- modeller_usage - salilab.org

Missing Residue Modeling for an Oligomer Inquiry
by Joel Subach 19 Sep '22

19 Sep '22

Hello, I missing residue modeled a loop region of a monomer from an oligomer heptamer and then oligomerized this new model monomer via GalaxyWeb into a heptamer, however, the generated heptamer´s RMSD to the PDB structure is a great 40 A. My understanding is that my above methodology is how Modeller would function best due to interfacing of multiple subunit problems if I tried to missing residue model all seven loops with missing residues. Is it possible to try and missing residue model the complete heptamer regardless due to my generated heptame exhibiting an unsatisfactory RMSD Value? Thanks

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Script to rank models by DOPE score
by Franceschini Ghilardi, Amanda (BIDMC - Lijun Sun - General Surg SF) 07 Sep '22

07 Sep '22

Hi, I generated 100 models of a protein and now I would like to select the 20 with the lowest DOPE score. I tried to use the script provided in the manual but it gave an error (see below). To generate the models (models were obtained sucessfully): # Comparative modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class import sys log.verbose() # request verbose output env = Environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True a = AutoModel(env, alnfile='ahr-mult.ali', knowns=('3f1o_pasA','3h7w_pasA','3h82_pasA'), sequence='AhR', assess_methods=(assess.DOPE)) a.starting_model= 1 # index of the first model a.ending_model = 100 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling To sort the models by DOPE score: # Comparative modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class import sys log.verbose() # request verbose output env = Environ() # create a new MODELLER environment to build this model in # Get a list of all successfully built models from a.output ok_models = [x for x in a.outputs if x['failure'] is None # Rank the models by DOPE score key = 'DOPE score' if sys.version_info[:2] == (2,3): ok_models.sort(lambda a,b: cmp(a[key], b[key])) else: ok_models.sort(key=lambda a: a[key]) # Get top model m = ok_models[0] print("Top model: %s (DOPE score %.3f)" % (m['name'], m[key])) Error shown: File "model-output.py", line 17 key = 'DOPE score' ^ SyntaxError: invalid syntax I also tried to combine the scripts as shown in the manual (same error): # Comparative modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class import sys log.verbose() # request verbose output env = Environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True a = AutoModel(env, alnfile='ahr-mult.ali', knowns=('3f1o_pasA','3h7w_pasA','3h82_pasA'), sequence='AhR', assess_methods=(assess.DOPE)) a.starting_model= 1 # index of the first model a.ending_model = 100 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling # Get a list of all succesfully built models from a.output ok_models = [x for x in a.outputs if x['failure'] is None # Rank the models by DOPE score key = 'DOPE score' if sys.version_info[:2] == (2,3): ok_models.sort(lambda a,b: cmp(a[key], b[key])) else: ok_models.sort(key=lambda a: a[key]) # Get top model m = ok_models[0] print("Top model: %s (DOPE score %.3f)" % (m['name'], m[key])) Error shown: File "model-output.py", line 27 key = 'DOPE score' ^ SyntaxError: invalid syntax Please, any help to fix this issue with python coding would be appreciated (I have both python 2.7.13rc1 and python 3.8.9 installed). Best, Amanda F. Ghilardi

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Missing Residue Modeling Indentation Error and A Not Defined Error Inquiry
by Joel Subach 07 Sep '22

07 Sep '22

Hello I am modeling missing residues and without moving the nonmissing residues and am receiving the below errors within my iTerm after copying and pasting in the bottom text. Please let me know how I can repair this script in my text file before pasting it in the iTerm to run? Thanks:) joelsubach@Joels-MacBook-Air 7dwbOPM_Monomer_LP % /usr/bin/python3 Python 3.8.9 (default, Apr 13 2022, 08:48:06) [Clang 13.1.6 (clang-1316.0.21.2.5)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from modeller import * >>> from modeller.automodel import * # Load the AutoModel class >>> >>> log.verbose() >>> env = Environ() MODELLER 10.3, 2022/07/08, r12388 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2022 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, Darwin Joels-MacBook-Air.local 21.6.0 arm64 Date and time of compilation : 2022/07/08 12:37:28 MODELLER executable type : mac11arm64-gnu Job starting time (YY/MM/DD HH:MM:SS): 2022/09/02 16:50:46 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL10v3}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL10v3}/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 ${MODINSTALL10v3}/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 ${MODINSTALL10v3}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL10v3}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL10v3}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL10v3}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL10v3}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL10v3}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL10v3}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 >>> >>> # directories for input atom files >>> env.io.atom_files_directory = ['.', '../atom_files'] >>> >>> class MyModel(AutoModel): ... def select_atoms(self): ... return Selection(self.residue_range('88:A', '99:A') ... ... a = MyModel(env, alnfile = 'alignment.ali', File "<stdin>", line 5 a = MyModel(env, alnfile = 'alignment.ali', ^ SyntaxError: invalid syntax >>> knowns = '7dwbOPM_chainA', sequence = '7dwbOPM_chainA_fill') File "<stdin>", line 1 knowns = '7dwbOPM_chainA', sequence = '7dwbOPM_chainA_fill') ^ IndentationError: unexpected indent >>> a.starting_model = 1 Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'a' is not defined >>> a.ending_model = 1 Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'a' is not defined >>> >>> a.make() TEXT FILE BELOW: from modeller import * from modeller.automodel import * # Load the AutoModel class log.verbose() env = Environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(AutoModel): def select_atoms(self): return Selection(self.residue_range('88:A', '99:A') a = MyModel(env, alnfile = 'alignment.ali', knowns = '7dwbOPM_chainA', sequence = '7dwbOPM_chainA_fill') a.starting_model = 1 a.ending_model = 1 a.make()

