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Re: "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:
> 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: 


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