Preparing coordinate file for deposition in PDB
MAIN can not write all for deposition necessary records, however it can offer you a substantial help when be their generation. With the help of following scripts you can:
get_closest.com macro starts with the usual "read.com to retrieve coordinate, cell constants and symmetry group information. It is assumed that solvent molecules are located at the end of the file. If it is not so either reorganize your file or skip the solvent part of PDB file preparation.
The following command files get_closest.com and water_close.com generate for each solvent molecule all symmetry equivalent positions and keep only the position closest to a protein atom.
The results are written to "to_pdb.pdb" file.
The command file attach_solvent.com reads the results from the previous step "to_pdb.pdb" file and writes results in "to_pdb_2.pdb".
The command file write_by_pair.com writes all protein segments together with their closets solvent molecules.
Renaming atoms and residues, creation of unusual bonds
Input file is "to_pdb_2.pdb" and output "to_pdb_deposit.pdb". This is the last step where residue and atom names should be adjusted to PDB rules. You do not have to worry about HET records. Program compares each residue name with the list of standard PDB residue names (Appendix C of PDB Atomic coordinate and bibliographic entry format description, Feb-1992).
Program generates RESIDUE list on the segment basis. The residue lists are followed by the ATOM, ATZERO and HETATOM records. Chain identifier is the first letter from the segment name. Cell constants, symmetry operations, disulfides and other connections are written as well. Be careful by calculation of covalent bonds, since each non-disulfide covalent bond connection will be written to the file.
The write_pdb_deposit.com macro is only an example that should be tailored. Particularly pay attention to the CRYST record - space group is simply set to P21.