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HELP - Modeling the binding site in presence of ligands
by Franceschini Ghilardi, Amanda (BIDMC - Lijun Sun - General Surg SF) 31 Aug '22

31 Aug '22

Hi, I am having issues reproducing the Advanced Tutorial provided at https://salilab.org/modeller/tutorial/advanced.html I could not figure out how to write/fix a script to align the 1emd_bs.pdb template with the TvLDH model previously obtained. I have searched in the manual and I could not find how to generate a python script that will give the right alignment. My input files and script used are shown below: TvLDH PIR file obtained in the previous steps of the tutorial: >P1;4mdhA structureX:4mdh_fit.pdb:1:A:+333:A:MOL_ID 1; MOLECULE CYTOPLASMIC MALATE DEHYDROGENASE; CHAIN A, B; EC 1.1.1.37; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC SUS SCROFA; ORGANISM_COMMON PIG; ORGANISM_TAXID 9823: 2.50: 0.17 -SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITP--MMGVLDGVLMELQDCALPLLKDVIATDK EEIAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIP KENFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEF ITTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIIS-DGNSYGVPDDLLYSFPVTIK-DKT WKIVEGLPINDFSREKMDLTAKELAEEKETAFEFLSSA* >P1;1bdmA structureX:1bdm_fit.pdb:0:A:+318:A:MOL_ID 1; MOLECULE MALATE DEHYDROGENASE; CHAIN A, B; EC 1.1.1.37; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC THERMUS THERMOPHILUS; ORGANISM_TAXID 274; EXPRESSION_SYSTEM_VECTOR_TYPE BACTERIUM: 1.80: 0.17 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQ--AMKALEGVVMELEDCAFPLLAGLEATDD PDVAFKDADYALLVGAAPR---------LQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLN PRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSIMFPDLFHAEVD----GRPALELV-DMEWYEKVF IPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPS-QGE-YGIPEGIVYSFPVTAK-DGA YRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLI-* >P1;1b8pA structureX:1b8p_fit.pdb:3:A:+327:A:MOL_ID 1; MOLECULE PROTEIN (MALATE DEHYDROGENASE); CHAIN A:MOL_ID 1; ORGANISM_SCIENTIFIC AQUASPIRILLUM ARCTICUM; ORGANISM_TAXID 87645: 1.90: 0.17 -KTPMRVAVTGAAGQICYSLLFRIANGDMLGKDQPVILQLLEIPNEKAQKALQGVMMEIDDCAFPLLAGMTAHAD PMTAFKDADVALLVGARPRGPGMERKDLLEANAQIFTVQGKAIDAVASRNIKVLVVGNPANTNAYIAMKSAPSLP AKNFTAMLRLDHNRALSQIAAKTGKPVSSIEKLFVWGNHSPTMYADYRYAQID----GASVKDMINDDAWNRDTF LPTVGKRGAAIIDARGVSSAASAANAAIDHIHDWVLGTAG-KWTTMGIPS-DGS-YGIPEGVIFGFPVTTE-NGE YKIVQGLSIDAFSQERINVTLNELLEEQNGVQ-HLLG-* >P1;TvLDH sequence:TvLDH:: :: :::-1.00:-1.00 MSEPAHVLITGAAGQIGYILSHWIAGGELYG-DRPVVLHLFDIPP--AMNRLTALTMELEDCAFPHLAGYVATTE PEAAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPTVKVLVIGNPDNTNCEIAMLHAKNLK PENFSSLSMLDHNRAYYEVASKLGVHVHDIHDIIVWGNHGESMVADLTQATFTKDGKTQKVVDVL-DHDYVFDTF FKKIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGH IHVVEGFKVNDWLREKLAFTENDLFHEKEIALEHLAQ-* 1emd_bs.pdb: REMARK ************************************* REMARK ONLY RESIDUES FOR THE LOOP AND HETATM REMARK ************************************* HEADER OXIDOREDUCTASE(NAD(A)-CHOH(D)) 25-MAR-93 1EMD 1EMD 2 COMPND MALATE DEHYDROGENASE (E.C.1.1.1.37) 1EMD 3 SOURCE (ESCHERICHIA COLI) 1EMD 4 AUTHOR M.D.HALL,L.J.BANASZAK 1EMD 5 REVDAT 1 31-OCT-93 1EMD 0 1EMD 6 JRNL AUTH M.D.HALL,L.J.BANASZAK 1EMD 7 JRNL TITL CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF 1EMD 8 JRNL TITL 2 ESCHERICHIA $COLI MALATE DEHYDROGENASE, CITRATE 1EMD 9 JRNL TITL 3 AND /NAD$ AT 1.9 ANGSTROMS RESOLUTION 1EMD 10 JRNL REF TO BE PUBLISHED 1EMD 11 JRNL REFN 353 1EMD 12 ATOM 534 N GLY 78 12.415 -10.954 6.308 1.00 19.62 1EMD 636 ATOM 535 CA GLY 78 12.332 -11.837 7.468 1.00 20.84 1EMD 637 ATOM 536 C GLY 78 10.926 -12.368 7.753 1.00 21.39 1EMD 638 ATOM 537 O GLY 78 9.932 -11.883 7.199 1.00 21.67 1EMD 639 ATOM 538 N VAL 79 10.825 -13.294 8.701 1.00 19.80 1EMD 640 ATOM 539 CA VAL 79 9.547 -13.950 9.006 1.00 22.26 1EMD 641 ATOM 540 C VAL 79 8.741 -13.142 10.035 1.00 21.75 1EMD 642 ATOM 541 O VAL 79 9.336 -12.504 10.907 1.00 24.34 1EMD 643 ATOM 542 CB VAL 79 9.805 -15.379 9.566 1.00 21.55 1EMD 644 ATOM 543 CG1 VAL 79 8.515 -16.157 9.649 1.00 21.32 1EMD 645 ATOM 544 CG2 VAL 79 10.799 -16.117 8.667 1.00 23.69 1EMD 646 ATOM 545 N ARG 80 7.417 -13.094 9.877 1.00 24.64 1EMD 647 ATOM 546 CA ARG 80 6.491 -12.559 10.904 1.00 24.91 1EMD 648 ATOM 547 C ARG 80 6.222 -13.592 12.023 1.00 24.51 1EMD 649 ATOM 548 O ARG 80 6.188 -14.796 11.755 1.00 20.95 1EMD 650 ATOM 549 CB ARG 80 5.134 -12.195 10.291 1.00 23.85 1EMD 651 ATOM 550 CG ARG 80 5.168 -11.202 9.163 1.00 34.96 1EMD 652 ATOM 551 CD ARG 80 3.778 -10.566 8.908 1.00 36.03 1EMD 653 ATOM 552 NE ARG 80 3.447 -10.526 7.493 1.00 41.06 1EMD 654 ATOM 553 CZ ARG 80 2.212 -10.520 6.994 1.00 46.64 1EMD 655 ATOM 554 NH1 ARG 80 1.210 -9.982 7.683 1.00 47.32 1EMD 656 ATOM 555 NH2 ARG 80 2.022 -10.855 5.719 1.00 46.01 1EMD 657 ATOM 556 N ARG 81 5.878 -13.128 13.226 1.00 20.99 1EMD 658 ATOM 557 CA ARG 81 5.483 -14.067 14.275 1.00 21.55 1EMD 659 ATOM 558 C ARG 81 4.016 -14.475 14.207 1.00 19.83 1EMD 660 ATOM 559 O ARG 81 3.225 -13.901 13.451 1.00 18.35 1EMD 661 ATOM 560 CB ARG 81 5.829 -13.534 15.670 1.00 22.85 1EMD 662 ATOM 561 CG ARG 81 5.108 -12.260 16.093 1.00 23.92 1EMD 663 ATOM 562 CD ARG 81 5.550 -11.831 17.517 1.00 25.18 1EMD 664 ATOM 563 NE ARG 81 5.154 -10.458 17.835 1.00 22.76 1EMD 665 ATOM 564 CZ ARG 81 4.396 -10.096 18.865 1.00 23.94 1EMD 666 ATOM 565 NH1 ARG 81 4.084 -10.986 19.806 1.00 23.41 1EMD 667 ATOM 566 NH2 ARG 81 4.030 -8.821 19.002 1.00 17.44 1EMD 668 ATOM 567 N LYS 82 3.715 -15.609 14.827 1.00 20.02 1EMD 669 ATOM 568 CA LYS 82 2.343 -16.116 14.887 1.00 22.20 1EMD 670 ATOM 569 C LYS 82 1.786 -15.902 16.307 1.00 19.41 1EMD 671 ATOM 570 O LYS 82 2.571 -15.795 17.255 1.00 19.35 1EMD 672 ATOM 571 CB LYS 82 2.339 -17.613 14.527 1.00 27.09 1EMD 673 ATOM 