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[modeller_usage] DNA atoms changed by modeller

Hello all,

I have a PDB with a small protein-DNA complex... I induce a point mutation
in the protein and then save the mutated PDB. The DNA molecule remains
untouched.

I noticed my original pdb defines the first base (adenine) with 18 atoms -
but the output modeller builds 21 atoms. The first 3 atoms are added.

I believe the original input is missing the phosphate group. But I want
modeller to leave the DNA alone the way it is. Is there a way to set
modeller to leave some chains untouched in the output?

Thanks in advance
Pedro

*MODIFIED BY MODELLER*
*A*

*TOM      1  P    DA B   1      11.378  26.105  39.925  1.00  0.00
  PATOM      2  OP1  DA B   1      11.702  25.899  40.057  1.00  0.00
    OATOM      3  OP2  DA B   1      12.983  26.076  41.112  1.00  0.00
      O*
ATOM      4  O5'  DA B   1      12.613  25.783  40.890  1.00 27.98
  O
ATOM      5  C5'  DA B   1      13.939  25.889  40.375  1.00 25.91
  C

*ORIGINAL*
CRYST1   45.400   56.200  130.800  90.00  90.00  90.00 C 2 2 21
ATOM      1  O5' DA  B   1      12.613  25.783  40.890  1.00 27.98
  O
ATOM      2  C5' DA  B   1      13.939  25.889  40.375  1.00 25.91
  C
ATOM      3  C4' DA  B   1      14.898  24.947  41.083  1.00 26.90
  C
ATOM      4  O4' DA  B   1      14.923  25.240  42.497  1.00 26.42
  O
ATOM      5  C3' DA  B   1      14.466  23.490  40.907  1.00 27.31
  C
ATOM      6  O3' DA  B   1      15.624  22.725  40.560  1.00 29.53
  O
ATOM      7  C2' DA  B   1      13.955  23.125  42.294  1.00 25.13
  C
ATOM      8  C1' DA  B   1      14.747  24.029  43.236  1.00 24.42
  C
ATOM      9  N9  DA  B   1      14.020  24.367  44.474  1.00 21.51
  N
ATOM     10  C8  DA  B   1      14.404  24.071  45.742  1.00 20.32
  C
ATOM     11  N7  DA  B   1      13.590  24.502  46.649  1.00 21.20
  N
ATOM     12  C5  DA  B   1      12.581  25.132  45.948  1.00 20.03
  C
ATOM     13  C6  DA  B   1      11.424  25.786  46.361  1.00 20.34
  C
ATOM     14  N6  DA  B   1      11.075  25.916  47.640  1.00 20.30
  N
ATOM     15  N1  DA  B   1      10.641  26.293  45.396  1.00 21.27
  N
ATOM     16  C2  DA  B   1      10.993  26.155  44.127  1.00 20.67
  C
ATOM     17  N3  DA  B   1      12.054  25.563  43.615  1.00 21.50
  N
ATOM     18  C4  DA  B   1      12.825  25.060  44.609  1.00 21.31
  C
Hello all,

I have a PDB with a small protein-DNA complex... I induce a point mutation in the protein and then save the mutated PDB. The DNA molecule remains untouched.

I noticed my original pdb defines the first base (adenine) with 18 atoms - but the output modeller builds 21 atoms. The first 3 atoms are added.

I believe the original input is missing the phosphate group. But I want modeller to leave the DNA alone the way it is. Is there a way to set modeller to leave some chains untouched in the output?

Thanks in advance
Pedro

MODIFIED BY MODELLER
ATOM      1  P    DA B   1      11.378  26.105  39.925  1.00  0.00            P
ATOM      2  OP1  DA B   1      11.702  25.899  40.057  1.00  0.00           O
ATOM      3  OP2  DA B   1      12.983  26.076  41.112  1.00  0.00           O
ATOM      4  O5'  DA B   1      12.613  25.783  40.890  1.00 27.98           O
ATOM      5  C5'  DA B   1      13.939  25.889  40.375  1.00 25.91           C

ORIGINAL
CRYST1   45.400   56.200  130.800  90.00  90.00  90.00 C 2 2 21      
ATOM      1  O5' DA  B   1      12.613  25.783  40.890  1.00 27.98           O  
ATOM      2  C5' DA  B   1      13.939  25.889  40.375  1.00 25.91           C  
ATOM      3  C4' DA  B   1      14.898  24.947  41.083  1.00 26.90           C  
ATOM      4  O4' DA  B   1      14.923  25.240  42.497  1.00 26.42           O  
ATOM      5  C3' DA  B   1      14.466  23.490  40.907  1.00 27.31           C  
ATOM      6  O3' DA  B   1      15.624  22.725  40.560  1.00 29.53           O  
ATOM      7  C2' DA  B   1      13.955  23.125  42.294  1.00 25.13           C  
ATOM      8  C1' DA  B   1      14.747  24.029  43.236  1.00 24.42           C  
ATOM      9  N9  DA  B   1      14.020  24.367  44.474  1.00 21.51           N  
ATOM     10  C8  DA  B   1      14.404  24.071  45.742  1.00 20.32           C  
ATOM     11  N7  DA  B   1      13.590  24.502  46.649  1.00 21.20           N  
ATOM     12  C5  DA  B   1      12.581  25.132  45.948  1.00 20.03           C  
ATOM     13  C6  DA  B   1      11.424  25.786  46.361  1.00 20.34           C  
ATOM     14  N6  DA  B   1      11.075  25.916  47.640  1.00 20.30           N  
ATOM     15  N1  DA  B   1      10.641  26.293  45.396  1.00 21.27           N  
ATOM     16  C2  DA  B   1      10.993  26.155  44.127  1.00 20.67           C  
ATOM     17  N3  DA  B   1      12.054  25.563  43.615  1.00 21.50           N  
ATOM     18  C4  DA  B   1      12.825  25.060  44.609  1.00 21.31           C  

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