Dear Dr. Andras Fiser,
Thank you for your suggestion. Yes, after I add SET FINAL_MALIGN3D = 1 in the top file, the final model is much close to the template, but still not superposed, but this is not the main problem.
I also noticed that the backbone conformation of the model and the template is different. This is what I would like to overcome if possible. Probably I missed something in my top file if modeller can do this kind of work. Here is my top file.
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL= 1 1 1 1 SET ALNFILE = 'peptide_1.ali' # alignment filename SET KNOWNS = '1dkxB' # codes of the templates SET SEQUENCE = 'peptide_1' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom fileSET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate)
CALL ROUTINE = 'model' # do homology modelling
SET FINAL_MALIGN3D = 1
And I also attached the model and template.
Thank you for your time.
Sincerely,
Xiao-Ping Zhang
Andras Fiser wrote:
> Hi > > STARTING and ENDING model variables define how many models to generate. Because > the structure optimization is stochastic (MD simulation) you can expect minor > differences among different structures, especially if you have such regions in > the structure which are not very well defined by restraints (segments with > insertions, vicinity of deletions or loosely defined substrates relative to > the template etc.). > > These variables also define the extension of your model files as it was noted > by Azat: technically it is useful if you run modeling under different > circumstances, e.g. generate 10 models with one ligand between 1-10, than > generate 10 models using different ligand or templates (Starting MODEL=11, > ENDING_MODEL=20) etc. > > > I am modeling a very short peptide with modeller4. If I set > > STARTING_MODEL=1, ENDING_MODEL=10, I get 10 models which have different > > orientations and spatial location. If I would like to get a model which > > can overlap with the original model (maximum uses the template > > coordinates), how to do it? And is it possible to keep the backbone in > > the same conformation of original peptide ? > > if you include in your top file: > SET FINAL_MALIGN3D = 1 > > modeller will automatically superpose all your models onto the template and > generate the *fit files which contains strcutures whith supeprosed coordinates. > > or you can write a short top script to superpose any number of structures from > any sources generated, as explained in the manual under MALIGN3D and SUPERPOSE > commands. > > Andras > > -- > , > Andras Fiser, PhD # phone: (212) 327 7206 > The Rockefeller University # fax: (212) 327 7540 > Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu > New York, NY 10021-6399, USA # http://salilab.org/~andras
****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden
Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se