572 CG LYS 82 2.269 -17.880 13.018 1.00 35.82 1EMD 674 ATOM 573 CD LYS 82 1.936 -19.341 12.681 1.00 41.18 1EMD 675 ATOM 574 CE LYS 82 1.569 -19.525 11.183 1.00 44.85 1EMD 676 ATOM 575 NZ LYS 82 0.273 -18.882 10.777 1.00 44.18 1EMD 677 ATOM 576 N PRO 83 0.442 -15.943 16.487 1.00 15.65 1EMD 678 ATOM 577 CA PRO 83 -0.191 -15.844 17.819 1.00 18.45 1EMD 679 ATOM 578 C PRO 83 0.401 -16.773 18.889 1.00 20.34 1EMD 680 ATOM 579 O PRO 83 0.664 -17.949 18.625 1.00 24.22 1EMD 681 ATOM 580 CB PRO 83 -1.659 -16.164 17.541 1.00 17.53 1EMD 682 ATOM 581 CG PRO 83 -1.852 -15.763 16.104 1.00 16.27 1EMD 683 ATOM 582 CD PRO 83 -0.562 -16.221 15.450 1.00 17.44 1EMD 684 ATOM 583 N GLY 84 0.746 -16.207 20.043 1.00 18.01 1EMD 685 ATOM 584 CA GLY 84 1.412 -16.995 21.055 1.00 16.89 1EMD 686 ATOM 585 C GLY 84 2.918 -16.853 21.039 1.00 21.24 1EMD 687 ATOM 586 O GLY 84 3.569 -17.305 21.983 1.00 21.18 1EMD 688 ATOM 587 N MET 85 3.479 -16.191 20.016 1.00 20.08 1EMD 689 ATOM 588 CA MET 85 4.937 -15.916 19.967 1.00 21.41 1EMD 690 ATOM 589 C MET 85 5.332 -14.519 20.459 1.00 19.19 1EMD 691 ATOM 590 O MET 85 4.603 -13.552 20.260 1.00 23.12 1EMD 692 ATOM 591 CB MET 85 5.491 -16.067 18.541 1.00 22.93 1EMD 693 ATOM 592 CG MET 85 5.887 -17.470 18.134 1.00 29.87 1EMD 694 ATOM 593 SD MET 85 6.012 -17.637 16.320 1.00 30.30 1EMD 695 ATOM 594 CE MET 85 7.646 -17.066 16.101 1.00 31.32 1EMD 696 ATOM 595 N ASP 86 6.552 -14.406 20.963 1.00 17.83 1EMD 697 ATOM 596 CA ASP 86 7.184 -13.110 21.212 1.00 20.54 1EMD 698 ATOM 597 C ASP 86 8.110 -12.747 20.044 1.00 22.97 1EMD 699 ATOM 598 O ASP 86 8.672 -13.635 19.391 1.00 22.20 1EMD 700 ATOM 599 CB ASP 86 8.016 -13.169 22.507 1.00 20.52 1EMD 701 ATOM 600 CG ASP 86 8.225 -11.792 23.154 1.00 23.20 1EMD 702 ATOM 601 OD1 ASP 86 7.632 -10.786 22.697 1.00 27.60 1EMD 703 ATOM 602 OD2 ASP 86 8.990 -11.721 24.142 1.00 25.53 1EMD 704 ATOM 603 N ARG 87 8.434 -11.463 19.938 1.00 20.11 1EMD 705 ATOM 604 CA ARG 87 9.378 -10.982 18.935 1.00 20.92 1EMD 706 ATOM 605 C ARG 87 10.737 -11.683 19.009 1.00 20.37 1EMD 707 ATOM 606 O ARG 87 11.265 -12.128 17.995 1.00 18.28 1EMD 708 ATOM 607 CB ARG 87 9.522 -9.443 19.028 1.00 21.05 1EMD 709 ATOM 608 CG ARG 87 8.153 -8.730 18.869 1.00 19.50 1EMD 710 ATOM 609 CD ARG 87 8.201 -7.351 18.181 1.00 21.27 1EMD 711 ATOM 610 NE ARG 87 7.855 -6.298 19.115 1.00 22.81 1EMD 712 ATOM 611 CZ ARG 87 6.649 -6.119 19.658 1.00 21.38 1EMD 713 ATOM 612 NH1 ARG 87 6.585 -6.030 20.976 1.00 20.02 1EMD 714 ATOM 613 NH2 ARG 87 5.692 -5.506 18.970 1.00 16.21 1EMD 715 ATOM 614 N SER 88 11.200 -11.953 20.221 1.00 17.44 1EMD 716 ATOM 615 CA SER 88 12.476 -12.622 20.409 1.00 15.95 1EMD 717 ATOM 616 C SER 88 12.458 -14.053 19.873 1.00 16.93 1EMD 718 ATOM 617 O SER 88 13.508 -14.648 19.641 1.00 16.56 1EMD 719 ATOM 618 CB SER 88 12.819 -12.656 21.893 1.00 17.62 1EMD 720 ATOM 619 OG SER 88 11.750 -13.252 22.622 1.00 19.78 1EMD 721 ATOM 620 N