Description of ATOMS.DAT
Coordinate file (M.I.T. style), called HD-type. For subsequent use in
FRODO, it is good practice to start a new residue with the atom P and
to finish it with the atom O(3'). It is also helpful to group the atoms
in the order phosphate, sugar, base, although the atom order within
each group is irrelevant. To manipulate a HD-type file, use the program
"MANIP".
With "MANIP", you can :
- add or change the occupancy,
- put the correct values for the atomic factor (KS),
- set the temperature factors per group,
- renumber the atoms,
- extract atoms by type or group,
- apply a symmetry operation.
NN,ATOM,KS,X,Y,Z,BF,Q
(I5,2X,A8,I3,5F10.4)
NN : atom #
ATOM : residue name (A1), number (I3), and atom name (A4) for example ( C21O3' ). residue and atom names must correspond to those in the dictionary (see nomenclature)
X,Y,Z: coordinates
BF : temperature factor
Q : occupancy
The Van der Waals contacts are checked against the values given by Ramachandran to which 0.3 has been added (see line 10 of NUCLSQ.TXT ) :
|
|
C |
N |
O |
P |
Mg |
Na |
|
|
|
|
|
|
|
|
C |
|
3.40 |
3.20 |
3.10 |
3.70 |
3.60 |
3.60 |
N |
|
3.20 |
3.00 |
3.00 |
3.50 |
2.20 |
2.60 |
O |
|
3.10 |
3.00 |
3.10 |
3.50 |
2.20 |
2.60 |
P |
|
3.70 |
3.50 |
3.50 |
3.80 |
3.60 |
3.60 |
Mg |
|
3.60 |
2.20 |
2.20 |
3.60 |
3.60 |
3.60 |
Na |
|
3.60 |
2.60 |
2.60 |
3.60 |
3.60 |
3.60 |
If KS.GT.6, then contacts as if KS=4 (i.e. P).