Shadow Contact Map
(version 1.30)

Basically, follow standard PDB formatting. Here is a sample pdb file, so you can see the format expected by the webtool.
Your pdb file MUST conform to the following standards.

• No hidden characters. They can lead to unpredictable results. To avoid accidentally inserting them use a text editor such as vi, or emacs.
• If your file does not work with the page, only include lines that start with "ATOM" (to specify each atom), "TER" (to indicate a break between 2 chains) and "END" at the end of the file. Ligand atoms are also expected to be called ATOM, though they often appear as HETATMs in pdb files (leaving HETATM lines in your file will often lead to problems with the webtool).
• Chain identifiers are not used. If you have multiple chains, insert "TER" (left justified) between chains. The webtool will internally index the chains sequentially, starting with 1.
• Terminal oxygens (in proteins) are called, OXT and O (not O1 and O2).
• The file is not read past an "END" statement (ALL CAPS, left justified). If atoms appear after an END line, these atoms will not be included.

Recognized residues include:

• Protein residues : All 20 amino acids (3 letter codes are used).
• RNA residues: CYT or C, GUA or G, URA or U and ADE or A.
• Modified RNA residue: MIA (2-methylthio-N6 isopentenyl adenosine).
• DNA residues: DG, DC, DA and DT.
• Ligands: SAM (S-Adenosylemethionine), GNP (Gpp(NH)p), ATP, ADP, AMP, FUA (Fusidic Acid), GTP, GDP and BMG (Bound MaGnesium ions).
• We are preparing a complete description on the precise parameterization of the ligands.