374_> Non-standard residue type,position,sequence: w 374 2
read_al_374_> Non-standard residue type,position,sequence: w 375 2
read_al_374_> Non-standard residue type,position,sequence: w 376 2
read_al_374_> Non-standard residue type,position,sequence: w 377 2
read_al_374_> Non-standard residue type,position,sequence: w 378 2
read_al_374_> Non-standard residue type,position,sequence: w 379 2
read_al_374_> Non-standard residue type,position,sequence: w 380 2
read_al_374_> Non-standard residue type,position,sequence: w 381 2
read_al_374_> Non-standard residue type,position,sequence: w 382 2
read_al_374_> Non-standard residue type,position,sequence: w 383 2
read_al_374_> Non-standard residue type,position,sequence: w 384 2
read_al_374_> Non-standard residue type,position,sequence: w 385 2
read_al_374_> Non-standard residue type,position,sequence: w 386 2
read_al_374_> Non-standard residue type,position,sequence: w 387 2
read_al_374_> Non-standard residue type,position,sequence: w 388 2
read_al_374_> Non-standard residue type,position,sequence: w 389 2
read_al_374_> Non-standard residue type,position,sequence: w 390 2
read_al_374_> Non-standard residue type,position,sequence: w 391 2
read_al_374_> Non-standard residue type,position,sequence: w 392 2
read_al_374_> Non-standard residue type,position,sequence: w 393 2
read_al_374_> Non-standard residue type,position,sequence: w 394 2
read_al_374_> Non-standard residue type,position,sequence: w 395 2
read_al_374_> Non-standard residue type,position,sequence: w 396 2
read_al_374_> Non-standard residue type,position,sequence: w 397 2
read_al_374_> Non-standard residue type,position,sequence: w 398 2
read_al_374_> Non-standard residue type,position,sequence: w 399 2
read_al_374_> Non-standard residue type,position,sequence: w 400 2
read_al_374_> Non-standard residue type,position,sequence: w 401 2
read_al_374_> Non-standard residue type,position,sequence: w 402 2
read_al_374_> Non-standard residue type,position,sequence: w 403 2
read_al_374_> Non-standard residue type,position,sequence: w 404 2
read_al_374_> Non-standard residue type,position,sequence: w 405 2
read_al_374_> Non-standard residue type,position,sequence: w 406 2
read_al_374_> Non-standard residue type,position,sequence: w 407 2
read_al_374_> Non-standard residue type,position,sequence: w 408 2
read_al_374_> Non-standard residue type,position,sequence: w 409 2
read_al_374_> Non-standard residue type,position,sequence: w 410 2
read_al_374_> Non-standard residue type,position,sequence: w 411 2
read_al_374_> Non-standard residue type,position,sequence: w 412 2
read_al_374_> Non-standard residue type,position,sequence: w 413 2
read_al_374_> Non-standard residue type,position,sequence: w 414 2
read_al_374_> Non-standard residue type,position,sequence: w 415 2
read_al_374_> Non-standard residue type,position,sequence: w 416 2
read_al_374_> Non-standard residue type,position,sequence: w 417 2
read_al_374_> Non-standard residue type,position,sequence: w 418 2
read_al_374_> Non-standard residue type,position,sequence: w 419 2
read_al_374_> Non-standard residue type,position,sequence: w 420 2
read_al_374_> Non-standard residue type,position,sequence: w 421 2
read_al_374_> Non-standard residue type,position,sequence: w 422 2
read_al_374_> Non-standard residue type,position,sequence: w 423 2
read_al_374_> Non-standard residue type,position,sequence: w 424 2
read_al_374_> Non-standard residue type,position,sequence: w 425 2
read_al_374_> Non-standard residue type,position,sequence: w 426 2
read_al_374_> Non-standard residue type,position,sequence: w 427 2
read_al_374_> Non-standard residue type,position,sequence: w 428 2
read_al_374_> Non-standard residue type,position,sequence: w 429 2
read_al_374_> Non-standard residue type,position,sequence: w 430 2
read_al_374_> Non-standard residue type,position,sequence: w 431 2
read_al_374_> Non-standard residue type,position,sequence: w 432 2
read_al_374_> Non-standard residue type,position,sequence: w 433 2
read_al_374_> Non-standard residue type,position,sequence: w 434 2
read_al_374_> Non-standard residue type,position,sequence: w 435 2
read_al_374_> Non-standard residue type,position,sequence: w 436 2
read_al_374_> Non-standard residue type,position,sequence: w 437 2
read_al_374_> Non-standard residue type,position,sequence: w 438 2
read_al_374_> Non-standard residue type,position,sequence: w 439 2