ASP 89 11.271 -14.635 19.751 1.00 19.87 1EMD 722 ATOM 621 CA ASP 89 11.143 -15.996 19.228 1.00 21.29 1EMD 723 ATOM 622 C ASP 89 11.535 -16.061 17.750 1.00 23.26 1EMD 724 ATOM 623 O ASP 89 11.811 -17.137 17.216 1.00 21.43 1EMD 725 ATOM 624 CB ASP 89 9.702 -16.521 19.387 1.00 22.42 1EMD 726 ATOM 625 CG ASP 89 9.309 -16.759 20.850 1.00 25.19 1EMD 727 ATOM 626 OD1 ASP 89 10.197 -16.861 21.729 1.00 27.62 1EMD 728 ATOM 627 OD2 ASP 89 8.098 -16.832 21.123 1.00 27.76 1EMD 729 ATOM 628 N LEU 90 11.557 -14.898 17.099 1.00 24.46 1EMD 730 ATOM 629 CA LEU 90 11.942 -14.779 15.684 1.00 21.27 1EMD 731 ATOM 630 C LEU 90 13.467 -14.806 15.447 1.00 21.75 1EMD 732 ATOM 631 O LEU 90 13.917 -14.842 14.304 1.00 22.38 1EMD 733 ATOM 632 CB LEU 90 11.365 -13.484 15.129 1.00 16.46 1EMD 734 ATOM 633 CG LEU 90 10.124 -13.467 14.239 1.00 20.89 1EMD 735 ATOM 634 CD1 LEU 90 9.275 -14.694 14.402 1.00 19.81 1EMD 736 ATOM 635 CD2 LEU 90 9.342 -12.206 14.534 1.00 16.02 1EMD 737 ATOM 636 N PHE 91 14.263 -14.832 16.515 1.00 19.41 1EMD 738 ATOM 637 CA PHE 91 15.719 -14.757 16.387 1.00 22.11 1EMD 739 ATOM 638 C PHE 91 16.297 -15.856 15.490 1.00 23.27 1EMD 740 ATOM 639 O PHE 91 17.241 -15.627 14.745 1.00 22.74 1EMD 741 ATOM 640 CB PHE 91 16.386 -14.817 17.771 1.00 18.27 1EMD 742 ATOM 641 CG PHE 91 17.899 -14.817 17.730 1.00 19.04 1EMD 743 ATOM 642 CD1 PHE 91 18.606 -13.639 17.603 1.00 17.32 1EMD 744 ATOM 643 CD2 PHE 91 18.613 -15.993 17.892 1.00 22.27 1EMD 745 ATOM 644 CE1 PHE 91 19.991 -13.630 17.648 1.00 19.66 1EMD 746 ATOM 645 CE2 PHE 91 20.012 -15.989 17.944 1.00 20.80 1EMD 747 ATOM 646 CZ PHE 91 20.695 -14.808 17.828 1.00 19.38 1EMD 748 ATOM 647 N ASN 92 15.782 -17.069 15.609 1.00 25.49 1EMD 749 ATOM 648 CA ASN 92 16.399 -18.190 14.914 1.00 29.89 1EMD 750 ATOM 649 C ASN 92 16.228 -18.186 13.390 1.00 28.92 1EMD 751 ATOM 650 O ASN 92 17.150 -18.530 12.651 1.00 30.89 1EMD 752 ATOM 651 CB ASN 92 15.902 -19.494 15.516 1.00 32.12 1EMD 753 ATOM 652 CG ASN 92 16.384 -19.669 16.933 1.00 40.04 1EMD 754 ATOM 653 OD1 ASN 92 15.870 -19.019 17.842 1.00 44.62 1EMD 755 ATOM 654 ND2 ASN 92 17.518 -20.331 17.091 1.00 39.01 1EMD 756 ATOM 655 N VAL 93 15.102 -17.688 12.912 1.00 26.82 1EMD 757 ATOM 656 CA VAL 93 14.928 -17.537 11.475 1.00 28.41 1EMD 758 ATOM 657 C VAL 93 15.587 -16.273 10.879 1.00 29.43 1EMD 759 ATOM 658 O VAL 93 16.210 -16.345 9.815 1.00 32.33 1EMD 760 ATOM 659 CB VAL 93 13.435 -17.572 11.103 1.00 30.48 1EMD 761 ATOM 660 CG1 VAL 93 12.859 -18.932 11.445 1.00 30.99 1EMD 762 ATOM 661 CG2 VAL 93 12.666 -16.482 11.853 1.00 33.80 1EMD 763 ATOM 662 N ASN 94 15.598 -15.174 11.640 1.00 23.64 1EMD 764 ATOM 663 CA ASN 94 15.856 -13.845 11.070 1.00 22.04 1EMD 765 ATOM 664 C ASN 94 17.288 -13.345 11.260 1.00 20.44 1EMD 766 ATOM 665 O ASN 94 17.744 -12.481 10.513 1.00 22.53 1EMD 767 ATOM 666 CB ASN 94 14.873 -12.790 11.638 1.00 18.80 1EMD 768 ATOM 667 CG ASN 94 13.477 -12.874 