"STARTING_MODEL" and "ENDING_MODEL"

Xiao-Ping Zhang

22 May 2000 22 May '00

3:43 a.m.

Hi,

Sorry, I have noticed that someone already asked the following question two years ago and Azat Badretdinov had answered the it. But I still don't understand the meaning behind the STARTING_MODEL" and "ENDING_MODEL.

> > > >What exactly is the meaning behind setting "STARTING_MODEL" and > >"ENDING_MODEL"? Does setting the former to 1 and the latter to, say,

> >7 result in seven models being built with the 7th model being the most > >refined?

>No, it does not. STARTING and ENDING will determine the range of indeces >in .B???? file names of the models

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 ?

All suggestions are highly appreciated.

Thank you for your help.

****************************** 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

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Andras Fiser

22 May 22 May

12:52 p.m.

New subject: "STARTING_MODEL" and"ENDING_MODEL"

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

23 May 23 May

1:33 a.m.

New subject: "STARTING_MODEL" and"ENDING_MODEL"

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 ATOM 1667 CA ASN B 1 ATOM 1668 C ASN B 1 ATOM 1669 O ASN B 1 ATOM 1670 CB ASN B 1 ATOM 1671 CG ASN B 1 ATOM 1672 OD1 ASN B 1 ATOM 1673 ND2 ASN B 1 ATOM 1674 N ARG B 2 ATOM 1675 CA ARG B 2 ATOM 1676 C ARG B 2 ATOM 1677 O ARG B 2 ATOM 1678 CB ARG B 2 ATOM 1679 CG ARG B 2 ATOM 1680 CD ARG B 2 ATOM 1681 NE ARG B 2 ATOM 1682 CZ ARG B 2 ATOM 1683 NH1 ARG B 2 ATOM 1684 NH2 ARG B 2 ATOM 1685 N LEU B 3 ATOM 1686 CA LEU B 3 ATOM 1687 C LEU B 3 ATOM 1688 O LEU B 3 ATOM 1689 CB LEU B 3 ATOM 1690 CG LEU B 3 ATOM 1691 CD1 LEU B 3 ATOM 1692 CD2 LEU B 3 ATOM 1693 N LEU B 4 ATOM 1694 CA LEU B 4 ATOM 1695 C LEU B 4 ATOM 1696 O LEU B 4 ATOM 1697 CB LEU B 4 ATOM 1698 CG LEU B 4 ATOM 1699 CD1 LEU B 4 ATOM 1700 CD2 LEU B 4 ATOM 1701 N LEU B 5 ATOM 1702 CA LEU B 5 ATOM 1703 C LEU B 5 ATOM 1704 O LEU B 5 ATOM 1705 CB LEU B 5 ATOM 1706 CG LEU B 5 ATOM 1707 CD1 LEU B 5 ATOM 1708 CD2 LEU B 5 ATOM 1709 N THR B 6 ATOM 1710 CA THR B 6 ATOM 1711 C THR B 6 ATOM 1712 O THR B 6 ATOM 1713 CB THR B 6 ATOM 1714 OG1 THR B 6 ATOM 1715 CG2 THR B 6 ATOM 1716 N GLY B 7 ATOM 1717 CA GLY B 7 ATOM 1718 C GLY B 7 ATOM 1719 O GLY B 7 ATOM 1720 OXT GLY B 7 50.702 87.722 38.867 1.00 43.10 N 51.449 86.814 37.946 1.00 41.67 C 51.328 87.331 36.498 1.00 39.68 C 50.267 87.216 35.865 1.00 39.73 O 50.874 85.389 38.031 1.00 44.13 C 50.750 84.878 39.468 1.00 46.27 C 50.338 85.626 40.353 1.00 46.16 O 51.084 83.634 39.757 1.00 45.47 N 52.433 87.895 36.025 1.00 36.65 N 52.555 88.448 34.656 1.00 32.06 C 53.586 87.620 33.873 1.00 28.54 C 54.665 87.294 34.387 1.00 25.94 O 53.006 89.911 34.728 1.00 36.71 C 52.282 90.816 33.727 1.00 41.73 C 50.777 90.927 33.989 1.00 44.15 C 50.050 91.548 32.870 1.00 47.60 N 48.751 91.877 32.904 1.00 47.23 C 48.009 91.654 33.997 1.00 49.83 N 48.094 92.442 31.880 1.00 44.33 N 53.236 87.297 32.635 1.00 25.64 N 54.079 86.438 31.778 1.00 22.32 C 54.737 87.207 30.621 1.00 22.74 C 54.225 88.243 30.169 1.00 22.20 O 53.235 85.323 31.158 1.00 18.68 C 52.213 84.739 32.134 1.00 19.46 C 51.449 83.546 31.556 1.00 20.46 C 52.846 84.236 33.433 1.00 15.12 C 55.858 86.627 30.205 1.00 20.92 N 56.688 87.110 29.086 1.00 23.64 C 56.790 86.014 28.021 1.00 27.49 C 56.680 84.818 28.324 1.00 28.91 O 58.117 87.414 29.559 1.00 25.41 C 58.192 88.438 30.690 1.00 24.73 C 59.616 88.631 31.223 1.00 24.26 C 57.716 89.830 30.272 1.00 24.71 C 57.000 86.447 26.792 1.00 29.48 N 57.145 85.533 25.643 1.00 30.37 C 58.628 85.360 25.284 1.00 31.29 C 59.481 86.132 25.727 1.00 27.62 O 56.468 86.114 24.395 1.00 32.09 C 55.053 86.640 24.629 1.00 35.07 C 54.403 87.181 23.350 1.00 40.10 C 54.100 85.569 25.156 1.00 38.35 C 58.897 84.333 24.478 1.00 36.46 N 60.264 84.053 23.927 1.00 44.50 C 60.360 84.677 22.466 1.00 47.61 C 59.699 84.184 21.554 1.00 48.64 O 60.477 82.528 23.817 1.00 47.63 C 59.676 81.818 24.755 1.00 53.22 O 61.928 82.107 24.047 1.00 48.63 C 61.232 85.767 22.212 1.00 50.38 N 61.334 86.583 20.844 1.00 51.64 C 62.588 86.267 20.033 1.00 53.33 C 63.180 85.187 20.170 1.00 53.27 O 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