read_al_374_> Non-standard residue type,position,sequence: w 440 2
read_al_374_> Non-standard residue type,position,sequence: w 441 2
read_al_374_> Non-standard residue type,position,sequence: w 442 2
read_al_374_> Non-standard residue type,position,sequence: w 443 2
read_al_374_> Non-standard residue type,position,sequence: w 444 2
read_al_374_> Non-standard residue type,position,sequence: w 445 2
read_al_374_> Non-standard residue type,position,sequence: w 446 2
read_al_374_> Non-standard residue type,position,sequence: w 447 2
read_al_374_> Non-standard residue type,position,sequence: w 448 2
read_al_374_> Non-standard residue type,position,sequence: w 449 2
read_al_374_> Non-standard residue type,position,sequence: w 450 2
read_al_374_> Non-standard residue type,position,sequence: w 451 2
read_al_374_> Non-standard residue type,position,sequence: w 452 2
read_al_374_> Non-standard residue type,position,sequence: w 453 2
read_al_374_> Non-standard residue type,position,sequence: w 454 2
read_al_374_> Non-standard residue type,position,sequence: w 455 2
read_al_374_> Non-standard residue type,position,sequence: w 456 2
read_al_374_> Non-standard residue type,position,sequence: w 457 2
read_al_374_> Non-standard residue type,position,sequence: w 458 2
read_al_374_> Non-standard residue type,position,sequence: w 459 2
read_al_374_> Non-standard residue type,position,sequence: w 460 2
read_al_374_> Non-standard residue type,position,sequence: w 461 2
read_al_374_> Non-standard residue type,position,sequence: w 462 2
read_al_374_> Non-standard residue type,position,sequence: w 463 2
read_al_374_> Non-standard residue type,position,sequence: w 464 2
read_al_374_> Non-standard residue type,position,sequence: w 465 2
read_al_374_> Non-standard residue type,position,sequence: w 466 2
read_al_374_> Non-standard residue type,position,sequence: w 467 2
read_al_374_> Non-standard residue type,position,sequence: w 468 2
read_al_374_> Non-standard residue type,position,sequence: w 469 2
read_al_374_> Non-standard residue type,position,sequence: w 470 2
read_al_374_> Non-standard residue type,position,sequence: w 471 2
read_al_374_> Non-standard residue type,position,sequence: w 472 2
read_al_374_> Non-standard residue type,position,sequence: w 473 2
read_al_374_> Non-standard residue type,position,sequence: w 474 2
read_al_374_> Non-standard residue type,position,sequence: w 475 2
read_al_374_> Non-standard residue type,position,sequence: w 476 2
read_al_374_> Non-standard residue type,position,sequence: w 477 2
read_al_374_> Non-standard residue type,position,sequence: w 478 2
read_al_374_> Non-standard residue type,position,sequence: w 479 2
read_al_374_> Non-standard residue type,position,sequence: w 480 2
read_al_374_> Non-standard residue type,position,sequence: w 481 2
read_al_374_> Non-standard residue type,position,sequence: w 482 2
read_al_374_> Non-standard residue type,position,sequence: w 483 2
read_al_374_> Non-standard residue type,position,sequence: w 484 2
read_al_374_> Non-standard residue type,position,sequence: w 485 2
read_al_374_> Non-standard residue type,position,sequence: w 486 2
read_al_374_> Non-standard residue type,position,sequence: w 487 2
read_al_374_> Non-standard residue type,position,sequence: w 488 2
read_al_374_> Non-standard residue type,position,sequence: w 489 2
read_al_374_> Non-standard residue type,position,sequence: w 490 2
read_al_374_> Non-standard residue type,position,sequence: w 491 2
read_al_374_> Non-standard residue type,position,sequence: w 492 2
read_al_374_> Non-standard residue type,position,sequence: w 493 2
read_al_374_> Non-standard residue type,position,sequence: w 494 2
read_al_374_> Non-standard residue type,position,sequence: w 495 2
read_al_374_> Non-standard residue type,position,sequence: w 496 2
read_al_374_> Non-standard residue type,position,sequence: w 497 2
read_al_374_> Non-standard residue type,position,sequence: w 498 2
read_al_374_> Non-standard residue type,position,sequence: w 499 2
read_al_374_> Non-standard residue type,position,sequence: w 500 2
read_al_374_> Non-standard residue type,position,sequence: w 501 2
read_al_374_> Non-standard residue type,position,sequence: w 502 2
read_al_374_> Non-standard residue type,position,sequence: w 503 2
read_al_374_> Non-standard residue type,position,sequence: w 504 2
read_al_374_> Non-standard residue type,position,sequence: w 505 2
