Re: PDB ORIGX records

• Messages sorted by: [ date ][ subject ][ author ]
• Previous message: Paula Fitzgerald: "Re: PDB EXPDTA records"
• Maybe in reply to: Frances Bernstein: "PDB ORIGX records"

Frances Bernstein writes:

> PDB entries present on ORIGX records the transformation (3x3 matrix plus
> vector) that will generate the authors' submitted coordinates from the
> coordinates in the entry.  Apparently there are no fields in the mmCIF
> dictionary to carry this information.

A new category, DATABASE_PDB_MATRIX has been added, for the purpose of
storing the matrices and vectors from the PDB ORIGX and SCALE cards.  These
are rather specialized matrices, in that they represent transformations
between the coordinates submitted by the authors and crystallographic 
coordinates, hence they do not necessarily correspond to fractional-to-
orthogonal or orthogonal-to-fractional transformations (they depend instead
on what the author submitted, which back in the old days might have been
hand-measured inches from a Richard's box). 

For that reason we have chosen to treat them as PDB specific data items, and
named them accordingly.  What follows is just a portion of the newly added
part of the dictionary, to give you a feel for what we have done (and I
use "we" very loosely in this regard, as John did all of this work).

- - - - -

#########################
## DATABASE_PDB_MATRIX ##
#########################

save_DATABASE_PDB_MATRIX
    _category.description
;              The DATABASE_PDB_MATRIX category provides placeholders for
               transformation matrices and vectors used by the Protein Data
               Bank (PDB).

               These data items are included only for consistency with older
               PDB format files.  They should appear in a data block only if
               that data block was created by reformatting a PDB format file.
;
    _category.id                  database_pdb_matrix
    _category.mandatory_code      no
    _category_key.name          '_database_pdb_matrix.entry_id'
     loop_
    _category_group.id           'inclusive_group'
                                 'database_group'
                                 'pdb_group'
     save_

- - - - -

save__database_pdb_matrix.origx[1][1]
    _item_description.description
;              The [1][1] element of the PDB ORIGX matrix.
;

    _item.name                  '_database_pdb_matrix.origx[1][1]'
    _item.category_id             database_pdb_matrix
    _item.mandatory_code          no
    _item_default.value           1.0
    _item_sub_category.id         matrix
    _item_type.code               float
     save_

- - - - -

save__database_pdb_matrix.origx_vector[1]
    _item_description.description
;              The [1] element of the PDB ORIGX vector.
;
    _item.name                  '_database_pdb_matrix.origx_vector[1]'
    _item.category_id             database_pdb_matrix
    _item.mandatory_code          no
    _item_type.code               float
    _item_default.value           0.0
    _item_sub_category.id         vector
     save_

- - - - -

save__database_pdb_matrix.scale[1][1]
    _item_description.description
;              The [1][1] element of the PDB SCALE matrix.
;

    _item.name                  '_database_pdb_matrix.scale[1][1]'
    _item.category_id             database_pdb_matrix
    _item.mandatory_code          no
    _item_default.value           1.0
    _item_sub_category.id         matrix
    _item_type.code               float
     save_

- - - - -

save__database_pdb_matrix.scale_vector[1]
    _item_description.description
;              The [1] element of the PDB SCALE vector.
;
    _item.name                  '_database_pdb_matrix.scale_vector[1]'
    _item.category_id             database_pdb_matrix
    _item.mandatory_code          no
    _item_type.code               float
    _item_default.value           0.0
    _item_sub_category.id         vector
     save_
 
- - - - -

Paula

********************************************************************************
 Dr. Paula M. D. Fitzgerald  ______________ voice and FAX: (908) 594-5510
   Merck Research Laboratories ______________ email: paula_fitzgerald@merck.com
     P.O. Box 2000, Ry50-105     ______________ or bean@merck.com           
       Rahway, NJ 07065  USA 
         (for express mail use 126 E. Lincoln Ave. instead of P. O. Box 2000)  
********************************************************************************

• Previous message: Paula Fitzgerald: "Re: PDB EXPDTA records"
• Maybe in reply to: Frances Bernstein: "PDB ORIGX records"