Andras Fiser

12:44 p.m.

New subject: "STARTING_MODEL" and"ENDING_MODEL"

Dear Dr. Zhang,

I believe it is not necessarily a good idea to use modeller for a heptapeptide modeling based on another heptapeptide unless you are sure that they adopt a very similar conformation. I do not know what is your environment (is it a docked peptide on a protein surface, or is it in solvent etc.) but there is no guarantee that even the same heptapeptide will have the same conformation in different environments.

Modeller relies on utilising the idea of evolution, that full size, sequentially similar proteins in physiological environment (for which modeller basically does not account for) adopt similar folds, while small peptides rely more on energetic criteria, which is not what modeller was designed for.

Nevertheless:

> 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.

Modeller builds a model based on the given restraints derived from statistical observations of features from other proteins, from molecular mechanics forcefields and your template. These retrains will not necessarily guide the model to entirely the same conformation as the template. As i checked your model and template I would say that is pretty much what one would expect.

As I mentioned above, in case of such a short fragment one is fairly lost, having no solid reference, and maybe way off reality.

If you want to force modeling to deal only with sidechains and retain the same backbone conformation include in your top file:

SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT='@:@' 'X:X',; SELECTION_SEARCH='segment', PICK_ATOMS_SET=1, ; RES_TYPES='all', ATOM_TYPES='SDCH', ; SELECTION_FROM='all', SELECTION_STATUS='initialize' RETURN END_SUBROUTINE

but I mention again that to my opinion it is an inadequate use of Modeller. I would prefer some detailed mol mechanics or semi empirical forcefields as CHARMM, AMBER or ECEPP, preferably with solvent representation and exhaustive optimisation method.

Sincerely, Andras Fiser

> > # 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

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Andras Fiser
Xiao-Ping Zhang