read_al_374_> Non-standard residue type,position,sequence: w 506 2
read_al_374_> Non-standard residue type,position,sequence: w 507 2
read_al_374_> Non-standard residue type,position,sequence: w 508 2
read_al_374_> Non-standard residue type,position,sequence: w 509 2
read_al_374_> Non-standard residue type,position,sequence: w 510 2
read_al_374_> Non-standard residue type,position,sequence: w 511 2
read_al_374_> Non-standard residue type,position,sequence: w 512 2
read_al_374_> Non-standard residue type,position,sequence: w 513 2
read_al_374_> Non-standard residue type,position,sequence: w 514 2
read_al_374_> Non-standard residue type,position,sequence: w 515 2
read_al_374_> Non-standard residue type,position,sequence: w 516 2
read_al_374_> Non-standard residue type,position,sequence: w 517 2
read_al_374_> Non-standard residue type,position,sequence: w 518 2
read_al_374_> Non-standard residue type,position,sequence: w 519 2
read_al_374_> Non-standard residue type,position,sequence: w 520 2
read_al_374_> Non-standard residue type,position,sequence: w 521 2
read_al_374_> Non-standard residue type,position,sequence: w 522 2
read_al_374_> Non-standard residue type,position,sequence: w 523 2
read_al_374_> Non-standard residue type,position,sequence: w 524 2
read_al_374_> Non-standard residue type,position,sequence: w 525 2
read_al_374_> Non-standard residue type,position,sequence: w 526 2
read_al_374_> Non-standard residue type,position,sequence: w 527 2
read_al_374_> Non-standard residue type,position,sequence: w 528 2
read_al_374_> Non-standard residue type,position,sequence: w 529 2
read_al_374_> Non-standard residue type,position,sequence: w 530 2
read_al_374_> Non-standard residue type,position,sequence: w 531 2
read_al_374_> Non-standard residue type,position,sequence: w 532 2
read_al_374_> Non-standard residue type,position,sequence: w 533 2
read_al_374_> Non-standard residue type,position,sequence: w 534 2
read_al_374_> Non-standard residue type,position,sequence: w 535 2
read_al_374_> Non-standard residue type,position,sequence: w 536 2
read_al_374_> Non-standard residue type,position,sequence: w 537 2
read_al_374_> Non-standard residue type,position,sequence: w 538 2
read_al_374_> Non-standard residue type,position,sequence: w 539 2
read_al_374_> Non-standard residue type,position,sequence: w 540 2
read_al_374_> Non-standard residue type,position,sequence: w 541 2
read_al_374_> Non-standard residue type,position,sequence: w 542 2
read_al_374_> Non-standard residue type,position,sequence: w 543 2
read_al_374_> Non-standard residue type,position,sequence: w 544 2
read_al_374_> Non-standard residue type,position,sequence: w 545 2
read_al_374_> Non-standard residue type,position,sequence: w 546 2
read_al_374_> Non-standard residue type,position,sequence: w 547 2
read_al_374_> Non-standard residue type,position,sequence: w 548 2
read_al_374_> Non-standard residue type,position,sequence: w 549 2
read_al_374_> Non-standard residue type,position,sequence: w 550 2
read_al_374_> Non-standard residue type,position,sequence: w 551 2
read_al_374_> Non-standard residue type,position,sequence: w 552 2
read_al_374_> Non-standard residue type,position,sequence: w 553 2
read_al_374_> Non-standard residue type,position,sequence: w 554 2
read_al_374_> Non-standard residue type,position,sequence: w 555 2
read_al_374_> Non-standard residue type,position,sequence: w 556 2
read_al_374_> Non-standard residue type,position,sequence: w 557 2
read_al_374_> Non-standard residue type,position,sequence: w 558 2
read_al_374_> Non-standard residue type,position,sequence: w 559 2
read_al_374_> Non-standard residue type,position,sequence: w 560 2
read_al_374_> Non-standard residue type,position,sequence: w 561 2
read_al_374_> Non-standard residue type,position,sequence: w 562 2
read_al_374_> Non-standard residue type,position,sequence: w 563 2
read_al_374_> Non-standard residue type,position,sequence: w 564 2
read_al_374_> Non-standard residue type,position,sequence: w 565 2
read_al_374_> Non-standard residue type,position,sequence: w 566 2
read_al_374_> Non-standard residue type,position,sequence: w 567 2
read_al_374_> Non-standard residue type,position,sequence: w 568 2
read_al_374_> Non-standard residue type,position,sequence: w 569 2
Read the alignment from file : alignment.ali
Total number of alignment positions: 569
