Notes on editing PDB format

The essential fields of pdb format are CRYST1, HETATM (or ATOM), and CONECT (minimum that is needed). Also TITLE and COMPND fields can be included. Here is an example of these fields:

TITLE     The title
COMPND    compound name
REMARK    A remark
CRYST1    5.000    5.000    9.111  90.00  90.00 120.00 P63/mmc
ATOM    293 1HG  GLU A   18    -14.861  -4.847   0.361  1.00  0.00           H
HETATM    3  As                  0.000  -0.719   0.000
CONECT   10    1    2    3    4

The fields TITLE and COMPND begin at column 11.

Description of the field CRYST1:

• columns 7-15, 16-24, 25-33: a,b,c parameters of the unit cell in Angstroms (real9.3, but 9.4 is also acceptable)
• columns 34-40, 41-47, 48-54: α,β,γ parameters of the unit cell in degrees (real7.2)
• columns 56-66: space group (full Hermann-Mauguin symbol)

Minimal description of the coordinate section:

• columns 1-6: record name (string, HETATM or ATOM)
• columns 7-11: atom serial number (integer)
• columns 13-16: atom name (string), column 13 is reserved for a numerical prefix (e.g. TINKER does not read it)
• columns 18-20: residue name (string, for ATOM only)
• columns 23-26: residue sequence number (integer)
• columns 31-38,39-46,47-54: cartesian x,y,z coordinates in Angstroms (real8.3, but 8.4 is also acceptable)
• columns 55-60: occupancy (real6.2)
• columns 61-66: Temperature factor (real6.2)
• columns 79-80: charge on the atom (integer)

Description of the field CONECT:

• columns 7-11: atom serial number
• columns 12-16, 17-21, 22-26, 27-31: serial numbers of bonded atoms (up to 4 atoms)

Note that for generating crystals in Mercury program you should specify in pdb-file only one atom for each symmetry position.

Complete description of PDB format can be found here, see also Wikipedia.