[modeller_usage] ordering of atoms in the PDB

["Robin Stamler" <>]

Hello

 I’m sure this is answered somewhere but I couldn’t find it.

 

The ordering of atoms in a residue in Modeller output as in (a) is different from that usually seen in PDB files (b)

This is a problem when using the output in some other servers. Can the Modeller output be changed?

 

   Thanks

 Robin Stamler

 Dept Molecular Genetics

 University of Cincinnati

 

 

(a)

ATOM      1  N   ALA B   1      10.145  12.378   3.667  1.00 25.81      1SG  N+2

ATOM      2  CA  ALA B   1      11.592  12.105   3.515  1.00 25.81      1SG  C+3

ATOM      3  CB  ALA B   1      12.225  11.817   4.886  1.00 25.81      1SG  C+4

ATOM      4  C   ALA B   1      11.834  10.932   2.631  1.00 25.81      1SG  C+5

ATOM      5  O   ALA B   1      11.538  10.968   1.437  1.00 25.81      1SG  O+6

 

(b)

ATOM    586  N   ALA A  86     -33.616  77.292  18.556  1.00 27.93           N 

ATOM    587  CA  ALA A  86     -34.153  76.748  17.311  1.00 27.40           C 

ATOM    588  C   ALA A  86     -33.329  77.134  16.085  1.00 27.32           C 

ATOM    589  O   ALA A  86     -32.386  77.921  16.172  1.00 25.96           O 

ATOM    590  CB  ALA A  86     -35.591  77.205  17.124  1.00 24.83           C