11.030 1.00 17.17 1EMD 769 ATOM 668 OD1 ASN 94 13.214 -13.646 10.109 1.00 21.51 1EMD 770 ATOM 669 ND2 ASN 94 12.584 -12.050 11.523 1.00 15.87 1EMD 771 TER 670 ASN 94 1EMD2381 HETATM 2280 C1 LAC 313 5.426 -7.608 15.720 1.00 25.43 1EMD2382 HETATM 2281 O1A LAC 313 4.760 -7.292 16.696 1.00 22.77 1EMD2383 HETATM 2282 O1B LAC 313 5.710 -8.783 15.470 1.00 23.22 1EMD2384 HETATM 2283 C2 LAC 313 5.220 -6.691 14.572 1.00 22.61 1EMD2385 HETATM 2285 O2 LAC 313 7.150 -5.379 15.668 1.00 20.35 1EMD2387 HETATM 2284 C3 LAC 313 5.865 -5.268 14.934 1.00 23.43 1EMD2386 HETATM 2293 AP NAD 314 6.405 -11.130 4.954 0.69 26.19 1EMD2395 HETATM 2294 AO1 NAD 314 6.596 -12.584 5.180 0.69 27.85 1EMD2396 HETATM 2295 AO2 NAD 314 5.164 -10.631 4.350 0.69 19.49 1EMD2397 HETATM 2296 AO5* NAD 314 7.698 -10.375 4.274 0.69 28.25 1EMD2398 HETATM 2297 AC5* NAD 314 9.100 -10.752 4.424 0.69 26.99 1EMD2399 HETATM 2298 AC4* NAD 314 9.908 -10.815 3.112 0.69 30.23 1EMD2400 HETATM 2299 AO4* NAD 314 11.245 -11.256 3.417 0.69 29.14 1EMD2401 HETATM 2300 AC3* NAD 314 9.377 -11.852 2.102 0.69 30.36 1EMD2402 HETATM 2301 AO3* NAD 314 8.918 -11.300 0.864 0.69 31.71 1EMD2403 HETATM 2302 AC2* NAD 314 10.516 -12.828 1.856 0.69 30.56 1EMD2404 HETATM 2303 AO2* NAD 314 10.532 -13.467 0.558 0.69 32.13 1EMD2405 HETATM 2304 AC1* NAD 314 11.642 -11.888 2.199 0.69 29.49 1EMD2406 HETATM 2305 AN9 NAD 314 12.946 -12.548 2.294 0.69 30.68 1EMD2407 HETATM 2306 AC8 NAD 314 13.403 -13.455 3.186 0.69 30.38 1EMD2408 HETATM 2307 AN7 NAD 314 14.746 -13.503 3.170 0.69 29.26 1EMD2409 HETATM 2308 AC5 NAD 314 15.076 -12.598 2.249 0.69 30.31 1EMD2410 HETATM 2309 AC6 NAD 314 16.347 -12.115 2.003 0.69 27.98 1EMD2411 HETATM 2310 AN6 NAD 314 17.465 -12.733 2.307 0.69 26.75 1EMD2412 HETATM 2311 AN1 NAD 314 16.406 -11.054 1.195 0.69 30.45 1EMD2413 HETATM 2312 AC2 NAD 314 15.323 -10.531 0.634 0.69 29.90 1EMD2414 HETATM 2313 AN3 NAD 314 14.102 -10.997 0.817 0.69 30.17 1EMD2415 HETATM 2314 AC4 NAD 314 13.972 -12.018 1.668 0.69 30.56 1EMD2416 HETATM 2315 O3 NAD 314 6.470 -10.585 6.442 0.69 25.22 1EMD2417 HETATM 2316 NP NAD 314 6.574 -9.067 6.899 0.69 29.30 1EMD2418 HETATM 2317 NO1 NAD 314 5.404 -8.704 7.740 0.69 22.95 1EMD2419 HETATM 2318 NO2 NAD 314 6.770 -8.191 5.717 0.69 18.36 1EMD2420 HETATM 2319 NO5* NAD 314 7.869 -9.394 7.848 0.69 23.27 1EMD2421 HETATM 2320 NC5* NAD 314 8.765 -8.341 8.225 0.69 27.18 1EMD2422 HETATM 2321 NC4* NAD 314 9.965 -8.616 9.126 0.69 28.17 1EMD2423 HETATM 2322 NO4* NAD 314 10.320 -7.290 9.589 0.69 33.05 1EMD2424 HETATM 2323 NC3* NAD 314 9.643 -9.373 10.416 0.69 28.95 1EMD2425 HETATM 2324 NO3* NAD 314 10.803 -9.831 11.132 0.69 19.79 1EMD2426 HETATM 2325 NC2* NAD 314 8.983 -8.282 11.258 0.69 32.60 1EMD2427 HETATM 2326 NO2* NAD 314 8.693 -8.760 12.602 0.69 31.87 1EMD2428 HETATM 2327 NC1* NAD 314 10.080 -7.227 11.022 0.69 34.45 1EMD2429 HETATM 2328 NN1 NAD 314 9.747 -5.837 11.353 0.69 40.34 