[modeller_usage] HELP - Modeling the binding site in presence of ligands

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