ATOM 1666 N ASN B 1 50.702 87.722 38.867 1.00 43.10 N ATOM 1667 CA ASN B 1 51.449 86.814 37.946 1.00 41.67 C ATOM 1668 C ASN B 1 51.328 87.331 36.498 1.00 39.68 C ATOM 1669 O ASN B 1 50.267 87.216 35.865 1.00 39.73 O ATOM 1670 CB ASN B 1 50.874 85.389 38.031 1.00 44.13 C ATOM 1671 CG ASN B 1 50.750 84.878 39.468 1.00 46.27 C ATOM 1672 OD1 ASN B 1 50.338 85.626 40.353 1.00 46.16 O ATOM 1673 ND2 ASN B 1 51.084 83.634 39.757 1.00 45.47 N ATOM 1674 N ARG B 2 52.433 87.895 36.025 1.00 36.65 N ATOM 1675 CA ARG B 2 52.555 88.448 34.656 1.00 32.06 C ATOM 1676 C ARG B 2 53.586 87.620 33.873 1.00 28.54 C ATOM 1677 O ARG B 2 54.665 87.294 34.387 1.00 25.94 O ATOM 1678 CB ARG B 2 53.006 89.911 34.728 1.00 36.71 C ATOM 1679 CG ARG B 2 52.282 90.816 33.727 1.00 41.73 C ATOM 1680 CD ARG B 2 50.777 90.927 33.989 1.00 44.15 C ATOM 1681 NE ARG B 2 50.050 91.548 32.870 1.00 47.60 N ATOM 1682 CZ ARG B 2 48.751 91.877 32.904 1.00 47.23 C ATOM 1683 NH1 ARG B 2 48.009 91.654 33.997 1.00 49.83 N ATOM 1684 NH2 ARG B 2 48.094 92.442 31.880 1.00 44.33 N ATOM 1685 N LEU B 3 53.236 87.297 32.635 1.00 25.64 N ATOM 1686 CA LEU B 3 54.079 86.438 31.778 1.00 22.32 C ATOM 1687 C LEU B 3 54.737 87.207 30.621 1.00 22.74 C ATOM 1688 O LEU B 3 54.225 88.243 30.169 1.00 22.20 O ATOM 1689 CB LEU B 3 53.235 85.323 31.158 1.00 18.68 C ATOM 1690 CG LEU B 3 52.213 84.739 32.134 1.00 19.46 C ATOM 1691 CD1 LEU B 3 51.449 83.546 31.556 1.00 20.46 C ATOM 1692 CD2 LEU B 3 52.846 84.236 33.433 1.00 15.12 C ATOM 1693 N LEU B 4 55.858 86.627 30.205 1.00 20.92 N ATOM 1694 CA LEU B 4 56.688 87.110 29.086 1.00 23.64 C ATOM 1695 C LEU B 4 56.790 86.014 28.021 1.00 27.49 C ATOM 1696 O LEU B 4 56.680 84.818 28.324 1.00 28.91 O ATOM 1697 CB LEU B 4 58.117 87.414 29.559 1.00 25.41 C ATOM 1698 CG LEU B 4 58.192 88.438 30.690 1.00 24.73 C ATOM 1699 CD1 LEU B 4 59.616 88.631 31.223 1.00 24.26 C ATOM 1700 CD2 LEU B 4 57.716 89.830 30.272 1.00 24.71 C ATOM 1701 N LEU B 5 57.000 86.447 26.792 1.00 29.48 N ATOM 1702 CA LEU B 5 57.145 85.533 25.643 1.00 30.37 C ATOM 1703 C LEU B 5 58.628 85.360 25.284 1.00 31.29 C ATOM 1704 O LEU B 5 59.481 86.132 25.727 1.00 27.62 O ATOM 1705 CB LEU B 5 56.468 86.114 24.395 1.00 32.09 C ATOM 1706 CG LEU B 5 55.053 86.640 24.629 1.00 35.07 C ATOM 1707 CD1 LEU B 5 54.403 87.181 23.350 1.00 40.10 C ATOM 1708 CD2 LEU B 5 54.100 85.569 25.156 1.00 38.35 C ATOM 1709 N THR B 6 58.897 84.333 24.478 1.00 36.46 N ATOM 1710 CA THR B 6 60.264 84.053 23.927 1.00 44.50 C ATOM 1711 C THR B 6 60.360 84.677 22.466 1.00 47.61 C ATOM 1712 O THR B 6 59.699 84.184 21.554 1.00 48.64 O ATOM 1713 CB THR B 6 60.477 82.528 23.817 1.00 47.63 C ATOM 1714 OG1 THR B 6 59.676 81.818 24.755 1.00 53.22 O ATOM 1715 CG2 THR B 6 61.928 82.107 24.047 1.00 48.63 C ATOM 1716 N GLY B 7 61.232 85.767 22.212 1.00 50.38 N ATOM 1717 CA GLY B 7 61.334 86.583 20.844 1.00 51.64 C ATOM 1718 C GLY B 7 62.588 86.267 20.033 1.00 53.33 C ATOM 1719 O GLY B 7 63.180 85.187 20.170 1.00 53.27 O ATOM 1720 OXT GLY B 7 62.917 87.254 19.203 1.00 53.00 O