1EMD2430 HETATM 2329 NC2 NAD 314 10.008 -5.147 12.560 0.69 44.29 1EMD2431 HETATM 2330 NC3 NAD 314 9.629 -3.816 12.717 0.69 44.76 1EMD2432 HETATM 2331 NC7 NAD 314 9.879 -3.032 13.977 0.69 44.86 1EMD2433 HETATM 2332 NO7 NAD 314 9.185 -2.066 14.289 0.69 48.45 1EMD2434 HETATM 2333 NN7 NAD 314 10.925 -3.436 14.647 0.69 42.75 1EMD2435 HETATM 2334 NC4 NAD 314 8.913 -3.178 11.754 0.69 45.41 1EMD2436 HETATM 2335 NC5 NAD 314 8.584 -3.871 10.603 0.69 45.19 1EMD2437 HETATM 2336 NC6 NAD 314 9.015 -5.178 10.398 0.69 42.63 1EMD2438 END 1EMD2583 Python script to align template to the model: from modeller import * env = Environ() aln = Alignment(env) mdl = Model(env, file='1emd_bs', model_segment=('78','94')) aln.append_model(mdl, align_codes='1emdA', atom_files='1emd.pdb') aln.append(file='TvLDH-mult.ali', align_codes='TvLDH') env.io.hetatm = True aln.align2d(max_gap_length=50) aln.write(file='TvLDH-ligand.ali', alignment_format='PIR') aln.write(file='TvLDH-ligand.pap', alignment_format='PAP') Output PAP file: _aln.pos 10 20 30 40 50 60 1emdA ----------GV--------------------R--------------R-------------------- TvLDH MSEPAHVLITGAAGQIGYILSHWIAGGELYGDRPVVLHLFDIPPAMNRLTALTMELEDCAFPHLAGYV _consrvd * * * _aln.p 70 80 90 100 110 120 130 1emdA -----------------------KPG------------------------------------------ TvLDH ATTEPEAAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPTVKVLVIGNPDNTNC _consrvd *** _aln.pos 140 150 160 170 180 190 200 1emdA ---M-------------------DR------------------------------SDL---------- TvLDH EIAMLHAKNLKPENFSSLSMLDHNRAYYEVASKLGVHVHDIHDIIVWGNHGESMVADLTQATFTKDGK _consrvd * * ** _aln.pos 210 220 230 240 250 260 270 1emdA ---------------------------------F---------------------------------- TvLDH TQKVVDVLDHDYVFDTFFKKIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVP _consrvd * _aln.pos 280 290 300 310 320 330 1emdA --N-----------------------------VN--------------------------- TvLDH EGNPYGIKPGVVFSFPCNVDKEGHIHVVEGFKVNDWLREKLAFTENDLFHEKEIALEHLAQ _consrvd * ** Output PIR file: >P1;1emdA structureX:1emd.pdb:78: :+17: :MALATE DEHYDROGENASE (E.C.1.1.1.37):(ESCHERICHIA COLI):-1.00:-1.00 ----------GV--------------------R--------------R--------------------------- ----------------KPG---------------------------------------------M---------- ---------DR------------------------------SDL------------------------------- ------------F------------------------------------N------------------------- ----VN---------------------------* >P1;TvLDH sequence:TvLDH:: :: :::-1.00:-1.00 MSEPAHVLITGAAGQIGYILSHWIAGGELYGDRPVVLHLFDIPPAMNRLTALTMELEDCAFPHLAGYVATTEPEA AFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPTVKVLVIGNPDNTNCEIAMLHAKNLKPEN FSSLSMLDHNRAYYEVASKLGVHVHDIHDIIVWGNHGESMVADLTQATFTKDGKTQKVVDVLDHDYVFDTFFKKI GHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGHIHVV EGFKVNDWLREKLAFTENDLFHEKEIALEHLAQ* Best Regards, Amanda F. Ghilardi

