Re: TER suggestion

• Messages sorted by: [ date ][ subject ][ author ]
• Previous message: herbert_bernstein: ". and ?"
• In reply to: herbert_bernstein: "TER suggestion"

Folks: If I may add my two cents to the TER issue...

If you were to translate an exiting PDB ATOM record to a mmCIF
loop in the _ATOM_SITE category you get the following:


loop_
_atom_site.group_PDB
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.cartn_x
_atom_site.cartn_y
_atom_site.cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.footnote_id
_atom_site.entity_id
_atom_site.entity_seq_num
_atom_site.id
  ATOM  N  N    THR .   1 .  17.047  14.099   3.625  1.00 13.79  .    1  
1    1
  ATOM  C  CA   THR .   1 .  16.967  12.784   4.338  1.00 10.80  .    1  
1    2
  ATOM  C  C    THR .   1 .  15.685  12.755   5.133  1.00  9.19  .    1  
1    3
  ATOM  O  O    THR .   1 .  15.268  13.825   5.594  1.00  9.85  .    1  
1    4
  ATOM  C  CB   THR .   1 .  18.170  12.703   5.337  1.00 13.02  .    1  
1    5
  ATOM  O  OG1  THR .   1 .  19.334  12.829   4.463  1.00 15.06  .    1  
1    6
  ATOM  C  CG2  THR .   1 .  18.150  11.546   6.304  1.00 14.23  .    1  
1    7
  ATOM  N  N    THR .   2 .  15.115  11.555   5.265  1.00  7.81  .    1  
2    8
  ATOM  C  CA   THR .   2 .  13.856  11.469   6.066  1.00  8.31  .    1  
2    9
 
   [etc.]

The combination of _atom_site.entity_id, _atom_site.entity_seq_num
_atom_site.label_asym_id and _atom_site.id allows you to gather and order
a random set of atoms into ordered sets according to their entity type and
asym_id. You have, therefore, by definition uniquely defined the polypeptide
chains and a terminator is unnecessary. The invention of a dummy
atom or some other flag would seen unneccessary.

            cheers.. /Phil

• Previous message: herbert_bernstein: ". and ?"
• In reply to: herbert_bernstein: "TER suggestion"