REMARK Produced by MODELLER: unknown unknown 1 ATOM 1666 N ASN B 1 50.702 87.722 38.867 1.00 43.10 N ATOM 1667 CA ASN B 1 51.449 86.814 37.946 1.00 41.67 C ATOM 1668 C ASN B 1 51.328 87.331 36.498 1.00 39.68 C ATOM 1669 O ASN B 1 50.267 87.216 35.865 1.00 39.73 O ATOM 1670 CB ASN B 1 50.874 85.389 38.031 1.00 44.13 C ATOM 1671 CG ASN B 1 50.750 84.878 39.468 1.00 46.27 C ATOM 1672 OD1 ASN B 1 50.338 85.626 40.353 1.00 46.16 O ATOM 1673 ND2 ASN B 1 51.084 83.634 39.757 1.00 45.47 N ATOM 1674 N ARG B 2 52.433 87.895 36.025 1.00 36.65 N ATOM 1675 CA ARG B 2 52.555 88.448 34.656 1.00 32.06 C ATOM 1676 C ARG B 2 53.586 87.620 33.873 1.00 28.54 C ATOM 1677 O ARG B 2 54.665 87.294 34.387 1.00 25.94 O ATOM 1678 CB ARG B 2 53.006 89.911 34.728 1.00 36.71 C ATOM 1679 CG ARG B 2 52.282 90.816 33.727 1.00 41.73 C ATOM 1680 CD ARG B 2 50.777 90.927 33.989 1.00 44.15 C ATOM 1681 NE ARG B 2 50.050 91.548 32.870 1.00 47.60 N ATOM 1682 CZ ARG B 2 48.751 91.877 32.904 1.00 47.23 C ATOM 1683 NH1 ARG B 2 48.009 91.654 33.997 1.00 49.83 N ATOM 1684 NH2 ARG B 2 48.094 92.442 31.880 1.00 44.33 N ATOM 1685 N LEU B 3 53.236 87.297 32.635 1.00 25.64 N ATOM 1686 CA LEU B 3 54.079 86.438 31.778 1.00 22.32 C ATOM 1687 C LEU B 3 54.737 87.207 30.621 1.00 22.74 C ATOM 1688 O LEU B 3 54.225 88.243 30.169 1.00 22.20 O ATOM 1689 CB LEU B 3 53.235 85.323 31.158 1.00 18.68 C ATOM 1690 CG LEU B 3 52.213 84.739 32.134 1.00 19.46 C ATOM 1691 CD1 LEU B 3 51.449 83.546 31.556 1.00 20.46 C ATOM 1692 CD2 LEU B 3 52.846 84.236 33.433 1.00 15.12 C ATOM 1693 N LEU B 4 55.858 86.627 30.205 1.00 20.92 N ATOM 1694 CA LEU B 4 56.688 87.110 29.086 1.00 23.64 C ATOM 1695 C LEU B 4 56.790 86.014 28.021 1.00 27.49 C ATOM 1696 O LEU B 4 56.680 84.818 28.324 1.00 28.91 O ATOM 1697 CB LEU B 4 58.117 87.414 29.559 1.00 25.41 C ATOM 1698 CG LEU B 4 58.192 88.438 30.690 1.00 24.73 C ATOM 1699 CD1 LEU B 4 59.616 88.631 31.223 1.00 24.26 C ATOM 1700 CD2 LEU B 4 57.716 89.830 30.272 1.00 24.71 C ATOM 1701 N LEU B 5 57.000 86.447 26.792 1.00 29.48 N ATOM 1702 CA LEU B 5 57.145 85.533 25.643 1.00 30.37 C ATOM 1703 C LEU B 5 58.628 85.360 25.284 1.00 31.29 C ATOM 1704 O LEU B 5 59.481 86.132 25.727 1.00 27.62 O ATOM 1705 CB LEU B 5 56.468 86.114 24.395 1.00 32.09 C ATOM 1706 CG LEU B 5 55.053 86.640 24.629 1.00 35.07 C ATOM 1707 CD1 LEU B 5 54.403 87.181 23.350 1.00 40.10 C ATOM 1708 CD2 LEU B 5 54.100 85.569 25.156 1.00 38.35 C ATOM 1709 N THR B 6 58.897 84.333 24.478 1.00 36.46 N ATOM 1710 CA THR B 6 60.264 84.053 23.927 1.00 44.50 C ATOM 1711 C THR B 6 60.360 84.677 22.466 1.00 47.61 C ATOM 1712 O THR B 6 59.699 84.184 21.554 1.00 48.64 O ATOM 1713 CB THR B 6 60.477 82.528 23.817 1.00 47.63 C ATOM 1714 OG1 THR B 6 59.676 81.818 24.755 1.00 53.22 O ATOM 1715 CG2 THR B 6 61.928 82.107 24.047 1.00 48.63 C ATOM 1716 N GLY B 7 61.232 85.767 22.212 1.00 50.38 N ATOM 1717 CA GLY B 7 61.334 86.583 20.844 1.00 51.64 C ATOM 1718 C GLY B 7 62.588 86.267 20.033 1.00 53.33 C ATOM 1719 O GLY B 7 63.180 85.187 20.170 1.00 53.27 O ATOM 1720 OXT GLY B 7 62.917 87.254 19.203 1.00 53.00 O