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 2mnr_1 569 1 2mnr_1
2 3toy,_cha 569 1 3toy,_chain
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./2mnr_1.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 705678 689.139
0.673
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 705678 689.139 0.673
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 705849 689.306
0.673
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 706699 690.136
0.674
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 707957 691.364
0.675
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 709861 693.224
0.677
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 709861 693.224 0.677
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 709951 693.312
0.677
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 712807 696.101
0.680
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 712807 696.101 0.680
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 712942 696.232
0.680
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 717226 700.416
0.684
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 717226 700.416 0.684
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 717424 700.609
0.684
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 723850 706.885
0.690
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 723850 706.885 0.690
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 724147 707.175
0.691
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 733769 716.571
0.700
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 733769 716.571 0.700
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 734219 717.011
0.700
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 748669 731.122
0.714
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 748669 731.122 0.714
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 749344 731.781
0.715
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 771002 752.932
0.735
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 771002 752.932 0.735
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 772010 753.916
0.736
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 804514 785.658
0.767
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 804514 785.658 0.767
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 806026 787.135
0.769
read_pd_459W> Residue type MN not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
read_pd_459W> Residue type SO4 not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 806026 787.135 0.769
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 808294 789.350
0.771
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 857050 836.963
0.817
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 855671 835.616
0.816
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 334)
Alignment TFEGGAVIPDLPGVGIIWREKEIGKYLV..wwwwwwwwwwwwwwwwwwwwwwwwwwwwww
PDB TFEGGNAVIPDLPGVGIIWREKEIGKYLV..wwwwwwwwwwwwwwwwwwwwwwwwwwwww
Match ***** * ** *****************************
Alignment residue type 1 (A, ALA) does not match pdb
residue type 12 (N, ASN),
for align code 2mnr_1 (atom file 2mnr_1), pdb residue number " 336", chain "A"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 2mnr_1
No output models from Modeller; see log for Modeller text output.
> 2mnr3toy.cxs
Unknown command: 2mnr3toy.cxs
> save 2mnr3toy.cxs
OpenGL version: 4.1 INTEL-14.7.18
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
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Model Identifier: MacBookPro11,4
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.2 GHz
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L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 427.140.8.0.0
SMC Version (system): 2.29f24
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1419)
Kernel Version: Darwin 19.6.0
Time since boot: 4:35
Graphics/Displays:
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0d26
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Metal: Supported, feature set macOS GPUFamily1 v4
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ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
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sphinxcontrib-devhelp: 1.0.2
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wheel-filename: 1.3.0
File attachment: 2mnr3toy.cxs
2mnr3toy.cxs
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Added by email2trac