additional tokens needed for NMR coordinates

Frances Bernstein (bernstei@fcb.pdb.bnl.gov)
Tue, 7 Nov 1995 11:46:45 -0500 

     In the coordinate portion of entries that were determined
by NMR, the depositors often use the occupancy and B value
fields to store other information.  This can be confusing if
one runs a program that assumes that the B value field actually
contains a B value.  It would be most helpful if someone in the NMR
community would work with the mmCIF committee to define some mmCIF
tokens to store these quantities.  I realize that the NMR community
is working separately on defining a schema for their data but the
PDB is facing the reality of having to be able to convert all
coordinate entries (x-ray and NMR alike) to mmCIF.  The provision
of additional tokens that fit into the _atom_site category seems to
be the most appropriate way to handle this conversion.  People
interested in structures will want to have all coordinate entries
in one schema so that they will need only one program to input the
coordinates.

A typical example is in entry 1ATX but I am sure that other variations
will be found in examining other PDB NMR entries.  A brief search
found 104 currently available NMR entries that contain the word
'column' in a remark record; I looked at a few of these and they
are all entries where the occupancy or B value field was used for
something else.

REMARK   9 THE AVERAGE OF THE RMS DEVIATION VALUES IN A PAIRWISE        1ATX
108
REMARK   9 COMPARISON OF THE 8 NMR STRUCTURES AS DESCRIBED IN THE       1ATX
109
REMARK   9 PAPER CITED ON THE *JRNL* RECORDS ABOVE IS 1.4 ANGSTROMS     1ATX
110
REMARK   9 FOR THE BACKBONE ATOMS OF RESIDUES 1-7 AND 19-46, AND 1.5    1ATX
111
REMARK   9 ANGSTROMS IF THE HEAVY ATOMS OF 20 INTERIOR SIDECHAINS ARE   1ATX
112
REMARK   9 ADDED.  THE CONFORMATION OF THE FRAGMENT CONSISTING OF       1ATX
113
REMARK   9 RESIDUES 8-18 IS NOT WELL DETERMINED; THESE RESIDUES         1ATX
114
REMARK   9 PROBABLY FORM A LOOP WITH INCREASED MOBILITY.  (THE AVERAGE  1ATX
115
REMARK   9 STRUCTURAL CHANGE DURING THE RESTRAINED "AMBER" REFINEMENT   1ATX
116
REMARK   9 CORRESPONDS TO A RMS DEVIATION OF 0.4 ANGSTROMS.)  IN THIS   1ATX
117
REMARK   9 ENTRY AN OCCUPANCY (COLUMNS 55 TO 60) OF 1.00 IDENTIFIES     1ATX
118
REMARK   9 THE AMINO ACID RESIDUES THAT WERE USED IN THE CALCULATION    1ATX
119
REMARK   9 OF THE GLOBAL RMS DEVIATIONS.  FOR ALL OTHER RESIDUES THE    1ATX
120
REMARK   9 VALUE IS 0.00.                                               1ATX
121
REMARK  10                                                              1ATX
122
REMARK  10 AVERAGES OF THE ROOT-MEAN-SQUARE DEVIATIONS IN ANGSTROMS OF  1ATX
123
REMARK  10 THE INDIVIDUAL ATOMS OF EACH STRUCTURE RELATIVE TO THE       1ATX
124
REMARK  10 SEVEN OTHER STRUCTURES ARE LISTED IN THE TEMPERATURE FACTOR  1ATX
125
REMARK  10 FIELD (COLUMNS 61 TO 66) OF THE ATOM RECORDS.  THEY WERE     1ATX
126
REMARK  10 OBTAINED AFTER THE BACKBONE OF RESIDUES 1-7 AND 19-46 OF     1ATX
127
REMARK  10 THE SEVEN STRUCTURES HAD BEEN OPTIMALLY FIT TO THE           1ATX
128
REMARK  10 STRUCTURE FOR WHICH THE ATOMIC DEVIATION IS GIVEN.           1ATX
129

                                       Frances C. Bernstein