REMARK Produced by MODELLER: unknown unknown 1 REMARK Produced by MODELLER: unknown unknown 1 REMARK MODELLER OBJECTIVE FUNCTION: 26.9688 ATOM 1 N LEU 1 55.010 84.333 35.414 1.00 .65 1SG 2 ATOM 2 CA LEU 1 53.968 85.226 35.960 1.00 .65 1SG 3 ATOM 3 CB LEU 1 54.576 86.546 36.460 1.00 .65 1SG 4 ATOM 4 CG LEU 1 55.517 86.395 37.669 1.00 .65 1SG 5 ATOM 5 CD2 LEU 1 55.807 87.761 38.311 1.00 .65 1SG 6 ATOM 6 CD1 LEU 1 56.797 85.616 37.318 1.00 .65 1SG 7 ATOM 7 C LEU 1 52.984 85.564 34.899 1.00 .65 1SG 8 ATOM 8 O LEU 1 52.463 84.686 34.216 1.00 .65 1SG 9 ATOM 9 N ARG 2 52.699 86.870 34.759 1.00 .93 1SG 10 ATOM 10 CA ARG 2 51.769 87.286 33.762 1.00 .93 1SG 11 ATOM 11 CB ARG 2 51.341 88.752 33.924 1.00 .93 1SG 12 ATOM 12 CG ARG 2 49.987 89.081 33.293 1.00 .93 1SG 13 ATOM 13 CD ARG 2 48.810 88.536 34.111 1.00 .93 1SG 14 ATOM 14 NE ARG 2 48.986 89.024 35.510 1.00 .93 1SG 15 ATOM 15 CZ ARG 2 48.532 90.257 35.886 1.00 .93 1SG 16 ATOM 16 NH1 ARG 2 47.868 91.051 34.997 1.00 .93 1SG 17 ATOM 17 NH2 ARG 2 48.729 90.696 37.163 1.00 .93 1SG 18 ATOM 18 C ARG 2 52.490 87.139 32.464 1.00 .93 1SG 19 ATOM 19 O ARG 2 53.008 86.065 32.159 1.00 .93 1SG 20 ATOM 20 N ARG 3 52.564 88.223 31.668 1.00 .88 1SG 21 ATOM 21 CA ARG 3 53.229 88.095 30.409 1.00 .88 1SG 22 ATOM 22 CB ARG 3 52.989 89.248 29.411 1.00 .88 1SG 23 ATOM 23 CG ARG 3 53.492 90.618 29.887 1.00 .88 1SG 24 ATOM 24 CD ARG 3 53.730 91.607 28.738 1.00 .88 1SG 25 ATOM 25 NE ARG 3 52.428 92.217 28.346 1.00 .88 1SG 26 ATOM 26 CZ ARG 3 52.025 93.407 28.885 1.00 .88 1SG 27 ATOM 27 NH1 ARG 3 52.803 94.045 29.807 1.00 .88 1SG 28 ATOM 28 NH2 ARG 3 50.851 93.977 28.488 1.00 .88 1SG 29 ATOM 29 C ARG 3 54.698 88.058 30.662 1.00 .88 1SG 30 ATOM 30 O ARG 3 55.161 88.076 31.802 1.00 .88 1SG 31 ATOM 31 N ALA 4 55.461 87.968 29.562 1.00 .49 1SG 32 ATOM 32 CA ALA 4 56.886 87.958 29.616 1.00 .49 1SG 33 ATOM 33 CB ALA 4 57.464 86.858 30.523 1.00 .49 1SG 34 ATOM 34 C ALA 4 57.312 87.656 28.224 1.00 .49 1SG 35 ATOM 35 O ALA 4 56.570 87.027 27.470 1.00 .49 1SG 36 ATOM 36 N SER 5 58.516 88.102 27.828 1.00 .41 1SG 37 ATOM 37 CA SER 5 58.909 87.798 26.491 1.00 .41 1SG 38 ATOM 38 CB SER 5 59.982 88.738 25.914 1.00 .41 1SG 39 ATOM 39 OG SER 5 59.411 90.008 25.645 1.00 .41 1SG 40 ATOM 40 C SER 5 59.458 86.415 26.493 1.00 .41 1SG 41 ATOM 41 O SER 5 60.492 86.133 27.098 1.00 .41 1SG 42 ATOM 42 N LEU 6 58.736 85.510 25.810 1.00 .40 1SG 43 ATOM 43 CA LEU 6 59.134 84.144 25.669 1.00 .40 1SG 44 ATOM 44 CB LEU 6 57.933 83.183 25.626 1.00 .40 1SG 45 ATOM 45 CG LEU 6 57.147 83.103 26.955 1.00 .40 1SG 46 ATOM 46 CD2 LEU 6 58.071 82.759 28.139 1.00 .40 1SG 47 ATOM 47 CD1 LEU 6 55.963 82.127 26.846 1.00 .40 1SG 48 ATOM 48 C LEU 6 59.804 84.111 24.339 1.00 .40 1SG 49 ATOM 49 O LEU 6 60.999 83.838 24.235 1.00 .40 1SG 50 ATOM 50 N GLY 7 59.034 84.403 23.277 1.00 .24 1SG 51 ATOM 51 CA GLY 7 59.619 84.472 21.974 1.00 .24 1SG 52 ATOM 52 C GLY 7 59.258 83.201 21.229 1.00 .24 1SG 53 ATOM 53 O GLY 7 58.244 82.561 21.606 1.00 .24 1SG 54 ATOM 54 OXT GLY 7 59.994 82.858 20.266 1.00 .24 1SG 55 END