2 1

Missing Residues Modeling for an Oligomer Inquiry
by Joel Subach 30 Aug '22

30 Aug '22

Hello, I am trying to model missing residues for a heptamer via the below Modeller link, is Modeller able to model these 12-missing residues in each of the seven exterior cytoplasmic loop-regions via a properly formatted alignment.ali file or would modeling just the missing residues for a single monomer work best for Modeller? (I would then oligomerize the complete monomer elsewhere.) * I had read the below on the Modeller Forum that Modeller may not have the monomer interface modeling ability hence my inquiry. *https://salilab.org/modeller/wiki/Missing_residues <https://salilab.org/modeller/wiki/Missing_residues>*

2 2

Missing Residues Script File Inquiry
by Joel Subach 27 Aug '22

27 Aug '22

Hello must I create the script files to fill in missing residues? If not where would they be? Thanks:) Joel

2 4

Modeller 10.3 release
by Modeller Caretaker 13 Jul '22

13 Jul '22

A new version of Modeller, 10.3, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 10.3 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.3 is a minor update that fixes the mod10.3 compatibility script on macOS Monterey 12.3 or later (this script uses Python 2, which Apple removed in their 12.3 update). There are no changes for Linux or Windows systems relative to the 10.2 release. If you encounter bugs in Modeller 10.3, please see https://salilab.org/modeller/10.3/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply unsubscribe from the modeller_announce mailing list, or reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

1 0

refine a loop in a multi-chain complex
by Li Xue 11 Jul '22

11 Jul '22

Hello, I am trying to refine a loop in a multi-chain complex. During the refinement/remodelling phase of the loop, does modeller molPDF include non-bonded energies between chains? Or it will only include the energies within the loop? Many thanks. Best, Li

2 1

Error in multichain modeller
by Zara Saeed 23 Jun '22

23 Jun '22

I am using the following python file for multichain modelling. I am sending you my script, structure file and alignment file in the attachment. When I run this script it gives the following error. *raise KeyError("No such chain: %s" % indx)* *KeyError: 'No such chain: F'* I read about it in the modeller 's problem and came to know that it can be due to unavailability of chain breaker. But as you can see in my ali. file chain breaker is present in sequence. Can you identify the problem please? Best regards, zeenat

2 1

(no subject)
by LEE Seayoung 15 Jun '22

15 Jun '22

Dear Whom it may concern, I am writing this email to request you a suggestion about settings in Modeller. Currently, I have trouble in running Modeller program. It seems like the program doesn't have the right Pythonpath. In the error message, it says that referring to modv10, the pythonpath is system/library/framework........ and it turns out that corresponding file doesn't exist. I am using iMac (version12.4) and I need to use Modeller10.2. Would you please suggest me to resolve this problem? Thank you Sincerely Seayoung LEE

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